Common Fund Data Ecosystem (CFDE)
Common Fund Data Ecosystem (CFDE)
Get Program Updates
Program Publications
Publications Search by Program
Search Results
The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
| Title | Author | Journal Name | PubMedID | Journal Abbreviation | Publication Date | PubMedLink |
|---|---|---|---|---|---|---|
| Mondrian Abstraction and Language Model Embeddings for Differential Pathway Analysis. | Al Abir F, Chen JY | bioRxiv : the preprint server for biology | 38659966 | bioRxiv | 2024 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/38659966 |
| TabGraphSyn: Graph-Guided Latent Diffusion for High-Fidelity and Privacy-Conscious Clinical Data Generation. | Wu Z, Chen H, Chen JY | medRxiv : the preprint server for health sciences | 41503456 | medRxiv | 2025 Dec 29 | https://www.ncbi.nlm.nih.gov/pubmed/41503456 |
| Building an Ethical and Trustworthy Biomedical AI Ecosystem for the Translational and Clinical Integration of Foundation Models. | Sankar BS, Gilliland D, Rincon J, Hermjakob H, Yan Y, Adam I, Lemaster G, Wang D, Watson K, Bui A, Wang W, Ping P | Bioengineering (Basel, Switzerland) | 39451360 | Bioengineering (Basel) | 2024 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/39451360 |
| Multi-omics signature of healthy versus unhealthy lifestyles reveals associations with diseases. | Fu G, Rushing BR, Graves L, Nieman DC, Pellegrini M, Soldano M, Thompson MJ, Sakaguchi CA, Pathmasiri W, Sumner SJ | Human genomics | 40886004 | Hum Genomics | 2025 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/40886004 |
| UniProt: the Universal Protein Knowledgebase in 2025. | UniProt Consortium | Nucleic acids research | 39552041 | Nucleic Acids Res | 2025 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/39552041 |
| International Mouse Phenotyping Consortium: Investigating gene function and providing insights into human disease. | Wilson R, Ataç TB, Cheng TK, Frost A, Güneş O, Kan M, Keskivali-Bond P, Gómez FL, McLaughlin J, Mucha J, Munava T, Oliveira C, Pava D, Estrada JFP, Selkirk E, Vardal B, Wells S, Cacheiro P, Smedley D, Parkinson H | bioRxiv : the preprint server for biology | 41279104 | bioRxiv | 2025 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/41279104 |
| KSMoFinder - Knowledge graph embedding of proteins and motifs for predicting kinases of human phosphosites. | Anandakrishnan M, Ross KE, Chen C, Vijay-Shanker K, Wu CH | bioRxiv : the preprint server for biology | 41279605 | bioRxiv | 2025 Oct 23 | https://www.ncbi.nlm.nih.gov/pubmed/41279605 |
| International Mouse Phenotyping Consortium Portal: facilitating investigation of gene function and providing insights into human disease. | Wilson R, Bülbül Ataç T, Cheng TK, Frost A, Güneş O, Kan M, Keskivali-Bond P, López Gómez F, McLaughlin J, Mucha J, Munava T, Oliveira C, Pava D, Peña Estrada JF, Selkirk E, Vardal B, Wells S, Cacheiro P, Smedley D, Parkinson H | Nucleic acids research | 41231752 | Nucleic Acids Res | 2026 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/41231752 |
| KSMoFinder-knowledge graph embedding of proteins and motifs for predicting kinases of human phosphosites. | Anandakrishnan M, Ross KE, Chen C, Vijay-Shanker K, Wu CH | Bioinformatics advances | 41323648 | Bioinform Adv | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/41323648 |
| The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data. | Ahooyi TM, Stear B, Simmons JA, Metzger VT, Kumar P, Evangelista JE, Clarke DJB, Xie Z, Kim H, Jenkins SL, Maurya MR, Ramachandran S, Fahy E, Gillespie TH, Imam FT, Kokash N, Roth ME, Fullem R, Jevtic D, Mihajlovic A, Tiemeyer M, Bakker C, Schroeder AJ, Markowski J, Nedzel J, Hill DD, Terry J, Nemarich C, Boline J, Park PJ, Ardlie KG, Vora J, Mazumder R, Ranzinger R, de Bono B, Subramaniam S, Grethe JS, Yang JJ, Lambert CG, Resnick A, Milosavljevic A, Ma'ayan A, Silverstein JC, Taylor DM | bioRxiv : the preprint server for biology | 40832351 | bioRxiv | 2025 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/40832351 |
| Benchmarking Transformer Embedding Models for Biomedical Terminology Standardization. | Lahiri A, Shukla S, Stear B, Ahooyi TM, Beigel K, Margolskee E, Taylor D | Machine learning with applications | 40718094 | Mach Learn Appl | 2025 Sep | https://www.ncbi.nlm.nih.gov/pubmed/40718094 |
| Germline pathogenic variation impacts somatic alterations and patient outcomes in pediatric central nervous system tumors. | Corbett RJ, Kaufman RS, McQuaid SW, Vaksman Z, Phul S, Brown MA, Mason JL, Waszak SM, Zhang B, Zhong C, Blauel E, Desai H, Hausler R, Naqvi AS, Daggett JM, Sickler A, Cresswell-Clay EC, Sullivan PJ, Chroni A, Geng Z, Gonzalez EM, Zhu Y, Heath AP, Li M, Storm PB, Resnick AC, Maxwell KN, Cole KA, Waanders AJ, Bornhorst M, MacFarland SP, Rokita JL, Diskin SJ | Nature communications | 41271695 | Nat Commun | 2025 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/41271695 |
| ID-GBA: Subgraph Extension With Information Distance Guilt by Association in Complex Networks. | Obradovic P, Kovacevic V, Milosavljevic A, Petrosyan V | IEEE access : practical innovations, open solutions | 41810358 | IEEE Access | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/41810358 |
| The Open Pediatric Cancer Project. | Geng Z, Wafula E, Corbett RJ, Zhang Y, Jin R, Gaonkar KS, Shukla S, Rathi KS, Hill D, Lahiri A, Miller DP, Sickler A, Keith K, Blackden C, Chroni A, Brown MA, Kraya AA, Clark KL, Rood BR, Resnick AC, Van Kuren N, Maris JM, Farrel A, Koptyra MP, Trooskin GR, Coleman N, Zhu Y, Stefankiewicz S, Abdullaev Z, Chinwalla AT, Santi M, Naqvi AS, Mason JL, Koschmann CJ, Huang X, Diskin SJ, Aldape K, Farrow BK, Ma W, Zhang B, Ennis BM, Tasian S, Phul S, Lueder MR, Zhong C, Dybas JM, Wang P, Taylor D, Rokita JL | GigaScience | 40891528 | Gigascience | 2025 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/40891528 |
| Germline pathogenic variation impacts somatic alterations and patient outcomes in pediatric CNS tumors. | Corbett RJ, Kaufman RS, McQuaid SW, Vaksman Z, Phul S, Brown MA, Mason JL, Waszak SM, Zhang B, Zhong C, Blauel E, Desai H, Hausler R, Naqvi AS, Daggett JM, Sickler A, Cresswell-Clay EC, Sullivan PJ, Chroni A, Geng Z, Gonzalez EM, Zhu Y, Heath AP, Li M, Penn Medicine BioBank, Regeneron Genetics Center, Storm PB, Resnick AC, Maxwell KN, Cole KA, Waanders AJ, Bornhorst M, MacFarland SP, Rokita JL, Diskin SJ | medRxiv : the preprint server for health sciences | 39974082 | medRxiv | 2025 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/39974082 |
| Molecularly Targeted Small Molecule Inhibitor Therapy for Pediatric Acute Lymphoblastic Leukemia: A Comprehensive Review of Clinical Trials. | Peccatori N, Brivio E, Lissat A, Bautista Sirvent F, Salzer E, Biondi A, Fazio G, Rizzari C, Tasian SK, Zwaan CM | Cancers | 41154380 | Cancers (Basel) | 2025 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/41154380 |
| Gosling Designer: a Platform to Democratize Construction and Sharing of Genomics Data Visualization Tools. | L'Yi S, Conroy J, Misner P, Kouřil D, van den Brandt A, Choy L, Abdennur N, Gehlenborg N | ArXiv | 41281213 | ArXiv | 2025 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/41281213 |
| Comparative Evaluation of Deep Learning and Foundation Model Embeddings for Osteoarthritis Feature Classification in Knee Radiographs. | Chavoshi M, Trivedi H, Newsome J, Mansuri A, Li F, Dapamede T, Khosravi B, Gichoya J | Journal of imaging informatics in medicine | 40897834 | J Imaging Inform Med | 2025 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/40897834 |
| Artificial Intelligence and Intelligent Interventional Radiology: Fusion of Human and Machine. | Huth H, Saccenti L, Anibal J, Ukeh I, Kassin M, Gichoya J, Varble N, Li M, Karanian J, Turkbey B, Wood BJ | Journal of vascular and interventional radiology : JVIR | 41276375 | J Vasc Interv Radiol | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/41276375 |
| Impact of Label Noise from Large Language Model-generated Annotations on Evaluation of Diagnostic Model Performance. | Chavoshi M, Trivedi H, Mansuri A, Newsome J, Sanyika CR, Isaac RS, Li F, Dapamede T, Gichoya JW | Radiology. Artificial intelligence | 41441444 | Radiol Artif Intell | 2026 Mar | https://www.ncbi.nlm.nih.gov/pubmed/41441444 |
| Real-world performance evaluation of a commercial deep learning model for intracranial hemorrhage detection. | Chavoshi M, Mansuri A, Bala W, Brown-Mulry B, Dapamede T, Isaac R, Khosravi B, Li H, Li F, Moon JT, Robichaux C, Cohen-Addad DIG, Salastekar NV, Gichoya JW, Trivedi H | NPJ digital medicine | 41444826 | NPJ Digit Med | 2025 Dec 24 | https://www.ncbi.nlm.nih.gov/pubmed/41444826 |
| Improving Performance, Robustness, and Fairness of Radiographic AI Models with Finely-Controllable Synthetic Data. | Moroianu SL, Bluethgen C, Chambon P, Cherti M, Delbrouck JB, Paschali M, Price B, Gichoya J, Jitsev J, Langlotz CP, Chaudhari AS | Research square | 41356360 | Res Sq | 2025 Nov 24 | https://www.ncbi.nlm.nih.gov/pubmed/41356360 |
| Heimdall: A Modular Framework for Tokenization in Single-Cell Foundation Models. | Haber E, Alam S, Ho N, Liu R, Trop E, Liang S, Yang M, Krieger S, Ma J | bioRxiv : the preprint server for biology | 41292913 | bioRxiv | 2025 Nov 10 | https://www.ncbi.nlm.nih.gov/pubmed/41292913 |
| MIMYR: Generative modeling of missing tissue in spatial transcriptomics. | Deshpande A, Bei Z, Ma J, Krieger S | bioRxiv : the preprint server for biology | 41394599 | bioRxiv | 2025 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/41394599 |
| Unified integration of spatial transcriptomics across platforms with LLOKI. | Haber E, Deshpande A, Ma J, Krieger S | Genome research | 41233159 | Genome Res | 2025 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/41233159 |
| TissueNarrator: Generative Modeling of Spatial Transcriptomics with Large Language Models. | Liu S, Tang J, Ma J, Liang S | bioRxiv : the preprint server for biology | 41394628 | bioRxiv | 2025 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/41394628 |
| CAZyme3D: A Database of 3D Structures for Carbohydrate-active Enzymes. | Siva Shanmugam NR, Yin Y | Journal of molecular biology | 39961523 | J Mol Biol | 2025 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/39961523 |
| AcrDB update: Predicted 3D structures of anti-CRISPRs in human gut viromes. | Khatri M, Shanmugam NRS, Zhang X, Patel RSKR, Yin Y | Protein science : a publication of the Protein Society | 40400348 | Protein Sci | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/40400348 |
| dbCAN-HGM: CAZyme gene clusters in gut microbiomes of diverse human populations. | Yan Y, Patel RSKR, Shanmugam NRS, Akresi J, Yin Y | Nucleic acids research | 41263098 | Nucleic Acids Res | 2026 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/41263098 |
| Mucinolysome in gut microbiomes of farm animals and humans. | Akresi JE, Van Thanh Do T, Cui Z, Shanmugam NRS, Moraïs S, Mizrahi I, Bayer EA, Auchtung J, Yin Y | bioRxiv : the preprint server for biology | 41279399 | bioRxiv | 2025 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/41279399 |
| Linking spatial omics to patient phenotypes at the population scale by BSNMani: Bayesian scalar-on-network regression with manifold learning. | Liu T, Yang Y, Wu H, Unjitwattana T, Wang S, Kang J, Li Y, Garmire LX | medRxiv : the preprint server for health sciences | 41282833 | medRxiv | 2025 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/41282833 |
| PANCDetect: Early Detection of Pancreatic Cancer from Multimodal EHR data with LLM Embeddings. | Jin Z, Guo X, Wang Z, Yang Q, Yang X, Zhang X, Yin R, Garmire LX | medRxiv : the preprint server for health sciences | 41282750 | medRxiv | 2025 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/41282750 |
| Constructing and Using Cell Type Populations of the Human Reference Atlas. | Bueckle A, Herr BW 2nd, Chen L, Bolin D, Qaurooni D, Ginda M, Jain Y, Puig-Barbe A, Ardlie K, Wang F, Börner K | bioRxiv : the preprint server for biology | 40894635 | bioRxiv | 2025 Aug 20 | https://www.ncbi.nlm.nih.gov/pubmed/40894635 |
| Exploring endothelial cell environments across organs in spatially resolved omics data. | Jain Y, Jepson J, Chen R, Maier E, Herr BW 2nd, Puig-Barbe A, Quardokus EM, Qaurooni D, Yapp C, Ewing SL, Enninful A, Farzad N, Bueckle A, Easter QT, Matuck B, Zhu C, Monte EM, Purkerson JM, Jehrio M, Misra RS, Fan R, Ginty F, Karunamurthy A, Fan J, Campbell-Thompson M, Pryhuber GS, Byrd KM, Hickey JW, Börner K | bioRxiv : the preprint server for biology | 41040203 | bioRxiv | 2025 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/41040203 |
| Nuclear receptor-SINE B1 network modulates expanded pluripotency in blastoids and blastocysts. | Wong KW, Zeng Y, Tay E, Teo JHJ, Cipta NO, Hamashima K, Yi Y, Liu H, Warrier T, Le MTN, Ng SC, Li QJ, Li H, Loh YH | Nature communications | 39562549 | Nat Commun | 2024 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/39562549 |
| TIA1 Mediates Divergent Inflammatory Responses to Tauopathy in Microglia and Macrophages. | Webber CJ, van de Spek SJF, Cruz AL, Puri S, Zhang C, Aw JTM, Papadimitriou GZ, Roberts R, Jiang K, Tran TN, Zhang L, Taylor A, Wang Z, Porter J, Sotiropoulos I, Emili A, Silva J, Li H, Wolozin B | bioRxiv : the preprint server for biology | 39574689 | bioRxiv | 2024 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/39574689 |
| WIMOAD: Weighted Integration of Multi-Omics Data with Meta Learning for Alzheimer's Disease Diagnosis. | Xiao H, Wang J, Wan S | bioRxiv : the preprint server for biology | 39386613 | bioRxiv | 2025 Apr 9 | https://www.ncbi.nlm.nih.gov/pubmed/39386613 |
| A review of artificial intelligence-based brain age estimation and its applications for related diseases. | Azzam M, Xu Z, Liu R, Li L, Meng Soh K, Challagundla KB, Wan S, Wang J | Briefings in functional genomics | 39436320 | Brief Funct Genomics | 2025 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/39436320 |
| RanBALL: An Ensemble Random Projection Model for Identifying Subtypes of B-Cell Acute Lymphoblastic Leukemia. | Li L, Xiao H, Wu X, Tang Z, Khoury JD, Wang J, Wan S | bioRxiv : the preprint server for biology | 39386448 | bioRxiv | 2025 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/39386448 |
| MOTLAB: A Weighted Multi-Omics Transfer Learning Approach to Mitigate Breast Cancer Racial Disparities. | Baek MJ, Li L, Band V, Wang J, Wan S | bioRxiv : the preprint server for biology | 41509387 | bioRxiv | 2025 Dec 25 | https://www.ncbi.nlm.nih.gov/pubmed/41509387 |
| Multi-omics based artificial intelligence for cancer research. | Li L, Sun M, Wang J, Wan S | Advances in cancer research | 39271266 | Adv Cancer Res | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/39271266 |
| Functional Connectivity Alterations in Cocaine Use Disorder: Insights from the Triple Network Model and the Addictions Neuroclinical Assessment Framework. | Xu Z, Li L, Liu R, Azzam M, Wan S, Wang J | bioRxiv : the preprint server for biology | 39605468 | bioRxiv | 2024 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/39605468 |
| SAMP: Identifying antimicrobial peptides by an ensemble learning model based on proportionalized split amino acid composition. | Feng J, Sun M, Liu C, Zhang W, Xu C, Wang J, Wang G, Wan S | Briefings in functional genomics | 39573886 | Brief Funct Genomics | 2024 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/39573886 |
| AttentionAML: An Attention-based Deep Learning Framework for Accurate Molecular Categorization of Acute Myeloid Leukemia. | Li L, Khoury JD, Wang J, Wan S | bioRxiv : the preprint server for biology | 40475602 | bioRxiv | 2025 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/40475602 |
| Leveraging Artificial Intelligence and Large Language Models for Cancer Immunotherapy. | Wu X, Sun M, Li L, Wang J, Wan S | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 41736575 | Adv Sci (Weinh) | 2026 Feb 25 | https://www.ncbi.nlm.nih.gov/pubmed/41736575 |
| A Comprehensive Review on RNA Subcellular Localization Prediction. | Zhang C, Zhu X, Peterson N, Wang J, Wan S | ArXiv | 40313658 | ArXiv | 2025 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/40313658 |
| MetaPaCS: A Novel Meta-Learning Framework for Pancreatic Cancer Subtype Identification. | Peterson NB, Sun M, Wu X, Wang J, Wan S | bioRxiv : the preprint server for biology | 41509399 | bioRxiv | 2026 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/41509399 |
| RaMBat: Accurate identification of medulloblastoma subtypes from diverse data sources with severe batch effects. | Sun M, Wang J, Wan S | Molecular oncology | 41571436 | Mol Oncol | 2026 Apr | https://www.ncbi.nlm.nih.gov/pubmed/41571436 |
| A Multi-Modal Transfer Learning Framework to Reduce Health Disparities in Prostate Adenocarcinoma. | Li L, Wang J, Wan S | bioRxiv : the preprint server for biology | 41446223 | bioRxiv | 2025 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/41446223 |
| Accurate identification of medulloblastoma subtypes from diverse data sources with severe batch effects by RaMBat. | Sun M, Wang J, Wan S | bioRxiv : the preprint server for biology | 40060540 | bioRxiv | 2025 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/40060540 |
| RanBALL: An Ensemble Machine Learning Framework for Accurate Subtype Identification of Pediatric B-Cell Acute Lymphoblastic Leukemia. | Li L, Xiao H, Wu X, Tang Z, Khoury JD, Wang J, Wan S | Advanced intelligent systems (Weinheim an der Bergstrasse, Germany) | 41246237 | Adv Intell Syst | 2025 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/41246237 |
| RPSLearner: A Novel Approach Based on Random Projection and Deep Stacking Learning for Categorizing Non-Small Cell Lung Cancer. | Wu X, Wang J, Wan S | Advanced intelligent systems (Weinheim an der Bergstrasse, Germany) | 41347120 | Adv Intell Syst | 2025 Oct 5 | https://www.ncbi.nlm.nih.gov/pubmed/41347120 |
| Enhancer selectivity in space and time: from enhancer-promoter interactions to promoter activation. | Yang JH, Hansen AS | Nature reviews. Molecular cell biology | 38413840 | Nat Rev Mol Cell Biol | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/38413840 |
| Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function. | Narducci DN, Hansen AS | Molecular cell | 39708803 | Mol Cell | 2025 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/39708803 |
| Developing a general AI model for integrating diverse genomic modalities and comprehensive genomic knowledge. | Zhang Z, Bao X, Jiang L, Luo X, Zhang Z, Yin J, Zhao M, Wang Y, Comai A, Waldhaus J, Hansen AS, Li W, Liu J | Nucleic acids research | 41277691 | Nucleic Acids Res | 2025 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/41277691 |
| Developing a general AI model for integrating diverse genomic modalities and comprehensive genomic knowledge. | Zhang Z, Bao X, Jiang L, Luo X, Wang Y, Comai A, Waldhaus J, Hansen AS, Li W, Liu J | bioRxiv : the preprint server for biology | 40462903 | bioRxiv | 2025 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/40462903 |
| Chromatin Dynamics are Highly Subdiffusive Across Seven Orders of Magnitude. | Mazzocca M, Narducci DN, Grosse-Holz S, Matthias J, Hansen AS | bioRxiv : the preprint server for biology | 40463058 | bioRxiv | 2025 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/40463058 |
| Genome structure mapping with high-resolution 3D genomics and deep learning. | Hong CKY, Feng F, Ramanathan V, Liu J, Hansen AS | bioRxiv : the preprint server for biology | 40654659 | bioRxiv | 2025 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/40654659 |
| Genome-wide absolute quantification of chromatin looping. | Jusuf JM, Grosse-Holz S, Gabriele M, Mach P, Flyamer IM, Zechner C, Giorgetti L, Mirny LA, Hansen AS | bioRxiv : the preprint server for biology | 39935886 | bioRxiv | 2025 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/39935886 |
| Distance matters: How protein regulators facilitate enhancer-promoter interactions and transcription. | Nagano M, Hansen AS | Cell genomics | 40081334 | Cell Genom | 2025 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/40081334 |
| Dynamics of microcompartment formation at the mitosis-to-G1 transition. | Goel VY, Aboreden NG, Jusuf JM, Zhang H, Mori LP, Mirny LA, Blobel GA, Banigan EJ, Hansen AS | bioRxiv : the preprint server for biology | 39345388 | bioRxiv | 2024 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/39345388 |
| LDB1 establishes multi-enhancer networks to regulate gene expression. | Aboreden NG, Lam JC, Goel VY, Wang S, Wang X, Midla SC, Quijano A, Keller CA, Giardine BM, Hardison RC, Zhang H, Hansen AS, Blobel GA | bioRxiv : the preprint server for biology | 39229045 | bioRxiv | 2024 Aug 24 | https://www.ncbi.nlm.nih.gov/pubmed/39229045 |
| Dynamics of microcompartment formation at the mitosis-to-G1 transition. | Goel VY, Aboreden NG, Jusuf JM, Zhang H, Mori LP, Mirny LA, Blobel GA, Banigan EJ, Hansen AS | Nature structural & molecular biology | 41107486 | Nat Struct Mol Biol | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/41107486 |
| A functional genomic framework to elucidate novel causal metabolic dysfunction-associated fatty liver disease genes. | Saliba-Gustafsson P, Justesen JM, Ranta A, Sharma D, Bielczyk-Maczynska E, Li J, Najmi LA, Apodaka M, Aspichueta P, Björck HM, Eriksson P, Schurr TM, Franco-Cereceda A, Gloudemans M, Mujica E, den Hoed M, Assimes TL, Quertermous T, Carcamo-Orive I, Park CY, Knowles JW | Hepatology (Baltimore, Md.) | 39190705 | Hepatology | 2025 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/39190705 |
| Label-Free Detection of Lipid Accumulation in Cells Using Magnetic Levitation. | Moncal KK, Najmi LA, Gupta R, Ramarao M, Knowles JW, Park CY, Durmus NG | Advanced biology | 40017001 | Adv Biol (Weinh) | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40017001 |
| Many Journeys Originating at the Same Source to Arrive at Solutions to the Common Problem of High Lipoprotein(a). | Luxama JW, Knowles JW | Circulation. Genomic and precision medicine | 40130305 | Circ Genom Precis Med | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/40130305 |
| Endurance Training Enhances Sex-Specific Cardioprotective Metabolism. | Brochet P, Montalvo S, Lindholm ME, Jimenez-Morales D, Jin CA, Rasmussen BB, Kraus WE, Yan Z, Wheeler MT, Katz DH | Circulation research | 40859825 | Circ Res | 2025 Sep 12 | https://www.ncbi.nlm.nih.gov/pubmed/40859825 |
| Exercise intensity modulates the human plasma secretome and interorgan communication. | Olsen L, Botella J, Barrows D, Romero E, Baird K, Katayama M, Kilic E, Peralta C, Sanford H, Farrell L, Axelrod CL, Plucińska K, Walker J, Yan L, Fredrickson K, Pourquie O, Robbins JM, Vinogradova EV, Kirwan JP, Zierath JR, Krook A, Gerszten RE, Bishop DJ, Cohen P | bioRxiv : the preprint server for biology | 41278785 | bioRxiv | 2025 Oct 23 | https://www.ncbi.nlm.nih.gov/pubmed/41278785 |
| Discovery of optimal cell type classification marker genes from single cell RNA sequencing data. | Liu A, Peng B, Pankajam AV, Duong TE, Pryhuber G, Scheuermann RH, Zhang Y | bioRxiv : the preprint server for biology | 38712147 | bioRxiv | 2024 Jun 26 | https://www.ncbi.nlm.nih.gov/pubmed/38712147 |
| A Multimodal Spatial and Epigenomic Atlas of Human Adult Lung Topography. | Duong TE, Diep D, Conklin KY, Bui I, Purkerson JM, Boone E, Olness J, Patel S, Peng B, Kern C, Zhao Z, Misra RS, Huyck HL, Verheyden JM, Borok Z, Zhang Y, Scheuermann RH, Zhu Q, Deutsch G, Hagood J, Sun X, Zhang K, Pryhuber GS | bioRxiv : the preprint server for biology | 40475598 | bioRxiv | 2025 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/40475598 |
| Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage. | Börner K, Blood PD, Silverstein JC, Ruffalo M, Satija R, Teichmann SA, Pryhuber GJ, Misra RS, Purkerson JM, Fan J, Hickey JW, Molla G, Xu C, Zhang Y, Weber GM, Jain Y, Qaurooni D, Kong Y, HRA Team, Bueckle A, Herr BW 2nd | Nature methods | 40082611 | Nat Methods | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/40082611 |
| Discovery of optimal cell type classification marker genes from single cell RNA sequencing data. | Liu A, Peng B, Pankajam AV, Duong TE, Pryhuber G, Scheuermann RH, Zhang Y | BMC methods | 40893796 | BMC Methods | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/40893796 |
| Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage. | Börner K, Blood PD, Silverstein JC, Ruffalo M, Satija R, Teichmann SA, Pryhuber G, Misra RS, Purkerson J, Fan J, Hickey JW, Molla G, Xu C, Zhang Y, Weber G, Jain Y, Qaurooni D, Kong Y, HRA Team, Bueckle A, Herr BW 2nd | bioRxiv : the preprint server for biology | 38826261 | bioRxiv | 2024 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/38826261 |
| Benchmarking single cell transcriptome matching methods for incremental growth of reference atlases. | Hu J, Peng B, Pankajam AV, Xu B, Deshpande VA, Bueckle A, Herr BW 2nd, Börner K, Dupont C, Scheuermann RH, Zhang Y | bioRxiv : the preprint server for biology | 40568082 | bioRxiv | 2025 Apr 16 | https://www.ncbi.nlm.nih.gov/pubmed/40568082 |
| NRCAM variant defined by microexon skipping is a targetable cell surface proteoform in high-grade gliomas. | Sehgal P, Naqvi AS, Higgins M, Liu J, Harvey K, Jarroux J, Kim T, Mankaliye B, Mishra P, Watterson G, Fine J, Davis J, Hayer KE, Castro A, Mogbo A, Drummer C 4th, Martinez D, Koptyra MP, Ang Z, Wang K, Farrel A, Quesnel-Vallieres M, Barash Y, Spangler JB, Rokita JL, Resnick AC, Tilgner HU, De Raedt T, Powell DJ Jr, Thomas-Tikhonenko A | Cell reports | 40782352 | Cell Rep | 2025 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/40782352 |
| Alternative splicing in pediatric central nervous system tumors highlights oncofetal candidate CLK1 exon 4. | Naqvi AS, Sullivan PJ, Corbett RJ, Sehgal P, Conkrite KL, Rathi KS, Ennis BM, Hayer KE, Zhang B, Brown MA, Miller DP, Sickler A, Kraya AA, Coleman KL, Dybas JM, Geng Z, Blackden C, Arif S, Chroni A, Lahiri A, Hollawell ML, Storm PB, Haydar D, Foster JB, Koptyra M, Madsen PJ, Diskin SJ, Thomas-Tikhonenko A, Resnick AC, Rokita JL | Neuro-oncology pediatrics | 41908886 | Neurooncol Pediatr | 2026 Jan | https://www.ncbi.nlm.nih.gov/pubmed/41908886 |
| Characterization of aberrant splicing in pediatric central nervous system tumors reveals CLK1 as a candidate oncogenic dependency. | Naqvi AS, Sullivan PJ, Corbett RJ, Sehgal P, Conkrite KL, Rathi KS, Ennis BM, Hayer KE, Zhang B, Brown MA, Miller DP, Sickler A, Kraya AA, Coleman KL, Dybas JM, Geng Z, Blackden C, Arif S, Chroni A, Lahiri A, Hollawell ML, Storm PB, Haydar D, Foster JB, Koptyra M, Madsen PJ, Diskin SJ, Thomas-Tikhonenko A, Resnick AC, Rokita JL | bioRxiv : the preprint server for biology | 39149264 | bioRxiv | 2025 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/39149264 |
| NRCAM variant defined by microexon skipping is a targetable cell surface proteoform in high-grade gliomas. | Sehgal P, Naqvi AS, Higgins M, Liu J, Harvey K, Jarroux J, Kim T, Mankaliye B, Mishra P, Watterson G, Fine J, Davis J, Hayer KE, Castro A, Mogbo A, Drummer C, Martinez D, Koptyra MP, Ang Z, Wang K, Farrel A, Quesnel-Vallieres M, Barash Y, Spangler JB, Rokita JL, Resnick AC, Tilgner HU, De Raedt T, Powell DJ, Thomas-Tikhonenko A | bioRxiv : the preprint server for biology | 39868324 | bioRxiv | 2025 Aug 4 | https://www.ncbi.nlm.nih.gov/pubmed/39868324 |
| Immunological biomarkers of aging. | Wu F, Mu WC, Markov NT, Fuentealba M, Halaweh H, Senchyna F, Manwaring-Mueller MN, Winer DA, Furman D | Journal of immunology (Baltimore, Md. : 1950) | 40443365 | J Immunol | 2025 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/40443365 |
| A blood-based epigenetic clock for intrinsic capacity predicts mortality and is associated with clinical, immunological and lifestyle factors. | Fuentealba M, Rouch L, Guyonnet S, Lemaitre JM, de Souto Barreto P, Vellas B, Andrieu S, Furman D | Nature aging | 40467932 | Nat Aging | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40467932 |
| An expanded registry of candidate cis-regulatory elements. | Moore JE, Pratt HE, Fan K, Phalke N, Fisher J, Elhajjajy SI, Andrews G, Gao M, Shedd N, Fu Y, Lacadie MC, Meza J, Khandpekar M, Ganna M, Choudhury E, Swofford R, Phan H, Ramirez CC, Campbell M, Likhite M, Farrell NP, Weimer AK, Pampari A, Ramalingam V, Reese F, Borsari B, Yu X, Wattenberg E, Ruiz-Romero M, Razavi-Mohseni M, Xu J, Galeev T, Colubri A, Beer MA, Guigó R, Gerstein MB, Engreitz JM, Ljungman M, Reddy TE, Snyder MP, Epstein CB, Gaskell E, Bernstein BE, Dickel DE, Visel A, Pennacchio LA, Mortazavi A, Kundaje A, Weng Z | Nature | 41501460 | Nature | 2026 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/41501460 |
| High-throughput in silico screen uncovers key regulators of 3D genome architecture. | Bai J, Lyu Q, Tan J, Issner R, Tischer B, Liu H, Goel V, Ling X, Bernstein BE, Tsirigos A, Hansen AS, Xia B | bioRxiv : the preprint server for biology | 41415375 | bioRxiv | 2025 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/41415375 |
| Multimodal learning decodes the global binding landscape of chromatin-associated proteins. | Tan J, Fu X, Ling X, Mo S, Bai J, Rabadán R, Fenyö D, Boeke JD, Tsirigos A, Xia B | bioRxiv : the preprint server for biology | 40832322 | bioRxiv | 2025 Aug 17 | https://www.ncbi.nlm.nih.gov/pubmed/40832322 |
| reguloGPT: Harnessing GPT for Knowledge Graph Construction of Molecular Regulatory Pathways. | Wu X, Zeng Y, Das A, Jo S, Zhang T, Patel P, Zhang J, Gao SJ, Pratt D, Chiu YC, Huang Y | bioRxiv : the preprint server for biology | 38313267 | bioRxiv | 2024 Jan 30 | https://www.ncbi.nlm.nih.gov/pubmed/38313267 |
| Cell type prediction with neighborhood-enhanced cellular embedding using deep learning on hematoxylin and eosin-stained images. | Phan NN, Wang H, Nayak T, Ye Z, Chiu YC, Jin Y, Huang Y, Chen Y | Computational and structural biotechnology journal | 40735431 | Comput Struct Biotechnol J | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40735431 |
| shinyDeepDR: A user-friendly R Shiny app for predicting anti-cancer drug response using deep learning. | Wang LJ, Ning M, Nayak T, Kasper MJ, Monga SP, Huang Y, Chen Y, Chiu YC | Patterns (New York, N.Y.) | 38370127 | Patterns (N Y) | 2024 Feb 9 | https://www.ncbi.nlm.nih.gov/pubmed/38370127 |
| High-Throughput Empirical and Virtual Screening To Discover Novel Inhibitors of Polyploid Giant Cancer Cells in Breast Cancer. | Ma Y, Shih CH, Cheng J, Chen HC, Wang LJ, Tan Y, Zhang Y, Brown DD, Oesterreich S, Lee AV, Chiu YC, Chen YC | Analytical chemistry | 40040372 | Anal Chem | 2025 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/40040372 |
| Inferring Drug-Gene Relationships in Cancer Using Literature-Augmented Large Language Models. | Lai YJ, Wang LJ, Yasaka TM, Shin Y, Ning M, Tan Y, Shih CH, Guo Y, Chen PY, Galloway H, Liu Z, Das A, Tseng GC, Monga SP, Huang Y, Chiu YC | Cancer research communications | 40293950 | Cancer Res Commun | 2025 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/40293950 |
| Effects of Lamina-Chromatin Attachment on Super Long-Range Chromatin Interactions. | Delafrouz P, Farooq H, Du L, Ma A, Liang J | bioRxiv : the preprint server for biology | 40027763 | bioRxiv | 2025 Feb 17 | https://www.ncbi.nlm.nih.gov/pubmed/40027763 |
| Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations. | Du L, Farooq H, Delafrouz P, Liang J | Bioinformatics (Oxford, England) | 39891345 | Bioinformatics | 2025 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/39891345 |
| ChromPolymerDB: A High-Resolution Database of Single-Cell 3D Chromatin Structures for Functional Genomics. | Chen M, Du L, Zhao S, Ye B, Delafrouz P, Farooq H, Chattopadhyay D, Marai GE, Shao Z, Liang J, Czajkowsky DM, Chronis C | bioRxiv : the preprint server for biology | 41256645 | bioRxiv | 2025 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/41256645 |
| ChromPolymerDB: a high-resolution database of single-cell 3D chromatin structures for functional genomics. | Chen M, Du L, Zhao S, Ye B, Delafrouz P, Farooq H, Chattopadhyay D, Marai GE, Shao Z, Liang J, Czajkowsky DM, Chronis C | Nucleic acids research | 41251144 | Nucleic Acids Res | 2026 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/41251144 |
| African Green Monkeys Respond to Synthetic Aβ Oligomers with Persistent Alzheimer's-like Activation. | Brown BRP, Li X, Grasty MR, Lopez IR, Dzigurski S, Geradi MN, Weed MR, Elsworth JD, Lawrence M, Gürsoy G, Miranker AD | bioRxiv : the preprint server for biology | 41279249 | bioRxiv | 2025 Oct 8 | https://www.ncbi.nlm.nih.gov/pubmed/41279249 |
| Estimating the size of long tandem repeat expansions from short reads with ScatTR. | Al-Abri R, Gürsoy G | Genome research | 40841169 | Genome Res | 2025 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/40841169 |
| ScatTR: Estimating the Size of Long Tandem Repeat Expansions from Short-Reads. | Al-Abri R, Gürsoy G | bioRxiv : the preprint server for biology | 40027646 | bioRxiv | 2025 Feb 20 | https://www.ncbi.nlm.nih.gov/pubmed/40027646 |
| Computational Analysis of the Gut Microbiota-Mediated Drug Metabolism. | Chum S, Naveira Montalvo A, Hassoun S | bioRxiv : the preprint server for biology | 39764061 | bioRxiv | 2025 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/39764061 |
| Transcriptomic Meta-analysis Identifies Long Non-Coding RNAs Mediating Zika's Oncolytic Impact in Glioblastoma Multiforme. | Kousa YA, Singh S, Horvath A, Tomasso F, Nazarian J, Henderson L, Mansour TA | bioRxiv : the preprint server for biology | 39372798 | bioRxiv | 2024 Aug 4 | https://www.ncbi.nlm.nih.gov/pubmed/39372798 |
| Transcriptional risk scores in Alzheimer's disease: From pathology to cognition. | Pyun JM, Park YH, Wang J, Bennett DA, Bice PJ, Kim JP, Kim S, Saykin AJ, Nho K | Alzheimer's & dementia : the journal of the Alzheimer's Association | 37563770 | Alzheimers Dement | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/37563770 |
| Accurate estimation of rare cell type fractions from tissue omics data via hierarchical deconvolution. | Huang P, Cai M, Lu X, McKennan C, Wang J | bioRxiv : the preprint server for biology | 36993280 | bioRxiv | 2023 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/36993280 |
| EMixed: Probabilistic Multi-Omics Cellular Deconvolution of Bulk Omics Data. | Cai M, Zhao K, Huang P, Celedón JC, McKennan C, Chen W, Wang J | Journal of data science : JDS | 41112940 | J Data Sci | 2025 Feb 26 | https://www.ncbi.nlm.nih.gov/pubmed/41112940 |
| BLEND: Probabilistic Cellular Deconvolution with Automated Reference Selection. | Huang P, Cai M, McKennan C, Wang J | bioRxiv : the preprint server for biology | 39149243 | bioRxiv | 2024 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/39149243 |
| scMD facilitates cell type deconvolution using single-cell DNA methylation references. | Cai M, Zhou J, McKennan C, Wang J | Communications biology | 38168620 | Commun Biol | 2024 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/38168620 |
| scMD: cell type deconvolution using single-cell DNA methylation references. | Cai M, Zhou J, McKennan C, Wang J | bioRxiv : the preprint server for biology | 37577715 | bioRxiv | 2023 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/37577715 |
| BLEND: probabilistic cellular deconvolution with individualized single-cell reference integration. | Huang P, Cai M, McKennan C, Wang J | Genome biology | 41039482 | Genome Biol | 2025 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/41039482 |
| Machine learning-predicted chromatin organization landscape across pediatric tumors. | Gjoni K, Zhang S, Yan RE, Zhang B, Miller D, Greenfield JP, Resnick A, Dahmane N, Pollard KS | Scientific reports | 41904260 | Sci Rep | 2026 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/41904260 |
| Comparing chromatin contact maps at scale: methods and insights. | Gunsalus LM, McArthur E, Gjoni K, Kuang S, Pittman M, Capra JA, Pollard KS | bioRxiv : the preprint server for biology | 37066196 | bioRxiv | 2023 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/37066196 |
| SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models. | Gjoni K, Pollard KS | Bioinformatics (Oxford, England) | 38796686 | Bioinformatics | 2024 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/38796686 |
| De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes. | Gjoni K, Ren X, Everitt A, Shen Y, Pollard KS | bioRxiv : the preprint server for biology | 39574698 | bioRxiv | 2024 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/39574698 |
| SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models. | Gjoni K, Pollard KS | bioRxiv : the preprint server for biology | 37961123 | bioRxiv | 2023 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/37961123 |
| Comparing chromatin contact maps at scale: methods and insights. | Gunsalus LM, McArthur E, Gjoni K, Kuang S, Pittman M, Capra JA, Pollard KS | Research square | 37292728 | Res Sq | 2023 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/37292728 |
| Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling. | Yan RE, Corman A, Katgara L, Wang X, Xue X, Gajic ZZ, Sam R, Farid M, Friedman SM, Choo J, Raimondi I, Ganesan S, Katsevich E, Greenfield JP, Dahmane N, Sanjana NE | Nature biotechnology | 39572737 | Nat Biotechnol | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39572737 |
| Comparing chromatin contact maps at scale: methods and insights. | Gjoni K, Gunsalus LM, Kuang S, McArthur E, Pittman M, Capra JA, Pollard KS | Nature methods | 40108448 | Nat Methods | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/40108448 |
| Flnc: Machine Learning Improves the Identification of Novel Long Noncoding RNAs from Stand-Alone RNA-Seq Data. | Li Z, Zhou P, Kwon E, Fitzgerald KA, Weng Z, Zhou C | Non-coding RNA | 36287122 | Noncoding RNA | 2022 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/36287122 |
| LibGen: Generating High Quality Spectral Libraries of Natural Products for EAD-, UVPD-, and HCD-High Resolution Mass Spectrometers. | Kong F, Keshet U, Shen T, Rodriguez E, Fiehn O | Analytical chemistry | 37939222 | Anal Chem | 2023 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/37939222 |
| High-Resolution Mass Spectrometry for Human Exposomics: Expanding Chemical Space Coverage. | Lai Y, Koelmel JP, Walker DI, Price EJ, Papazian S, Manz KE, Castilla-Fernández D, Bowden JA, Nikiforov V, David A, Bessonneau V, Amer B, Seethapathy S, Hu X, Lin EZ, Jbebli A, McNeil BR, Barupal D, Cerasa M, Xie H, Kalia V, Nandakumar R, Singh R, Tian Z, Gao P, Zhao Y, Froment J, Rostkowski P, Dubey S, Coufalíková K, Seličová H, Hecht H, Liu S, Udhani HH, Restituito S, Tchou-Wong KM, Lu K, Martin JW, Warth B, Godri Pollitt KJ, Klánová J, Fiehn O, Metz TO, Pennell KD, Jones DP, Miller GW | Environmental science & technology | 38984754 | Environ Sci Technol | 2024 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/38984754 |
| Metabolomic characterization of human glioblastomas and patient plasma: a pilot study. | Liu YA, Aboud O, Dahabiyeh LA, Bloch O, Fiehn O | F1000Research | 39371551 | F1000Res | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/39371551 |
| Alternative Identification of Glycosides Using MS/MS Matching with an In Silico-Modified Aglycone Mass Spectra Library. | Rodríguez EP, Li Y, Vaniya A, Shih PM, Fiehn O | Analytical chemistry | 37390485 | Anal Chem | 2023 Jul 18 | https://www.ncbi.nlm.nih.gov/pubmed/37390485 |
| Flash entropy search to query all mass spectral libraries in real time. | Li Y, Fiehn O | Nature methods | 37735567 | Nat Methods | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37735567 |
| A pilot study on metabolomic characterization of human glioblastomas and patient plasma. | Liu A, Aboud O, Dahabiyeh LA, Bloch O, Fiehn O | Research square | 36945517 | Res Sq | 2023 Mar 10 | https://www.ncbi.nlm.nih.gov/pubmed/36945517 |
| Differences in the Stool Metabolome between Vegans and Omnivores: Analyzing the NIST Stool Reference Material. | Cumeras R, Shen T, Valdiviez L, Tippins Z, Haffner BD, Fiehn O | Metabolites | 37623865 | Metabolites | 2023 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/37623865 |
| De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens. | Weiskittel TM, Ung CY, Correia C, Zhang C, Li H | Genome research | 34876496 | Genome Res | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/34876496 |
| Deciphering tumour microenvironment and elucidating the origin of cancer cells in ovarian clear cell carcinoma. | Kamaraj US, Gautam P, Cheng T, Chin TS, Tay SK, Ho TH, Nadarajah R, Goh RCH, Wong SL, Mantoo S, Busmanis I, Li H, Le MT, Li QJ, Lim EH, Loh YH | bioRxiv : the preprint server for biology | 39149248 | bioRxiv | 2024 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/39149248 |
| Glycogen synthase kinase 3 activity enhances liver inflammation in MASH. | Khoury M, Guo Q, Furuta K, Correia C, Meroueh C, Kim Lee HS, Warasnhe K, Valenzuela-Pérez L, Mazar AP, Kim I, Noh YK, Holmes H, Romero MF, Sussman CR, Pavelko KD, Islam S, Bamidele AO, Hirsova P, Li H, Ibrahim SH | JHEP reports : innovation in hepatology | 38882600 | JHEP Rep | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/38882600 |
| Artificial Clinic Intelligence (ACI): A Generative AI-Powered Modeling Platform to Optimize Patient Cohort Enrichment and Clinical Trial Optimization. | Ung CY, Correia C, Zhang Z, Caya C, Zhu S, Billadeau DD, Li H | Cancers | 41228335 | Cancers (Basel) | 2025 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/41228335 |
| Manifold medicine: A schema that expands treatment dimensionality. | Ung CY, Weiskittel TM, Correia C, Kaufmann SH, Li H | Drug discovery today | 34600126 | Drug Discov Today | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/34600126 |
| Network Biology-Inspired Machine Learning Features Predict Cancer Gene Targets and Reveal Target Coordinating Mechanisms. | Weiskittel TM, Cao A, Meng-Lin K, Lehmann Z, Feng B, Correia C, Zhang C, Wisniewski P, Zhu S, Yong Ung C, Li H | Pharmaceuticals (Basel, Switzerland) | 37242535 | Pharmaceuticals (Basel) | 2023 May 16 | https://www.ncbi.nlm.nih.gov/pubmed/37242535 |
| Senescent alveolar macrophages promote early-stage lung tumorigenesis. | Prieto LI, Sturmlechner I, Graves SI, Zhang C, Goplen NP, Yi ES, Sun J, Li H, Baker DJ | Cancer cell | 37267954 | Cancer Cell | 2023 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/37267954 |
| Multiorgan locked-state model of chronic diseases and systems pharmacology opportunities. | Ung CY, Correia C, Li H, Adams CM, Westendorf JJ, Zhu S | Drug discovery today | 37967790 | Drug Discov Today | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/37967790 |
| Codon specific readthrough as a mechanism of BRCA2 restoration in acquired PARP inhibitor and chemotherapy resistance. | McGehee CD, Meng XW, Wu X, Correia C, Venkatachalam A, Flatten KS, Peterson KL, Patel AG, Rossman OK, Wong C, Hurley RM, Wagner JM, Schneider PA, Dai H, Poirier GG, Hendrickson AEW, Swisher EM, Pandey A, Li H, Kaufmann SH | Nucleic acids research | 41099700 | Nucleic Acids Res | 2025 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/41099700 |
| The Rise of Hypothesis-Driven Artificial Intelligence in Oncology. | Xianyu Z, Correia C, Ung CY, Zhu S, Billadeau DD, Li H | Cancers | 38398213 | Cancers (Basel) | 2024 Feb 18 | https://www.ncbi.nlm.nih.gov/pubmed/38398213 |
| SPIN-AI: A Deep Learning Model That Identifies Spatially Predictive Genes. | Meng-Lin K, Ung CY, Zhang C, Weiskittel TM, Wisniewski P, Zhang Z, Tan SH, Yeo KS, Zhu S, Correia C, Li H | Biomolecules | 37371475 | Biomolecules | 2023 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/37371475 |
| Manifold epigenetics: A conceptual model that guides engineering strategies to improve whole-body regenerative health. | Ung CY, Correia C, Billadeau DD, Zhu S, Li H | Frontiers in cell and developmental biology | 36866271 | Front Cell Dev Biol | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/36866271 |
| Single-nucleus multiomic mapping of m(6)A methylomes and transcriptomes in native populations of cells with sn-m6A-CT. | Hamashima K, Wong KW, Sam TW, Teo JHJ, Taneja R, Le MTN, Li QJ, Hanna JH, Li H, Loh YH | Molecular cell | 37657444 | Mol Cell | 2023 Aug 25 | https://www.ncbi.nlm.nih.gov/pubmed/37657444 |
| Loop Catalog: a comprehensive HiChIP database of human and mouse samples. | Reyna J, Fetter K, Ignacio R, Ali Marandi CC, Ma A, Rao N, Jiang Z, Figueroa DS, Bhattacharyya S, Ay F | bioRxiv : the preprint server for biology | 38746164 | bioRxiv | 2025 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/38746164 |
| Loop Catalog: a comprehensive HiChIP database of human and mouse samples. | Reyna J, Fetter K, Ignacio R, Marandi CCA, Ma A, Rao N, Jiang Z, Figueroa DS, Bhattacharyya S, Ay F | Genome biology | 40542429 | Genome Biol | 2025 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/40542429 |
| The underappreciated diversity of bile acid modifications. | Mohanty I, Mannochio-Russo H, Schweer JV, El Abiead Y, Bittremieux W, Xing S, Schmid R, Zuffa S, Vasquez F, Muti VB, Zemlin J, Tovar-Herrera OE, Moraïs S, Desai D, Amin S, Koo I, Turck CW, Mizrahi I, Kris-Etherton PM, Petersen KS, Fleming JA, Huan T, Patterson AD, Siegel D, Hagey LR, Wang M, Aron AT, Dorrestein PC | Cell | 38471500 | Cell | 2024 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/38471500 |
| ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization. | Shahneh MRZ, Strobel M, Vitale GA, Geibel C, Abiead YE, Garg N, Wagner B, Forchhammer K, Aron A, Phelan VV, Petras D, Wang M | Journal of the American Society for Mass Spectrometry | 38830143 | J Am Soc Mass Spectrom | 2024 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/38830143 |
| Leptochelins A-C, Cytotoxic Metallophores Produced by Geographically Dispersed Leptothoe Strains of Marine Cyanobacteria. | Avalon NE, Reis MA, Thornburg CC, Williamson RT, Petras D, Aron AT, Neuhaus GF, Al-Hindy M, Mitrevska J, Ferreira L, Morais J, El Abiead Y, Glukhov E, Alexander KL, Vulpanovici FA, Bertin MJ, Whitner S, Choi H, Spengler G, Blinov K, Almohammadi AM, Shaala LA, Kew WR, Paša-Tolić L, Youssef DTA, Dorrestein PC, Vasconcelos V, Gerwick L, McPhail KL, Gerwick WH | Journal of the American Chemical Society | 38918178 | J Am Chem Soc | 2024 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/38918178 |
| The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns. | Salido RA, Zhao HN, McDonald D, Mannochio-Russo H, Zuffa S, Oles RE, Aron AT, El Abiead Y, Farmer S, González A, Martino C, Mohanty I, Parker CW, Patel L, Portal Gomes PW, Schmid R, Schwartz T, Zhu J, Barratt MR, Rubins KH, Chu H, Karouia F, Venkateswaran K, Dorrestein PC, Knight R | Cell | 40020666 | Cell | 2025 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/40020666 |
| A universal language for finding mass spectrometry data patterns. | Damiani T, Jarmusch AK, Aron AT, Petras D, Phelan VV, Zhao HN, Bittremieux W, Acharya DD, Ahmed MMA, Bauermeister A, Bertin MJ, Boudreau PD, Borges RM, Bowen BP, Brown CJ, Chagas FO, Clevenger KD, Correia MSP, Crandall WJ, Crüsemann M, Fahy E, Fiehn O, Garg N, Gerwick WH, Gilbert JR, Globisch D, Gomes PWP, Heuckeroth S, James CA, Jarmusch SA, Kakhkhorov SA, Kang KB, Kessler N, Kersten RD, Kim H, Kirk RD, Kohlbacher O, Kontou EE, Liu K, Lizama-Chamu I, Luu GT, Luzzatto Knaan T, Mannochio-Russo H, Marty MT, Matsuzawa Y, McAvoy AC, McCall LI, Mohamed OG, Nahor O, Neuweger H, Niedermeyer THJ, Nishida K, Northen TR, Overdahl KE, Rainer J, Reher R, Rodriguez E, Sachsenberg TT, Sanchez LM, Schmid R, Stevens C, Subramaniam S, Tian Z, Tripathi A, Tsugawa H, van der Hooft JJJ, Vicini A, Walter A, Weber T, Xiong Q, Xu T, Pluskal T, Dorrestein PC, Wang M | Nature methods | 40355727 | Nat Methods | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/40355727 |
| Reproducible mass spectrometry data processing and compound annotation in MZmine 3. | Heuckeroth S, Damiani T, Smirnov A, Mokshyna O, Brungs C, Korf A, Smith JD, Stincone P, Dreolin N, Nothias LF, Hyötyläinen T, Orešič M, Karst U, Dorrestein PC, Petras D, Du X, van der Hooft JJJ, Schmid R, Pluskal T | Nature protocols | 38769143 | Nat Protoc | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/38769143 |
| Unified and Standardized Mass Spectrometry Data Processing in Python Using spectrum_utils. | Bittremieux W, Levitsky L, Pilz M, Sachsenberg T, Huber F, Wang M, Dorrestein PC | Journal of proteome research | 36688502 | J Proteome Res | 2023 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/36688502 |
| A guide to reverse metabolomics-a framework for big data discovery strategy. | Charron-Lamoureux V, Mannochio-Russo H, Lamichhane S, Xing S, Patan A, Portal Gomes PW, Rajkumar P, Deleray V, Caraballo-Rodríguez AM, Chua KV, Lee LS, Liu Z, Ching J, Wang M, Dorrestein PC | Nature protocols | 40021805 | Nat Protoc | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/40021805 |
| Defining the Roles of Cardiokines in Human Aging and Age-Associated Diseases. | Srivastava H, Pozzoli M, Lau E | Frontiers in aging | 35821831 | Front Aging | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35821831 |
| Protein prediction models support widespread post-transcriptional regulation of protein abundance by interacting partners. | Srivastava H, Lippincott MJ, Currie J, Canfield R, Lam MPY, Lau E | PLoS computational biology | 36356032 | PLoS Comput Biol | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/36356032 |
| Proteogenomics reveals sex-biased aging genes and coordinated splicing in cardiac aging. | Han Y, Wennersten SA, Wright JM, Ludwig RW, Lau E, Lam MPY | American journal of physiology. Heart and circulatory physiology | 35930447 | Am J Physiol Heart Circ Physiol | 2022 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/35930447 |
| SALVE: prediction of interorgan communication with transcriptome latent space representation. | Pavelka J, Voong CK, Schaal P, Lam MPY, Lau E | American journal of physiology. Heart and circulatory physiology | 41191057 | Am J Physiol Heart Circ Physiol | 2025 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/41191057 |
| Harmonizing Labeling and Analytical Strategies to Obtain Protein Turnover Rates in Intact Adult Animals. | Hammond DE, Simpson DM, Franco C, Wright Muelas M, Waters J, Ludwig RW, Prescott MC, Hurst JL, Beynon RJ, Lau E | Molecular & cellular proteomics : MCP | 35636728 | Mol Cell Proteomics | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35636728 |
| Association studies of up to 1.2 million individuals yield new insights into the genetic etiology of tobacco and alcohol use. | Liu M, Jiang Y, Wedow R, Li Y, Brazel DM, Chen F, Datta G, Davila-Velderrain J, McGuire D, Tian C, Zhan X, 23andMe Research Team, HUNT All-In Psychiatry, Choquet H, Docherty AR, Faul JD, Foerster JR, Fritsche LG, Gabrielsen ME, Gordon SD, Haessler J, Hottenga JJ, Huang H, Jang SK, Jansen PR, Ling Y, Mägi R, Matoba N, McMahon G, Mulas A, Orrù V, Palviainen T, Pandit A, Reginsson GW, Skogholt AH, Smith JA, Taylor AE, Turman C, Willemsen G, Young H, Young KA, Zajac GJM, Zhao W, Zhou W, Bjornsdottir G, Boardman JD, Boehnke M, Boomsma DI, Chen C, Cucca F, Davies GE, Eaton CB, Ehringer MA, Esko T, Fiorillo E, Gillespie NA, Gudbjartsson DF, Haller T, Harris KM, Heath AC, Hewitt JK, Hickie IB, Hokanson JE, Hopfer CJ, Hunter DJ, Iacono WG, Johnson EO, Kamatani Y, Kardia SLR, Keller MC, Kellis M, Kooperberg C, Kraft P, Krauter KS, Laakso M, Lind PA, Loukola A, Lutz SM, Madden PAF, Martin NG, McGue M, McQueen MB, Medland SE, Metspalu A, Mohlke KL, Nielsen JB, Okada Y, Peters U, Polderman TJC, Posthuma D, Reiner AP, Rice JP, Rimm E, Rose RJ, Runarsdottir V, Stallings MC, Stančáková A, Stefansson H, Thai KK, Tindle HA, Tyrfingsson T, Wall TL, Weir DR, Weisner C, Whitfield JB, Winsvold BS, Yin J, Zuccolo L, Bierut LJ, Hveem K, Lee JJ, Munafò MR, Saccone NL, Willer CJ, Cornelis MC, David SP, Hinds DA, Jorgenson E, Kaprio J, Stitzel JA, Stefansson K, Thorgeirsson TE, Abecasis G, Liu DJ, Vrieze S | Nature genetics | 30643251 | Nat Genet | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30643251 |
| Rare genetic variants explain missing heritability in smoking. | Jang SK, Evans L, Fialkowski A, Arnett DK, Ashley-Koch AE, Barnes KC, Becker DM, Bis JC, Blangero J, Bleecker ER, Boorgula MP, Bowden DW, Brody JA, Cade BE, Jenkins BWC, Carson AP, Chavan S, Cupples LA, Custer B, Damrauer SM, David SP, de Andrade M, Dinardo CL, Fingerlin TE, Fornage M, Freedman BI, Garrett ME, Gharib SA, Glahn DC, Haessler J, Heckbert SR, Hokanson JE, Hou L, Hwang SJ, Hyman MC, Judy R, Justice AE, Kaplan RC, Kardia SLR, Kelly S, Kim W, Kooperberg C, Levy D, Lloyd-Jones DM, Loos RJF, Manichaikul AW, Gladwin MT, Martin LW, Nouraie M, Melander O, Meyers DA, Montgomery CG, North KE, Oelsner EC, Palmer ND, Payton M, Peljto AL, Peyser PA, Preuss M, Psaty BM, Qiao D, Rader DJ, Rafaels N, Redline S, Reed RM, Reiner AP, Rich SS, Rotter JI, Schwartz DA, Shadyab AH, Silverman EK, Smith NL, Smith JG, Smith AV, Smith JA, Tang W, Taylor KD, Telen MJ, Vasan RS, Gordeuk VR, Wang Z, Wiggins KL, Yanek LR, Yang IV, Young KA, Young KL, Zhang Y, Liu DJ, Keller MC, Vrieze S | Nature human behaviour | 35927319 | Nat Hum Behav | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/35927319 |
| Integrating 3D genomic and epigenomic data to enhance target gene discovery and drug repurposing in transcriptome-wide association studies. | Khunsriraksakul C, McGuire D, Sauteraud R, Chen F, Yang L, Wang L, Hughey J, Eckert S, Dylan Weissenkampen J, Shenoy G, Marx O, Carrel L, Jiang B, Liu DJ | Nature communications | 35672318 | Nat Commun | 2022 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/35672318 |
| Multi-ancestry and multi-trait genome-wide association meta-analyses inform clinical risk prediction for systemic lupus erythematosus. | Khunsriraksakul C, Li Q, Markus H, Patrick MT, Sauteraud R, McGuire D, Wang X, Wang C, Wang L, Chen S, Shenoy G, Li B, Zhong X, Olsen NJ, Carrel L, Tsoi LC, Jiang B, Liu DJ | Nature communications | 36750564 | Nat Commun | 2023 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/36750564 |
| Genetic diversity fuels gene discovery for tobacco and alcohol use. | Saunders GRB, Wang X, Chen F, Jang SK, Liu M, Wang C, Gao S, Jiang Y, Khunsriraksakul C, Otto JM, Addison C, Akiyama M, Albert CM, Aliev F, Alonso A, Arnett DK, Ashley-Koch AE, Ashrani AA, Barnes KC, Barr RG, Bartz TM, Becker DM, Bielak LF, Benjamin EJ, Bis JC, Bjornsdottir G, Blangero J, Bleecker ER, Boardman JD, Boerwinkle E, Boomsma DI, Boorgula MP, Bowden DW, Brody JA, Cade BE, Chasman DI, Chavan S, Chen YI, Chen Z, Cheng I, Cho MH, Choquet H, Cole JW, Cornelis MC, Cucca F, Curran JE, de Andrade M, Dick DM, Docherty AR, Duggirala R, Eaton CB, Ehringer MA, Esko T, Faul JD, Fernandes Silva L, Fiorillo E, Fornage M, Freedman BI, Gabrielsen ME, Garrett ME, Gharib SA, Gieger C, Gillespie N, Glahn DC, Gordon SD, Gu CC, Gu D, Gudbjartsson DF, Guo X, Haessler J, Hall ME, Haller T, Harris KM, He J, Herd P, Hewitt JK, Hickie I, Hidalgo B, Hokanson JE, Hopfer C, Hottenga J, Hou L, Huang H, Hung YJ, Hunter DJ, Hveem K, Hwang SJ, Hwu CM, Iacono W, Irvin MR, Jee YH, Johnson EO, Joo YY, Jorgenson E, Justice AE, Kamatani Y, Kaplan RC, Kaprio J, Kardia SLR, Keller MC, Kelly TN, Kooperberg C, Korhonen T, Kraft P, Krauter K, Kuusisto J, Laakso M, Lasky-Su J, Lee WJ, Lee JJ, Levy D, Li L, Li K, Li Y, Lin K, Lind PA, Liu C, Lloyd-Jones DM, Lutz SM, Ma J, Mägi R, Manichaikul A, Martin NG, Mathur R, Matoba N, McArdle PF, McGue M, McQueen MB, Medland SE, Metspalu A, Meyers DA, Millwood IY, Mitchell BD, Mohlke KL, Moll M, Montasser ME, Morrison AC, Mulas A, Nielsen JB, North KE, Oelsner EC, Okada Y, Orrù V, Palmer ND, Palviainen T, Pandit A, Park SL, Peters U, Peters A, Peyser PA, Polderman TJC, Rafaels N, Redline S, Reed RM, Reiner AP, Rice JP, Rich SS, Richmond NE, Roan C, Rotter JI, Rueschman MN, Runarsdottir V, Saccone NL, Schwartz DA, Shadyab AH, Shi J, Shringarpure SS, Sicinski K, Skogholt AH, Smith JA, Smith NL, Sotoodehnia N, Stallings MC, Stefansson H, Stefansson K, Stitzel JA, Sun X, Syed M, Tal-Singer R, Taylor AE, Taylor KD, Telen MJ, Thai KK, Tiwari H, Turman C, Tyrfingsson T, Wall TL, Walters RG, Weir DR, Weiss ST, White WB, Whitfield JB, Wiggins KL, Willemsen G, Willer CJ, Winsvold BS, Xu H, Yanek LR, Yin J, Young KL, Young KA, Yu B, Zhao W, Zhou W, Zöllner S, Zuccolo L, 23andMe Research Team, Biobank Japan Project, Batini C, Bergen AW, Bierut LJ, David SP, Gagliano Taliun SA, Hancock DB, Jiang B, Munafò MR, Thorgeirsson TE, Liu DJ, Vrieze S | Nature | 36477530 | Nature | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36477530 |
| Dissecting heritability, environmental risk, and air pollution causal effects using > 50 million individuals in MarketScan. | McGuire D, Markus H, Yang L, Xu J, Montgomery A, Berg A, Li Q, Carrel L, Liu DJ, Jiang B | Nature communications | 38918381 | Nat Commun | 2024 Jun 25 | https://www.ncbi.nlm.nih.gov/pubmed/38918381 |
| Construction and Application of Polygenic Risk Scores in Autoimmune Diseases. | Khunsriraksakul C, Markus H, Olsen NJ, Carrel L, Jiang B, Liu DJ | Frontiers in immunology | 35833142 | Front Immunol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35833142 |
| Assessing reproducibility of high-throughput experiments in the case of missing data. | Singh R, Zhang F, Li Q | Statistics in medicine | 35178743 | Stat Med | 2022 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/35178743 |
| Multi-ancestry transcriptome-wide association analyses yield insights into tobacco use biology and drug repurposing. | Chen F, Wang X, Jang SK, Quach BC, Weissenkampen JD, Khunsriraksakul C, Yang L, Sauteraud R, Albert CM, Allred NDD, Arnett DK, Ashley-Koch AE, Barnes KC, Barr RG, Becker DM, Bielak LF, Bis JC, Blangero J, Boorgula MP, Chasman DI, Chavan S, Chen YI, Chuang LM, Correa A, Curran JE, David SP, de las Fuentes L, Deka R, Duggirala R, Faul JD, Garrett ME, Gharib SA, Guo X, Hall ME, Hawley NL, He J, Hobbs BD, Hokanson JE, Hsiung CA, Hwang SJ, Hyde TM, Irvin MR, Jaffe AE, Johnson EO, Kaplan R, Kardia SLR, Kaufman JD, Kelly TN, Kleinman JE, Kooperberg C, Lee IT, Levy D, Lutz SM, Manichaikul AW, Martin LW, Marx O, McGarvey ST, Minster RL, Moll M, Moussa KA, Naseri T, North KE, Oelsner EC, Peralta JM, Peyser PA, Psaty BM, Rafaels N, Raffield LM, Reupena MS, Rich SS, Rotter JI, Schwartz DA, Shadyab AH, Sheu WH, Sims M, Smith JA, Sun X, Taylor KD, Telen MJ, Watson H, Weeks DE, Weir DR, Yanek LR, Young KA, Young KL, Zhao W, Hancock DB, Jiang B, Vrieze S, Liu DJ | Nature genetics | 36702996 | Nat Genet | 2023 Feb | https://www.ncbi.nlm.nih.gov/pubmed/36702996 |
| Deep learning enabled multi-organ segmentation of mouse embryos. | Rolfe SM, Whikehart SM, Maga AM | Biology open | 36802342 | Biol Open | 2023 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/36802342 |
| Streamlining Asymmetry Quantification in Fetal Mouse Imaging: A Semi-Automated Pipeline Supported by Expert Guidance. | Rolfe SM, Mao D, Maga AM | bioRxiv : the preprint server for biology | 39554050 | bioRxiv | 2024 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/39554050 |
| Streamlining asymmetry quantification in fetal mouse imaging: A semi-automated pipeline supported by expert guidance. | Rolfe SM, Mao D, Maga AM | Developmental dynamics : an official publication of the American Association of Anatomists | 40421888 | Dev Dyn | 2025 Aug | https://www.ncbi.nlm.nih.gov/pubmed/40421888 |
| Proteogenomic Markers of Chemotherapy Resistance and Response in Triple-Negative Breast Cancer. | Anurag M, Jaehnig EJ, Krug K, Lei JT, Bergstrom EJ, Kim BJ, Vashist TD, Huynh AMT, Dou Y, Gou X, Huang C, Shi Z, Wen B, Korchina V, Gibbs RA, Muzny DM, Doddapaneni H, Dobrolecki LE, Rodriguez H, Robles AI, Hiltke T, Lewis MT, Nangia JR, Nemati Shafaee M, Li S, Hagemann IS, Hoog J, Lim B, Osborne CK, Mani DR, Gillette MA, Zhang B, Echeverria GV, Miles G, Rimawi MF, Carr SA, Ademuyiwa FO, Satpathy S, Ellis MJ | Cancer discovery | 36001024 | Cancer Discov | 2022 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/36001024 |
| Proteogenomic analysis of the CALGB 40601 (Alliance) HER2+ breast cancer neoadjuvant trial reveals resistance biomarkers. | Jaehnig EJ, Fernandez-Martinez A, Vashist TD, Holt MV, Williams L, Lei JT, Moon CI, Kim BJ, Dou Y, Zhao H, Korchina V, Gibbs RA, Muzny DM, Doddapaneni H, Perou CM, Carey LA, Robles AI, Hyslop T, Wen Y, McCart L, Krek A, Petralia F, Miles G, Kavuri SM, Gillette MA, Mani DR, Carr SA, Zhang B, Ellis MJ, Satpathy S, Anurag M | Cell reports. Medicine | 40480221 | Cell Rep Med | 2025 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/40480221 |
| Potential and Progress of 2D Materials in Photomedicine for Cancer Treatment. | Bhatt HN, Pena-Zacarias J, Beaven E, Zahid MI, Ahmad SS, Diwan R, Nurunnabi M | ACS applied bio materials | 36753355 | ACS Appl Bio Mater | 2023 Feb 20 | https://www.ncbi.nlm.nih.gov/pubmed/36753355 |
| β-Glucan and Fatty Acid Based Mucoadhesive Carrier for Gastrointestinal Tract Specific Local and Sustained Drug Delivery. | Esquivel SV, Bhatt HN, Diwan R, Habib A, Lee WY, Khatun Z, Nurunnabi M | Biomolecules | 37238639 | Biomolecules | 2023 Apr 28 | https://www.ncbi.nlm.nih.gov/pubmed/37238639 |
| Liver fibrosis pathologies and potentials of RNA based therapeutics modalities. | Diwan R, Gaytan SL, Bhatt HN, Pena-Zacarias J, Nurunnabi M | Drug delivery and translational research | 38446352 | Drug Deliv Transl Res | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/38446352 |
| A photothermal driven chemotherapy for the treatment of metastatic melanoma. | Bhatt HN, Diwan R, Borrego EA, Pérez CAM, Varela-Ramirez A, Kumar R, Aguilera RJ, Nurunnabi M | Journal of controlled release : official journal of the Controlled Release Society | 37562554 | J Control Release | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37562554 |
| Myofibroblast specific targeting approaches to improve fibrosis treatment. | Beaven E, Kumar R, Bhatt HN, Esquivel SV, Nurunnabi M | Chemical communications (Cambridge, England) | 36445310 | Chem Commun (Camb) | 2022 Dec 8 | https://www.ncbi.nlm.nih.gov/pubmed/36445310 |
| Oral delivery of RNAi for cancer therapy. | Afrin H, Geetha Bai R, Kumar R, Ahmad SS, Agarwal SK, Nurunnabi M | Cancer metastasis reviews | 36971908 | Cancer Metastasis Rev | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/36971908 |
| Potentials of ionic liquids to overcome physical and biological barriers. | Beaven E, Kumar R, An JM, Mendoza H, Sutradhar SC, Choi W, Narayan M, Lee YK, Nurunnabi M | Advanced drug delivery reviews | 38104896 | Adv Drug Deliv Rev | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/38104896 |
| Cadherin-11 targeted cell-specific liposomes enabled skin fibrosis treatment by inducing apoptosis. | Bhatt HN, Diwan R, Estevao IL, Dong R, Smith J, Xiao C, Agarwal SK, Nurunnabi M | Journal of controlled release : official journal of the Controlled Release Society | 38648957 | J Control Release | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/38648957 |
| β-Glucan-Mediated Oral Codelivery of 5FU and Bcl2 siRNA Attenuates Stomach Cancer. | Afrin H, Esquivel SV, Kumar R, Zahid MI, Oporeza B, Rahman MF, Boland T, Nurunnabi M | ACS applied materials & interfaces | 37350332 | ACS Appl Mater Interfaces | 2023 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/37350332 |
| Emerging delivery approaches for targeted pulmonary fibrosis treatment. | Diwan R, Bhatt HN, Beaven E, Nurunnabi M | Advanced drug delivery reviews | 38065244 | Adv Drug Deliv Rev | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/38065244 |
| Mucoadhesive carriers for oral drug delivery. | Kumar R, Islam T, Nurunnabi M | Journal of controlled release : official journal of the Controlled Release Society | 36116580 | J Control Release | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/36116580 |
| Carbon Coated Iron-Cobalt Nanoparticles for Magnetic Particle Imaging. | Kumar R, Huda MN, Habib A, Nafiujjaman M, Woo HJ, Kim T, Nurunnabi M | ACS applied bio materials | 37554053 | ACS Appl Bio Mater | 2023 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/37554053 |
| Less-is-more: selecting transcription factor binding regions informative for motif inference. | Xu J, Gao J, Ni P, Gerstein M | Nucleic acids research | 38214231 | Nucleic Acids Res | 2024 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/38214231 |
| Ocular Phenotyping of Knockout Mice Identifies Genes Associated With Late Adult Retinal Phenotypes. | Hang A, Shao A, Shea M, Roux MJ, Imai-Leonard DM, Adams DJ, Amano T, Amarie OV, Berberovic Z, Bour R, Bower L, Leonard BC, Brown SD, Cho SY, Clementson-Mobbs S, D'Souza AJ, Dickinson M, Eskandarian M, Flenniken AM, Fuchs H, Gailus-Durner V, Heaney J, Hérault Y, Hrabe de Angelis M, Hsu CW, Jin S, Joynson R, Kang YK, Kim H, Masuya H, Nam KH, Noh H, Nutter LMJ, Palkova M, Prochazka J, Raishbrook MJ, Riet F, Salazar J, Seavitt JR, Sedlacek R, Selloum M, Seo KY, Seong JK, Shin HS, Shiroishi T, Sorg T, Stewart M, Tamura M, Tolentino H, Udensi U, Wells S, Wurst W, Yoshiki A, Meziane H, Yiu G, Sieving PA, Lanoue L, Lloyd KCK, McKerlie C, Moshiri A, International Mouse Phenotyping Consortium (IMPC) | Investigative ophthalmology & visual science | 40548636 | Invest Ophthalmol Vis Sci | 2025 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/40548636 |
| Systematic ocular phenotyping of 8,707 knockout mouse lines identifies genes associated with abnormal corneal phenotypes. | Vo P, Imai-Leonard DM, Yang B, Briere A, Shao A, Casanova MI, Adams D, Amano T, Amarie O, Berberovic Z, Bower L, Braun R, Brown S, Burrill S, Cho SY, Clementson-Mobbs S, D'Souza A, Dickinson M, Eskandarian M, Flenniken AM, Fuchs H, Gailus-Durner V, Heaney J, Hérault Y, Angelis MH, Hsu CW, Jin S, Joynson R, Kang YK, Kim H, Masuya H, Meziane H, Murray S, Nam KH, Noh H, Nutter LMJ, Palkova M, Prochazka J, Raishbrook MJ, Riet F, Ryan J, Salazar J, Seavey Z, Seavitt JR, Sedlacek R, Selloum M, Seo KY, Seong JK, Shin HS, Shiroishi T, Stewart M, Svenson K, Tamura M, Tolentino H, Udensi U, Wells S, White J, Willett A, Wotton J, Wurst W, Yoshiki A, International Mouse Phenotyping Consortium, Lanoue L, Lloyd KCK, Leonard BC, Roux MJ, McKerlie C, Moshiri A | BMC genomics | 39833678 | BMC Genomics | 2025 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/39833678 |
| Genome-wide screening reveals the genetic basis of mammalian embryonic eye development. | Chee JM, Lanoue L, Clary D, Higgins K, Bower L, Flenniken A, Guo R, Adams DJ, Bosch F, Braun RE, Brown SDM, Chin HG, Dickinson ME, Hsu CW, Dobbie M, Gao X, Galande S, Grobler A, Heaney JD, Herault Y, de Angelis MH, Mammano F, Nutter LMJ, Parkinson H, Qin C, Shiroishi T, Sedlacek R, Seong JK, Xu Y, International Mouse Phenotyping Consortium, Brooks B, McKerlie C, Lloyd KCK, Westerberg H, Moshiri A | BMC biology | 36737727 | BMC Biol | 2023 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/36737727 |
| Analysis of genome-wide knockout mouse database identifies candidate ciliopathy genes. | Higgins K, Moore BA, Berberovic Z, Adissu HA, Eskandarian M, Flenniken AM, Shao A, Imai DM, Clary D, Lanoue L, Newbigging S, Nutter LMJ, Adams DJ, Bosch F, Braun RE, Brown SDM, Dickinson ME, Dobbie M, Flicek P, Gao X, Galande S, Grobler A, Heaney JD, Herault Y, de Angelis MH, Chin HG, Mammano F, Qin C, Shiroishi T, Sedlacek R, Seong JK, Xu Y, IMPC Consortium, Lloyd KCK, McKerlie C, Moshiri A | Scientific reports | 36456625 | Sci Rep | 2022 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/36456625 |
| Arap1 loss causes retinal pigment epithelium phagocytic dysfunction and subsequent photoreceptor death. | Shao A, Lopez AJ, Chen J, Tham A, Javier S, Quiroz A, Frick S, Levine EM, Lloyd KCK, Leonard BC, Murphy CJ, Glaser TM, Moshiri A | Disease models & mechanisms | 35758026 | Dis Model Mech | 2022 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/35758026 |
| Systematic Ocular Phenotyping of Knockout Mouse Lines Identifies Genes Associated With Age-Related Corneal Dystrophies. | Briere A, Vo P, Yang B, Adams D, Amano T, Amarie O, Berberovic Z, Bower L, Brown SDM, Burrill S, Cho SY, Clementson-Mobbs S, D'souza A, Eskandarian M, Flenniken AM, Fuchs H, Gailus-Durner V, Hérault Y, Hrabe de Angelis M, Jin S, Joynson R, Kang YK, Kim H, Masuya H, Meziane H, Nam KH, Noh H, Nutter LMJ, Palkova M, Prochazka J, Raishbrook MJ, Riet F, Salazar J, Sedlacek R, Selloum M, Seo KY, Seong JK, Shin HS, Shiroishi T, Stewart M, Svenson K, Tamura M, Tolentino H, Wells S, Wurst W, Yoshiki A, Lanoue L, Lloyd KCK, Leonard BC, Roux MJ, McKerlie C, Moshiri A, International Mouse Phenotyping Consortium | Investigative ophthalmology & visual science | 40323269 | Invest Ophthalmol Vis Sci | 2025 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/40323269 |
| Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies. | Li X, Quick C, Zhou H, Gaynor SM, Liu Y, Chen H, Selvaraj MS, Sun R, Dey R, Arnett DK, Bielak LF, Bis JC, Blangero J, Boerwinkle E, Bowden DW, Brody JA, Cade BE, Correa A, Cupples LA, Curran JE, de Vries PS, Duggirala R, Freedman BI, Göring HHH, Guo X, Haessler J, Kalyani RR, Kooperberg C, Kral BG, Lange LA, Manichaikul A, Martin LW, McGarvey ST, Mitchell BD, Montasser ME, Morrison AC, Naseri T, O'Connell JR, Palmer ND, Peyser PA, Psaty BM, Raffield LM, Redline S, Reiner AP, Reupena MS, Rice KM, Rich SS, Sitlani CM, Smith JA, Taylor KD, Vasan RS, Willer CJ, Wilson JG, Yanek LR, Zhao W, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Lipids Working Group, Rotter JI, Natarajan P, Peloso GM, Li Z, Lin X | Nature genetics | 36564505 | Nat Genet | 2023 Jan | https://www.ncbi.nlm.nih.gov/pubmed/36564505 |
| A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies. | Li Z, Li X, Zhou H, Gaynor SM, Selvaraj MS, Arapoglou T, Quick C, Liu Y, Chen H, Sun R, Dey R, Arnett DK, Auer PL, Bielak LF, Bis JC, Blackwell TW, Blangero J, Boerwinkle E, Bowden DW, Brody JA, Cade BE, Conomos MP, Correa A, Cupples LA, Curran JE, de Vries PS, Duggirala R, Franceschini N, Freedman BI, Göring HHH, Guo X, Kalyani RR, Kooperberg C, Kral BG, Lange LA, Lin BM, Manichaikul A, Manning AK, Martin LW, Mathias RA, Meigs JB, Mitchell BD, Montasser ME, Morrison AC, Naseri T, O'Connell JR, Palmer ND, Peyser PA, Psaty BM, Raffield LM, Redline S, Reiner AP, Reupena MS, Rice KM, Rich SS, Smith JA, Taylor KD, Taub MA, Vasan RS, Weeks DE, Wilson JG, Yanek LR, Zhao W, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Lipids Working Group, Rotter JI, Willer CJ, Natarajan P, Peloso GM, Lin X | Nature methods | 36303018 | Nat Methods | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36303018 |
| FAVOR: functional annotation of variants online resource and annotator for variation across the human genome. | Zhou H, Arapoglou T, Li X, Li Z, Zheng X, Moore J, Asok A, Kumar S, Blue EE, Buyske S, Cox N, Felsenfeld A, Gerstein M, Kenny E, Li B, Matise T, Philippakis A, Rehm HL, Sofia HJ, Snyder G, NHGRI Genome Sequencing Program Variant Functional Annotation Working Group, Weng Z, Neale B, Sunyaev SR, Lin X | Nucleic acids research | 36350676 | Nucleic Acids Res | 2023 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/36350676 |
| Evaluating cancer cell line and patient-derived xenograft recapitulation of tumor and non-diseased tissue gene expression profiles in silico. | Williams AS, Wilk EJ, Fisher JL, Lasseigne BN | Cancer reports (Hoboken, N.J.) | 37533331 | Cancer Rep (Hoboken) | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37533331 |
| Ten simple rules for using public biological data for your research. | Oza VH, Whitlock JH, Wilk EJ, Uno-Antonison A, Wilk B, Gajapathy M, Howton TC, Trull A, Ianov L, Worthey EA, Lasseigne BN | PLoS computational biology | 36602970 | PLoS Comput Biol | 2023 Jan | https://www.ncbi.nlm.nih.gov/pubmed/36602970 |
| Evaluating cancer cell line and patient-derived xenograft recapitulation of tumor and non-diseased tissue gene expression profiles in silico. | Williams AS, Wilk EJ, Fisher JL, Lasseigne BN | bioRxiv : the preprint server for biology | 37090499 | bioRxiv | 2023 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/37090499 |
| Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes. | Fisher JL, Clark AD, Jones EF, Lasseigne BN | BMC pharmacology & toxicology | 38167211 | BMC Pharmacol Toxicol | 2024 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/38167211 |
| Considerations and challenges for sex-aware drug repurposing. | Fisher JL, Jones EF, Flanary VL, Williams AS, Ramsey EJ, Lasseigne BN | Biology of sex differences | 35337371 | Biol Sex Differ | 2022 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/35337371 |
| Signature reversion of three disease-associated gene signatures prioritizes cancer drug repurposing candidates. | Fisher JL, Wilk EJ, Oza VH, Gary SE, Howton TC, Flanary VL, Clark AD, Hjelmeland AB, Lasseigne BN | FEBS open bio | 38531616 | FEBS Open Bio | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38531616 |
| Prioritized polycystic kidney disease drug targets and repurposing candidates from pre-cystic and cystic mouse Pkd2 model gene expression reversion. | Wilk EJ, Howton TC, Fisher JL, Oza VH, Brownlee RT, McPherson KC, Cleary HL, Yoder BK, George JF, Mrug M, Lasseigne BN | Molecular medicine (Cambridge, Mass.) | 37217845 | Mol Med | 2023 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/37217845 |
| Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes. | Fisher JL, Clark AD, Jones EF, Lasseigne BN | bioRxiv : the preprint server for biology | 37362157 | bioRxiv | 2023 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/37362157 |
| Computational Advancements in Cancer Combination Therapy Prediction. | Flanary VL, Fisher JL, Wilk EJ, Howton TC, Lasseigne BN | JCO precision oncology | 37824797 | JCO Precis Oncol | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37824797 |
| The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository. | Powell CD, Moseley HNB | Metabolites | 33808985 | Metabolites | 2021 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/33808985 |
| kegg_pull: a software package for the RESTful access and pulling from the Kyoto Encyclopedia of Gene and Genomes. | Huckvale E, Moseley HNB | BMC bioinformatics | 36870946 | BMC Bioinformatics | 2023 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/36870946 |
| An Ensemble Spectral Prediction (ESP) model for metabolite annotation. | Li X, Zhou Chen Y, Kalia A, Zhu H, Liu LP, Hassoun S | Bioinformatics (Oxford, England) | 39180771 | Bioinformatics | 2024 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/39180771 |
| Petagraph: A large-scale unifying knowledge graph framework for integrating biomolecular and biomedical data. | Stear BJ, Mohseni Ahooyi T, Simmons JA, Kollar C, Hartman L, Beigel K, Lahiri A, Vasisht S, Callahan TJ, Nemarich CM, Silverstein JC, Taylor DM | Scientific data | 39695169 | Sci Data | 2024 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/39695169 |
| Connecting high-resolution 3D chromatin organization with epigenomics. | Feng F, Yao Y, Wang XQD, Zhang X, Liu J | Nature communications | 35440119 | Nat Commun | 2022 Apr 19 | https://www.ncbi.nlm.nih.gov/pubmed/35440119 |
| Social and scientific motivations to move beyond groups in allele frequencies: The TOPMed experience. | Nelson SC, Gogarten SM, Fullerton SM, Isasi CR, Mitchell BD, North KE, Rich SS, Taylor MRG, Zöllner S, Sofer T | American journal of human genetics | 36055210 | Am J Hum Genet | 2022 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/36055210 |
| LMOD2-related dilated cardiomyopathy presenting in late infancy. | Lay E, Azamian MS, Denfield SW, Dreyer W, Spinner JA, Kearney D, Zhang L, Worley KC, Bi W, Lalani SR | American journal of medical genetics. Part A | 35188328 | Am J Med Genet A | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35188328 |
| Clinical exome sequencing uncovers a high frequency of Mendelian disorders in infants with stroke: A retrospective analysis. | Kumar RD, Meng L, Liu P, Miyake CY, Worley KC, Bi W, Lalani SR | American journal of medical genetics. Part A | 36065636 | Am J Med Genet A | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/36065636 |
| Promoting validation and cross-phylogenetic integration in model organism research. | Cheng KC, Burdine RD, Dickinson ME, Ekker SC, Lin AY, Lloyd KCK, Lutz CM, MacRae CA, Morrison JH, O'Connor DH, Postlethwait JH, Rogers CD, Sanchez S, Simpson JH, Talbot WS, Wallace DC, Weimer JM, Bellen HJ | Disease models & mechanisms | 36125045 | Dis Model Mech | 2022 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/36125045 |
| A fast, scalable and versatile tool for analysis of single-cell omics data. | Zhang K, Zemke NR, Armand EJ, Ren B | Nature methods | 38191932 | Nat Methods | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38191932 |
| Predictive analyses of regulatory sequences with EUGENe. | Klie A, Laub D, Talwar JV, Stites H, Jores T, Solvason JJ, Farley EK, Carter H | Nature computational science | 38177592 | Nat Comput Sci | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/38177592 |
| RummaGEO: Automatic Mining of Human and Mouse Gene Sets from GEO. | Marino GB, Clarke DJB, Deng EZ, Ma'ayan A | bioRxiv : the preprint server for biology | 38645198 | bioRxiv | 2024 Apr 13 | https://www.ncbi.nlm.nih.gov/pubmed/38645198 |
| Creating an Interactive Web Interface for Networks Stored in Knowledge Graph Databases. | Evangelista JE, Lutsky AD, Byrd AI, Clarke DJB, Prabhakaran A, Jenkins SL, Ma'ayan A | Current protocols | 40956607 | Curr Protoc | 2025 Sep | https://www.ncbi.nlm.nih.gov/pubmed/40956607 |
| Molecular Atlas of HER2+ Breast Cancer Cells Treated with Endogenous Ligands: Temporal Insights into Mechanisms of Trastuzumab Resistance. | Mukund K, Alva-Ornelas JA, Maddox AL, Murali D, Veraksa D, Saftics A, Tomsic J, Frankhouser D, Razo M, Jovanovic-Talisman T, Seewaldt VL, Subramaniam S | Cancers | 38339304 | Cancers (Basel) | 2024 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/38339304 |
| Molecular signatures and signaling interactions of the hair follicle stem cell niche. | Ghuwalewala S, Cao J, Rezza A, Rangl M, Kwiatkowski A, Brown A, Grisanti L, Heitman N, Schober M, Wang Z, Ma'ayan A, Almet AA, Plikus MV, Rendl M | The Journal of investigative dermatology | 41407191 | J Invest Dermatol | 2025 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/41407191 |
| lncRNAlyzr: Enrichment Analysis for lncRNA Sets. | Evangelista JE, Ali-Nasser T, Malek LE, Xie Z, Marino GB, Bester AC, Ma'ayan A | Journal of molecular biology | 40133794 | J Mol Biol | 2025 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/40133794 |
| A novel subtyping method for TNBC with implications for prognosis and therapy. | Mesrizadeh Z, Mukund K, Zabaleta J, Del Valle L, Tomsic J, Neuhausen S, Ding YC, Seewaldt V, Ochoa A, Miele L, Subramaniam S | bioRxiv : the preprint server for biology | 40672200 | bioRxiv | 2025 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/40672200 |
| Playbook workflow builder: Interactive construction of bioinformatics workflows. | Clarke DJB, Evangelista JE, Xie Z, Marino GB, Byrd AI, Maurya MR, Srinivasan S, Yu K, Petrosyan V, Roth ME, Milinkov M, King CH, Vora JK, Keeney J, Nemarich C, Khan W, Lachmann A, Ahmed N, Agris A, Pan J, Ramachandran S, Fahy E, Esquivel E, Mihajlovic A, Jevtic B, Milinovic V, Kim S, McNeely P, Wang T, Wenger E, Brown MA, Sickler A, Zhu Y, Jenkins SL, Blood PD, Taylor DM, Resnick AC, Mazumder R, Milosavljevic A, Subramaniam S, Ma'ayan A | PLoS computational biology | 40179105 | PLoS Comput Biol | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/40179105 |
| Rummagene: massive mining of gene sets from supporting materials of biomedical research publications. | Clarke DJB, Marino GB, Deng EZ, Xie Z, Evangelista JE, Ma'ayan A | Communications biology | 38643247 | Commun Biol | 2024 Apr 20 | https://www.ncbi.nlm.nih.gov/pubmed/38643247 |
| GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets. | Marino GB, Olaiya S, Evangelista JE, Clarke DJB, Ma'ayan A | GigaScience | 40208796 | Gigascience | 2025 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/40208796 |
| Protocol for using Multiomics2Targets to identify targets and driver kinases for cancer cohorts profiled with multi-omics assays. | Marino GB, Deng EZ, Clarke DJB, Diamant I, Resnick AC, Ma W, Wang P, Ma'ayan A | STAR protocols | 39565691 | STAR Protoc | 2024 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/39565691 |
| L2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engine. | Marino GB, Evangelista JE, Clarke DJB, Ma'ayan A | Nucleic acids research | 40308216 | Nucleic Acids Res | 2025 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/40308216 |
| Spatially distinct cellular and molecular landscapes define prognosis in triple negative breast cancer. | Mukund K, Veraksa D, Frankhouser D, Yang L, Tomsic J, Pillai R, Atti S, Mesrizadeh Z, Schmolze D, Wu XC, LeBlanc MA, Miele L, Ochoa A, Seewaldt V, Subramaniam S | bioRxiv : the preprint server for biology | 39990419 | bioRxiv | 2025 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/39990419 |
| A Gene Set Foundation Model Pre-Trained on a Massive Collection of Diverse Gene Sets. | Clarke DJB, Marino GB, Ma'ayan A | bioRxiv : the preprint server for biology | 40501705 | bioRxiv | 2025 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/40501705 |
| Dex-Benchmark: datasets and code to evaluate algorithms for transcriptomics data analysis. | Xie Z, Chen C, Ma'ayan A | PeerJ | 37953774 | PeerJ | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37953774 |
| Toxicology knowledge graph for structural birth defects. | Evangelista JE, Clarke DJB, Xie Z, Marino GB, Utti V, Jenkins SL, Ahooyi TM, Bologa CG, Yang JJ, Binder JL, Kumar P, Lambert CG, Grethe JS, Wenger E, Taylor D, Oprea TI, de Bono B, Ma'ayan A | Communications medicine | 37460679 | Commun Med (Lond) | 2023 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/37460679 |
| RummaGEO: Automatic mining of human and mouse gene sets from GEO. | Marino GB, Clarke DJB, Lachmann A, Deng EZ, Ma'ayan A | Patterns (New York, N.Y.) | 39569206 | Patterns (N Y) | 2024 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/39569206 |
| The molecular chronology of mammary epithelial cell fate switching. | Vallmajo-Martin Q, Ma Z, Srinivasan S, Murali D, Dravis C, Mukund K, Subramaniam S, Wahl GM, Lytle NK | bioRxiv : the preprint server for biology | 39415993 | bioRxiv | 2024 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/39415993 |
| ChEA-KG: Human Transcription Factor Regulatory Network with a Knowledge Graph Interactive User Interface. | Byrd AI, Evangelista JE, Lachmann A, Chung HY, Jenkins SL, Ma'ayan A | bioRxiv : the preprint server for biology | 40832173 | bioRxiv | 2025 Aug 12 | https://www.ncbi.nlm.nih.gov/pubmed/40832173 |
| GlycoSiteMiner: an ML/AI-assisted literature mining-based pipeline for extracting glycosylation sites from PubMed abstracts. | Kahsay R, Bhuiyan U, Au CCH, Edwards N, Johnson L, Kulkarni S, Martinez K, Ranzinger R, Vijay-Shanker K, Vora J, Warner K, Tiemeyer M, Mazumder R | Glycobiology | 40401984 | Glycobiology | 2025 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/40401984 |
| exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers. | LaPlante EL, Stürchler A, Fullem R, Chen D, Starner AC, Esquivel E, Alsop E, Jackson AR, Ghiran I, Pereira G, Rozowsky J, Chang J, Gerstein MB, Alexander RP, Roth ME, Franklin JL, Coffey RJ, Raffai RL, Mansuy IM, Stavrakis S, deMello AJ, Laurent LC, Wang YT, Tsai CF, Liu T, Jones J, Van Keuren-Jensen K, Van Nostrand E, Mateescu B, Milosavljevic A | Cell genomics | 37228754 | Cell Genom | 2023 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/37228754 |
| KG2ML: integrating knowledge graphs and positive unlabeled learning for identifying disease-associated genes. | Kumar P, Metzger VT, Purushotham ST, Kedia P, Bologa CG, Lambert CG, Yang JJ | Frontiers in bioinformatics | 41584517 | Front Bioinform | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/41584517 |
| DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. | Kropiwnicki E, Lachmann A, Clarke DJB, Xie Z, Jagodnik KM, Ma'ayan A | BMC bioinformatics | 35183110 | BMC Bioinformatics | 2022 Feb 19 | https://www.ncbi.nlm.nih.gov/pubmed/35183110 |
| KG2ML: Integrating Knowledge Graphs and Positive Unlabeled Learning for Identifying Disease-Associated Genes. | Kumar P, Metzger VT, Purushotham ST, Kedia P, Bologa CG, Lambert CG, Yang JJ | medRxiv : the preprint server for health sciences | 40166563 | medRxiv | 2025 Mar 17 | https://www.ncbi.nlm.nih.gov/pubmed/40166563 |
| Getting Started with the IDG KMC Datasets and Tools. | Kropiwnicki E, Binder JL, Yang JJ, Holmes J, Lachmann A, Clarke DJB, Sheils T, Kelleher KJ, Metzger VT, Bologa CG, Oprea TI, Ma'ayan A | Current protocols | 35085427 | Curr Protoc | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/35085427 |
| Gene and drug landing page aggregator. | Clarke DJB, Kuleshov MV, Xie Z, Evangelista JE, Meyers MR, Kropiwnicki E, Jenkins SL, Ma'ayan A | Bioinformatics advances | 35368424 | Bioinform Adv | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35368424 |
| Tissue registration and exploration user interfaces in support of a human reference atlas. | Börner K, Bueckle A, Herr BW 2nd, Cross LE, Quardokus EM, Record EG, Ju Y, Silverstein JC, Browne KM, Jain S, Wasserfall CH, Jorgensen ML, Spraggins JM, Patterson NH, Weber GM | Communications biology | 36513738 | Commun Biol | 2022 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/36513738 |
| The HRA Organ Gallery Affords Immersive Superpowers for Building and Exploring the Human Reference Atlas with Virtual Reality. | Bueckle A, Qing C, Luley S, Kumar Y, Pandey N, Börner K | bioRxiv : the preprint server for biology | 36824790 | bioRxiv | 2023 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/36824790 |
| Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph. | Bueckle A, Herr BW 2nd, Hardi J, Quardokus EM, Musen MA, Börner K | Scientific data | 40592888 | Sci Data | 2025 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/40592888 |
| Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph for Linked Open Data. | Bueckle A, Herr BW 2nd, Hardi J, Quardokus EM, Musen MA, Börner K | bioRxiv : the preprint server for biology | 39764040 | bioRxiv | 2025 Feb 19 | https://www.ncbi.nlm.nih.gov/pubmed/39764040 |
| An open source knowledge graph ecosystem for the life sciences. | Callahan TJ, Tripodi IJ, Stefanski AL, Cappelletti L, Taneja SB, Wyrwa JM, Casiraghi E, Matentzoglu NA, Reese J, Silverstein JC, Hoyt CT, Boyce RD, Malec SA, Unni DR, Joachimiak MP, Robinson PN, Mungall CJ, Cavalleri E, Fontana T, Valentini G, Mesiti M, Gillenwater LA, Santangelo B, Vasilevsky NA, Hoehndorf R, Bennett TD, Ryan PB, Hripcsak G, Kahn MG, Bada M, Baumgartner WA Jr, Hunter LE | Scientific data | 38605048 | Sci Data | 2024 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/38605048 |
| 3D virtual reality vs. 2D desktop registration user interface comparison. | Bueckle A, Buehling K, Shih PC, Börner K | PloS one | 34705835 | PLoS One | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34705835 |
| Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas. | Herr BW 2nd, Hardi J, Quardokus EM, Bueckle A, Chen L, Wang F, Caron AR, Osumi-Sutherland D, Musen MA, Börner K | Scientific data | 36973309 | Sci Data | 2023 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/36973309 |
| The stability of the myelinating oligodendrocyte transcriptome is regulated by the nuclear lamina. | Pruvost M, Patzig J, Yattah C, Selcen I, Hernandez M, Park HJ, Moyon S, Liu S, Morioka MS, Shopland L, Al-Dalahmah O, Bendl J, Fullard JF, Roussos P, Goldman J, He Y, Dupree JL, Casaccia P | Cell reports | 37515770 | Cell Rep | 2023 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/37515770 |
| Spatially resolved metabolomics and isotope tracing reveal dynamic metabolic responses of dentate granule neurons with acute stimulation. | Miller A, York EM, Stopka SA, Martínez-François JR, Hossain MA, Baquer G, Regan MS, Agar NYR, Yellen G | Nature metabolism | 37798473 | Nat Metab | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37798473 |
| Modeling transcriptional regulation of the cell cycle using a novel cybernetic-inspired approach. | Raja R, Khanum S, Aboulmouna L, Maurya MR, Gupta S, Subramaniam S, Ramkrishna D | Biophysical journal | 38102827 | Biophys J | 2024 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/38102827 |
| Fatty acid metabolism promotes TRPV4 activity in lung microvascular endothelial cells in pulmonary arterial hypertension. | Philip N, Yun X, Pi H, Murray S, Hill Z, Fonticella J, Perez P, Zhang C, Pathmasiri W, Sumner S, Servinsky L, Jiang H, Huetsch JC, Oldham WM, Visovatti S, Leary PJ, Gharib SA, Brittain E, Simpson CE, Le A, Shimoda LA, Suresh K | American journal of physiology. Lung cellular and molecular physiology | 38226418 | Am J Physiol Lung Cell Mol Physiol | 2024 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/38226418 |
| Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3K-AKT pathway activation. | Rogava M, Aprati TJ, Chi WY, Melms JC, Hug C, Davis SH, Earlie EM, Chung C, Deshmukh SK, Wu S, Sledge G, Tang S, Ho P, Amin AD, Caprio L, Gurjao C, Tagore S, Ngo B, Lee MJ, Zanetti G, Wang Y, Chen S, Ge W, Melo LMN, Allies G, Rösler J, Gibney GT, Schmitz OJ, Sykes M, Creusot RJ, Tüting T, Schadendorf D, Röcken M, Eigentler TK, Molotkov A, Mintz A, Bakhoum SF, Beyaz S, Cantley LC, Sorger PK, Meckelmann SW, Tasdogan A, Liu D, Laughney AM, Izar B | Nature cancer | 38286827 | Nat Cancer | 2024 Mar | https://www.ncbi.nlm.nih.gov/pubmed/38286827 |
| Deletion of Kcnj16 altered transcriptomic and metabolomic profiles of Dahl salt-sensitive rats. | Xu B, Dissanayake LV, Levchenko V, Zietara A, Kravtsova O, Staruschenko A | iScience | 39328933 | iScience | 2024 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/39328933 |
| Taurine modulates host cell responses to Helicobacter pylori VacA toxin. | Westland MD, Schrimpe-Rutledge AC, Codreanu SG, Sherrod SD, McLean JA, McClain MS, Cover TL | Infection and immunity | 38975764 | Infect Immun | 2024 Aug 13 | https://www.ncbi.nlm.nih.gov/pubmed/38975764 |
| FDX2, an iron-sulfur cluster assembly factor, is essential to prevent cellular senescence, apoptosis or ferroptosis of ovarian cancer cells. | Miyahara S, Ohuchi M, Nomura M, Hashimoto E, Soga T, Saito R, Hayashi K, Sato T, Saito M, Yamashita Y, Shimada M, Yaegashi N, Yamada H, Tanuma N | The Journal of biological chemistry | 39151727 | J Biol Chem | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/39151727 |
| FGFR inhibition blocks NF-ĸB-dependent glucose metabolism and confers metabolic vulnerabilities in cholangiocarcinoma. | Zhen Y, Liu K, Shi L, Shah S, Xu Q, Ellis H, Balasooriya ER, Kreuzer J, Morris R, Baldwin AS, Juric D, Haas W, Bardeesy N | Nature communications | 38714664 | Nat Commun | 2024 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/38714664 |
| ndufs2(-/-) zebrafish have impaired survival, neuromuscular activity, morphology, and one-carbon metabolism treatable with folic acid. | Mitchell DV, Iadarola DM, Mathew ND, Keith K, Seiler C, Yu S, Kim MS, Woodard N, Anderson VE, Nakamaru-Ogiso E, Taylor DM, Falk MJ | bioRxiv : the preprint server for biology | 40791373 | bioRxiv | 2025 Jul 18 | https://www.ncbi.nlm.nih.gov/pubmed/40791373 |
| Metabolomics Network Analysis of Various Genotypes Associated with Schizophrenia Gene Variant. | Rajula HSR, Piras C, Kopeć KK, Noto A, Spada M, Lilliu K, Manchia M, Mussap M, Atzori L, Fanos V | Metabolites | 40863167 | Metabolites | 2025 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/40863167 |
| In vitro protocol demonstrating five functional steps of trained immunity in mice: Implications on biomarker discovery and translational research. | González-Pérez M, Baranda J, Pérez-Rodríguez L, Conde P, Calle-Fabregat C, Berges-Buxeda MJ, Dimitrov A, Arranz J, Rius-Rocabert S, Zotta A, Dopazo A, Poddar N, Wang X, Nistal-Villán E, Duivenvoorden R, Madsen JC, Williams DL, Hasson D, Lozano-Ojalvo D, Ginhoux F, O'Neill LAJ, Ochando J | Cell reports | 41014560 | Cell Rep | 2025 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/41014560 |
| Microglia-specific regulation of lipid metabolism in Alzheimer's disease revealed by microglial depletion in 5xFAD Mice. | Xu Z, Kiani Shabestari S, Barannikov S, Bieniek KF, Blurton-Jones M, Palavicini JP, Han X | Nature communications | 41093842 | Nat Commun | 2025 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/41093842 |
| Synaptic vesicle-omics in mice captures signatures of aging and synucleinopathy. | Gao V, Chlebowicz J, Gaskin K, Briano JA, Komer LE, Pineda A, Jhalani S, Ahmad S, Uwaifo E, Black LS, Haller JE, Przedborski S, Lane DA, Zhang S, Sharma M, Burré J | Nature communications | 40312501 | Nat Commun | 2025 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/40312501 |
| Multiomics analysis of the Silkworm cocoon shell. | Fragkou P, Martakos I, Rouni G, Vasilakos D, Koutsoukos E, Saviane A, Cappellozza S, Thomaidis NS, Kostakis MG, Samiotaki M, Kotsiantis S, Barcenas M, Dedos SG | Scientific data | 41068133 | Sci Data | 2025 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/41068133 |
| MYC is a regulator of androgen receptor inhibition-induced metabolic requirements in prostate cancer. | Crowell PD, Giafaglione JM, Jones AE, Nunley NM, Hashimoto T, Delcourt AML, Petcherski A, Agrawal R, Bernard MJ, Diaz JA, Heering KY, Huang RR, Low JY, Matulionis N, Navone NM, Ye H, Zoubeidi A, Christofk HR, Rettig MB, Reiter RE, Haffner MC, Boutros PC, Shirihai OS, Divakaruni AS, Goldstein AS | Cell reports | 37815914 | Cell Rep | 2023 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/37815914 |
| Endotype Characterization Reveals Mechanistic Differences Across Brain Regions in Sporadic Alzheimer's Disease. | Patel AO, Caldwell AB, Ramachandran S, Subramaniam S | Journal of Alzheimer's disease reports | 37849634 | J Alzheimers Dis Rep | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37849634 |
| Associations between maternal microbiome, metabolome and incidence of low-birth weight in Guatemalan participants from the Women First Trial. | Ruebel ML, Gilley SP, Yeruva L, Tang M, Frank DN, Garcés A, Figueroa L, Lan RS, Assress HA, Kemp JF, Westcott JLE, Hambidge KM, Shankar K, Krebs NF | Frontiers in microbiology | 39473842 | Front Microbiol | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/39473842 |
| Cancer-associated fibroblasts maintain critical pancreatic cancer cell lipid homeostasis in the tumor microenvironment. | Han X, Burrows M, Kim LC, Xu JP, Vostrejs W, Van Le TN, Poltorack C, Jiang Y, Cukierman E, Stanger BZ, Reiss KA, Shaffer SM, Mesaros C, Keith B, Simon MC | Cell reports | 39535921 | Cell Rep | 2024 Nov 26 | https://www.ncbi.nlm.nih.gov/pubmed/39535921 |
| Imidazole propionate is a driver and therapeutic target in atherosclerosis. | Mastrangelo A, Robles-Vera I, Mañanes D, Galán M, Femenía-Muiña M, Redondo-Urzainqui A, Barrero-Rodríguez R, Papaioannou E, Amores-Iniesta J, Devesa A, Lobo-González M, Carreras A, Beck KR, Ivarsson S, Gummesson A, Georgiopoulos G, Rodrigo-Tapias M, Martínez-Cano S, Fernández-López I, Nuñez V, Ferrarini A, Inohara N, Stamatelopoulos K, Benguría A, Cibrian D, Sánchez-Madrid F, Alonso-Herranz V, Dopazo A, Barbas C, Vázquez J, López JA, González-Martín A, Nuñez G, Stellos K, Bergström G, Bäckhed F, Fuster V, Ibañez B, Sancho D | Nature | 40670786 | Nature | 2025 Sep | https://www.ncbi.nlm.nih.gov/pubmed/40670786 |
| Dynamic metabolic and molecular changes during seasonal shrinking in Sorex araneus. | Thomas WR, Baldoni C, Zeng Y, Carlson D, Holm-Jacobsen J, Muturi M, von Elverfeldt D, Bennike TB, Dechmann DKN, Nieland J, Corthals AP, Dávalos LM | Genome research | 41188034 | Genome Res | 2026 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/41188034 |
| A taxon-specific measurement of disruption in a multi-modal study of microbiomes and metabolomes reveals system-wide dysbiosis preceding HIV-1 infection. | Fouladi F, Chen Y, Bera S, Jarmusch AK, Van Tyne D, Palella FJ, Margolick JB, Chew KW, Sun J, Martinson J, Rinaldo CR, Peddada SD | Nature communications | 41266305 | Nat Commun | 2025 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/41266305 |
| Spatially resolved metabolomics and isotope tracing reveal dynamic metabolic responses of dentate granule neurons with acute stimulation. | Miller A, York E, Stopka S, Martínez-François J, Hossain MA, Baquer G, Regan M, Agar N, Yellen G | Research square | 37546759 | Res Sq | 2023 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/37546759 |
| Modular and mechanistic changes across stages of colorectal cancer. | Rahiminejad S, Maurya MR, Mukund K, Subramaniam S | BMC cancer | 35448980 | BMC Cancer | 2022 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/35448980 |
| Immune Response in Severe and Non-Severe Coronavirus Disease 2019 (COVID-19) Infection: A Mechanistic Landscape. | Mukund K, Nayak P, Ashokkumar C, Rao S, Almeda J, Betancourt-Garcia MM, Sindhi R, Subramaniam S | Frontiers in immunology | 34721400 | Front Immunol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34721400 |
| GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. | Petras D, Phelan VV, Acharya D, Allen AE, Aron AT, Bandeira N, Bowen BP, Belle-Oudry D, Boecker S, Cummings DA Jr, Deutsch JM, Fahy E, Garg N, Gregor R, Handelsman J, Navarro-Hoyos M, Jarmusch AK, Jarmusch SA, Louie K, Maloney KN, Marty MT, Meijler MM, Mizrahi I, Neve RL, Northen TR, Molina-Santiago C, Panitchpakdi M, Pullman B, Puri AW, Schmid R, Subramaniam S, Thukral M, Vasquez-Castro F, Dorrestein PC, Wang M | Nature methods | 34862502 | Nat Methods | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/34862502 |
| DRMY1 promotes robust morphogenesis in Arabidopsis by sustaining the translation of cytokinin-signaling inhibitor proteins. | Kong S, Zhu M, Scarpin MR, Pan D, Jia L, Martinez RE, Alamos S, Vadde BVL, Garcia HG, Qian SB, Brunkard JO, Roeder AHK | Developmental cell | 39305905 | Dev Cell | 2024 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/39305905 |
| Integrated multi-omics unveil the impact of H-phosphinic analogs of glutamate and α-ketoglutarate on Escherichia coli metabolism. | Giovannercole F, Gafeira Gonçalves L, Armengaud J, Varela Coelho A, Khomutov A, De Biase D | The Journal of biological chemistry | 39307306 | J Biol Chem | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39307306 |
| Modeling enzyme competition in eicosanoid metabolism in macrophage cells using a cybernetic framework. | Khanum S, Gupta S, Maurya MR, Raja R, Aboulmouna L, Subramaniam S, Ramkrishna D | Journal of lipid research | 39395792 | J Lipid Res | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39395792 |
| Single-cell transcriptomics reveals stage- and side-specificity of gene modules in colorectal cancer. | Rahiminejad S, Mukund K, Maurya MR, Subramaniam S | Research square | 38826219 | Res Sq | 2024 May 24 | https://www.ncbi.nlm.nih.gov/pubmed/38826219 |
| Pyruvate dehydrogenase kinase 1 controls triacylglycerol hydrolysis in cardiomyocytes. | Atser MG, Wenyonu CD, Rowe EM, Leung CLK, Cen HH, Queathem ED, Liu LT, Moravcova R, Rogalski J, Perrin D, Crawford P, Foster LJ, Alcazar A, Johnson JD | bioRxiv : the preprint server for biology | 39464135 | bioRxiv | 2025 Feb 24 | https://www.ncbi.nlm.nih.gov/pubmed/39464135 |
| Biotin mitigates the development of manganese-induced, Parkinson's disease-related neurotoxicity in Drosophila and human neurons. | Lai Y, Reina-Gonzalez P, Maor G, Miller GW, Sarkar S | Science signaling | 39836750 | Sci Signal | 2025 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/39836750 |
| METTL3-mediated chromatin contacts promote stress granule phase separation through metabolic reprogramming during senescence. | Wang C, Tanizawa H, Hill C, Havas A, Zhang Q, Liao L, Hao X, Lei X, Wang L, Nie H, Qi Y, Tian B, Gardini A, Kossenkov AV, Goldman A, Berger SL, Noma KI, Adams PD, Zhang R | Nature communications | 38926365 | Nat Commun | 2024 Jun 26 | https://www.ncbi.nlm.nih.gov/pubmed/38926365 |
| Contribution of Circulating Host and Microbial Tryptophan Metabolites Toward Ah Receptor Activation. | Morgan EW, Dong F, Annalora AJ, Murray IA, Wolfe T, Erickson R, Gowda K, Amin SG, Petersen KS, Kris-Etherton PM, Marcus CB, Walk ST, Patterson AD, Perdew GH | International journal of tryptophan research : IJTR | 37441265 | Int J Tryptophan Res | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37441265 |
| Repeated exposure to eucalyptus wood smoke alters pulmonary gene and metabolic profiles in male Long-Evans rats. | Cochran SJ, Dunigan-Russell K, Hutton GM, Nguyen H, Schladweiler MC, Jones DP, Williams WC, Fisher AA, Gilmour MI, Dye JA, Smith MR, Miller CN, Gowdy KM | Toxicological sciences : an official journal of the Society of Toxicology | 38544285 | Toxicol Sci | 2024 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/38544285 |
| Metabolic reprogramming by histone deacetylase inhibition preferentially targets NRF2-activated tumors. | Karagiannis D, Wu W, Li A, Hayashi M, Chen X, Yip M, Mangipudy V, Xu X, Sánchez-Rivera FJ, Soto-Feliciano YM, Ye J, Papagiannakopoulos T, Lu C | Cell reports | 38165806 | Cell Rep | 2024 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/38165806 |
| Metabolic reprogramming enhances oxidative stress resistance in differentiating cardiomyocytes. | Novais LB, Rodrigues BRI, Pereira FOB, Amaral AG, Lapa SC, Maldonado LL, Víctor-Carvalho P, Moretto IA, Zamora-Obando HR, da Silva MC, Samogim AP, de Brito IR, de Souza Carvalho MDG, Campos ATP, de Moura Pereira Antunes MB, Cesar CL, Carvalho HF, Simionato AVC, de Thomaz AA, Santos AMD | Scientific reports | 41559164 | Sci Rep | 2026 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/41559164 |
| Stress exposure in the mdx mouse model of Duchenne muscular dystrophy provokes a widespread metabolic response. | Johnson EE, Ervasti JM | The FEBS journal | 39985215 | FEBS J | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39985215 |
| Autoimmune disease risk gene ANKRD55 promotes TH17 effector function through metabolic modulation. | Xu J, Kong L, Creasey EA, Rath S, Deng L, Avila-Pacheco J, Li C, Oliver BA, Dao TT, Shih AR, Daly MJ, Shalek AK, Clish CB, Graham DB, Deguine J, Xavier RJ | The Journal of experimental medicine | 40932625 | J Exp Med | 2025 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/40932625 |
| Early adipose tissue wasting in a preclinical model of human lung cancer cachexia. | Snoke DB, van der Velden JL, Bellafleur ER, Dearborn JS, Lenahan SM, Beal AE, Aboushousha R, Heininger SCJ, Ather JL, Mank MM, Sarausky H, Stephenson D, Reisz JA, D'Alessandro A, Majumdar D, Ahern TP, Xu K, Sandler KL, Landman BA, Janssen-Heininger YMW, Poynter ME, Seward DJ, Toth MJ | Cell reports | 40934088 | Cell Rep | 2025 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/40934088 |
| Nuclear receptor subfamily 4 group a member 2 induces a Warburg-like effect and promotes phospholipids synthesis in the mouse heart. | Ashraf S, Odogwu D, McPherson DD, Harmancey R | Physiological genomics | 41801102 | Physiol Genomics | 2026 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/41801102 |
| Matrix Linear Models for connecting metabolite composition to individual characteristics. | Farage G, Zhao C, Choi HY, Garrett TJ, Kechris K, Elam MB, Sen Ś | bioRxiv : the preprint server for biology | 38187579 | bioRxiv | 2023 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/38187579 |
| MetGENE: gene-centric metabolomics information retrieval tool. | Srinivasan S, Maurya MR, Ramachandran S, Fahy E, Subramaniam S | GigaScience | 37983749 | Gigascience | 2022 Dec 28 | https://www.ncbi.nlm.nih.gov/pubmed/37983749 |
| Methionine-SAM metabolism-dependent ubiquinone synthesis is crucial for ROS accumulation in ferroptosis induction. | Xia C, Peng P, Zhang W, Xing X, Jin X, Du J, Peng W, Hao F, Zhao Z, Dong K, Tian M, Feng Y, Ba X, Wei M, Wang Y | Nature communications | 39420002 | Nat Commun | 2024 Oct 17 | https://www.ncbi.nlm.nih.gov/pubmed/39420002 |
| Metabolic abnormalities in the bone marrow cells of young offspring born to mothers with obesity. | Phillips EA, Alharithi YJ, Kadam L, Coussens LM, Kumar S, Maloyan A | International journal of obesity (2005) | 38937647 | Int J Obes (Lond) | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/38937647 |
| Structural and systems characterization of phosphorylation on metabolic enzymes identifies sex-specific metabolic reprogramming in obesity. | Tamir TY, Chaudhary S, Li AX, Trojan SE, Flower CT, Vo P, Cui Y, Davis JC, Mukkamala RS, Venditti FN, Hillis AL, Toker A, Vander Heiden MG, Spinelli JB, Kennedy NJ, Davis RJ, White FM | bioRxiv : the preprint server for biology | 39257804 | bioRxiv | 2024 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/39257804 |
| Gut symbiont-derived sphingosine modulates vector competence in Aedes mosquitoes. | Sun X, Wang Y, Yuan F, Zhang Y, Kang X, Sun J, Wang P, Lu T, Sae Wang F, Gu J, Wang J, Xia Q, Zheng A, Zou Z | Nature communications | 39300135 | Nat Commun | 2024 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/39300135 |
| A Multiomics Evaluation of the Countermeasure Influence of 4-Week Cranberry Beverage Supplementation on Exercise-Induced Changes in Innate Immunity. | Nieman DC, Sakaguchi CA, Williams JC, Woo J, Omar AM, Mulani FA, Zhang Q, Pathmasiri W, Rushing BR, McRitchie S, Sumner SJ, Lawson J, Lambirth KC | Nutrients | 39408218 | Nutrients | 2024 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/39408218 |
| Differential impact of sex on regulation of skeletal muscle mitochondrial function and protein homeostasis by hypoxia-inducible factor-1α in normoxia. | Welch N, Mishra S, Bellar A, Kannan P, Gopan A, Goudarzi M, King J, Luknis M, Musich R, Agrawal V, Bena J, Koch CJ, Li L, Willard B, Shah YM, Dasarathy S | The Journal of physiology | 38761133 | J Physiol | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/38761133 |
| Deficiency of the lipid flippase ATP10A causes diet-induced dyslipidemia in female mice. | Norris AC, Yazlovitskaya EM, Zhu L, Rose BS, May JC, Gibson-Corley KN, McLean JA, Stafford JM, Graham TR | Scientific reports | 38172157 | Sci Rep | 2024 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/38172157 |
| Mannose controls mesoderm specification and symmetry breaking in mouse gastruloids. | Dingare C, Cao D, Yang JJ, Sozen B, Steventon B | Developmental cell | 38636516 | Dev Cell | 2024 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/38636516 |
| Metabolic abnormalities in the bone marrow cells of young offspring born to obese mothers. | Alina M, Phillips E, Alharithi Y, Kadam L, Coussens L, Kumar S | Research square | 38313293 | Res Sq | 2024 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/38313293 |
| Defining diurnal fluctuations in mouse choroid plexus and CSF at high molecular, spatial, and temporal resolution. | Fame RM, Kalugin PN, Petrova B, Xu H, Soden PA, Shipley FB, Dani N, Grant B, Pragana A, Head JP, Gupta S, Shannon ML, Chifamba FF, Hawks-Mayer H, Vernon A, Gao F, Zhang Y, Holtzman MJ, Heiman M, Andermann ML, Kanarek N, Lipton JO, Lehtinen MK | Nature communications | 37349305 | Nat Commun | 2023 Jun 22 | https://www.ncbi.nlm.nih.gov/pubmed/37349305 |
| Integrative multiomics reveals common endotypes across PSEN1, PSEN2, and APP mutations in familial Alzheimer's disease. | Valdes P, Caldwell AB, Liu Q, Fitzgerald MQ, Ramachandran S, Karch CM, Dominantly Inherited Alzheimer Network (DIAN), Galasko DR, Yuan SH, Wagner SL, Subramaniam S | Alzheimer's research & therapy | 39754192 | Alzheimers Res Ther | 2025 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/39754192 |
| Unveiling cellular changes in leukaemia cell lines after cannabidiol treatment through lipidomics. | Chamoso-Sanchez D, Panini M, Caroli C, Marani M, Corsi L, Rupérez FJ, Garcia A, Pellati F | Scientific reports | 39824876 | Sci Rep | 2025 Jan 17 | https://www.ncbi.nlm.nih.gov/pubmed/39824876 |
| Salivary Metabolomic Signatures in Pediatric Eosinophilic Esophagitis. | Hiremath G, Codreanu SG, Sherrod SD, Tyree R, Correa H, Choksi Y, McLean JA, Locke A | Allergy | 39707873 | Allergy | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39707873 |
| Untargeted metabolomics of 3xTg-AD neurotoxic astrocytes. | Carvalho D, Diaz-Amarilla P, Smith MR, Santi MD, Martinez-Busi M, Go YM, Jones DP, Duarte P, Savio E, Abin-Carriquiry JA, Arredondo F | Journal of proteomics | 39448026 | J Proteomics | 2025 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/39448026 |
| Ketogenic diet suppresses colorectal cancer through the gut microbiome long chain fatty acid stearate. | Tsenkova M, Brauer M, Pozdeev VI, Kasakin M, Busi SB, Schmoetten M, Cheung D, Meyers M, Rodriguez F, Gaigneaux A, Koncina E, Gilson C, Schlicker L, Herebian D, Schmitz M, de Nies L, Mayatepek E, Haan S, de Beaufort C, Cramer T, Meiser J, Linster CL, Wilmes P, Letellier E | Nature communications | 39979287 | Nat Commun | 2025 Feb 20 | https://www.ncbi.nlm.nih.gov/pubmed/39979287 |
| Pyruvate dehydrogenase kinase 1 controls triacylglycerol hydrolysis in cardiomyocytes. | Atser MG, Wenyonu CD, Rowe EM, Leung CLK, Cen HH, Queathem ED, Liu LT, Moravcova R, Rogalski J, Perrin D, Crawford P, Foster LJ, Alcazar A, Johnson JD | The Journal of biological chemistry | 40074083 | J Biol Chem | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/40074083 |
| OGDHL regulates tumor growth, neuroendocrine marker expression, and nucleotide abundance in prostate cancer. | Bernard MJ, Ruiz A, Diaz JA, Nunley NM, Dove RN, Zhang S, Lee E, Heering KY, Bopardikar S, Gallardo A, Hashimoto T, Agrawal R, Smith CM, Wilde BR, Matulionis N, Richards HM, Lee SCS, Sharifi MN, Lang JM, Zhao SG, Haffner MC, Shackelford DB, Boutros PC, Christofk HR, Goldstein AS | bioRxiv : the preprint server for biology | 40502162 | bioRxiv | 2025 Aug 22 | https://www.ncbi.nlm.nih.gov/pubmed/40502162 |
| Structural and systems characterization of phosphorylation on metabolic enzymes identifies sex-specific metabolic reprogramming in obesity. | Tamir TY, Chaudhary S, Li AX, Trojan SE, Flower CT, Vo P, Cui Y, Davis JC, Mukkamala R, Venditti FN, Hillis AL, Toker A, Vander Heiden MG, Spinelli JB, Kennedy NJ, Davis RJ, White FM | Molecular cell | 40441152 | Mol Cell | 2025 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/40441152 |
| An autoencoder learning method for predicting breast cancer subtypes. | Rostami Z, Mukund K, Masnadi-Shirazi M, Subramaniam S | PloS one | 40700427 | PLoS One | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40700427 |
| Untargeted plasma metabolite detection in sudden sensorineural hearing loss: identifying key metabolic signatures. | Ma R, Zhang H, Wang W, Yu C, Xiong G, Li Q, Wang Y, Zhou L, Zhang Y, Li M, Guo M | Frontiers in molecular biosciences | 40726995 | Front Mol Biosci | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40726995 |
| Metabolomic profiling reveals interindividual metabolic variability and its association with cardiovascular-kidney-metabolic syndrome risk. | Zhou M, Sun W, Gao Y, Jiang B, Sun T, Xu R, Zhang X, Wang Q, Xuan Q, Ma S | Cardiovascular diabetology | 40751246 | Cardiovasc Diabetol | 2025 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/40751246 |
| Intra-tumoral hypoxia promotes CD8(+) T cell dysfunction via chronic activation of integrated stress response transcription factor ATF4. | Alicea Pauneto CDM, Riesenberg BP, Gandy EJ, Kennedy AS, Clutton GT, Hem JW, Hurst KE, Hunt EG, Green JM, Miller BC, Angus SP, Johnson GL, Esther RJ, Guerriero JL, Gao P, Soto-Pantoja DR, Ferris RL, Modliszewski JL, Coleman MF, Chung HK, Milner JJ, Moschos SJ, Wiseman RL, Thaxton JE | Immunity | 41005293 | Immunity | 2025 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/41005293 |
| Cytosolic acetyl-coenzyme A is a signalling metabolite to control mitophagy. | Zhang Y, Shen X, Shen Y, Wang C, Yu C, Han J, Cao S, Qian L, Ma M, Huang S, Wen W, Yin M, Lei QY | Nature | 41225001 | Nature | 2026 Jan | https://www.ncbi.nlm.nih.gov/pubmed/41225001 |
| The SLC1A1/EAAT3 dicarboxylic amino acid transporter is an epigenetically dysregulated nutrient carrier that sustains oncogenic metabolic programs. | Grubb T, Koochaki P, Matar S, Ghandour F, Machaalani M, Saad E, Tang C, Reznik E, Khatun J, Salem C, Dubasik N, Orlando DA, Guenther MG, Parajuli G, Srivastava RM, Martinez SR, Coker JA, Kotecha RR, Hakimi AA, Asara JM, Chan TA, Vanharanta S, Stauffer SR, Kaelin WG Jr, Signoretti S, Choueiri TK, Chakraborty AA | Nature communications | 41238532 | Nat Commun | 2025 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/41238532 |
| Targeted Metabolomic Methods for (13)C Stable Isotope Labeling with Uniformly Labeled Glucose and Glutamine Using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS). | Jennings EQ, Rathmell WK, Rathmell JC | Journal of proteome research | 41264887 | J Proteome Res | 2025 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/41264887 |
| Exploring the interplay between running exercises, microbial diversity, and tryptophan metabolism along the microbiota-gut-brain axis. | Vazquez-Medina A, Rodriguez-Trujillo N, Ayuso-Rodriguez K, Marini-Martinez F, Angeli-Morales R, Caussade-Silvestrini G, Godoy-Vitorino F, Chorna N | Frontiers in microbiology | 38318337 | Front Microbiol | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38318337 |
| A nested case-control study of untargeted plasma metabolomics and lung cancer among never-smoking women within the prospective Shanghai Women's Health Study. | Rahman ML, Shu XO, Jones DP, Hu W, Ji BT, Blechter B, Wong JYY, Cai Q, Yang G, Gao YT, Zheng W, Rothman N, Walker D, Lan Q | International journal of cancer | 38651675 | Int J Cancer | 2024 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/38651675 |
| Fetal growth delay caused by loss of non-canonical imprinting is resolved late in pregnancy and culminates in offspring overgrowth. | Oberin R, Petautschnig S, Jarred EG, Qu Z, Tsai T, Youngson NA, Pulsoni G, Truong TT, Fernando D, Bildsoe H, Blücher RO, van den Buuse M, Gardner DK, Sims NA, Adelson DL, Western PS | eLife | 38813868 | Elife | 2024 May 30 | https://www.ncbi.nlm.nih.gov/pubmed/38813868 |
| Nucleotide metabolism in cancer cells fuels a UDP-driven macrophage cross-talk, promoting immunosuppression and immunotherapy resistance. | Scolaro T, Manco M, Pecqueux M, Amorim R, Trotta R, Van Acker HH, Van Haele M, Shirgaonkar N, Naulaerts S, Daniluk J, Prenen F, Varamo C, Ponti D, Doglioni G, Ferreira Campos AM, Fernandez Garcia J, Radenkovic S, Rouhi P, Beatovic A, Wang L, Wang Y, Tzoumpa A, Antoranz A, Sargsian A, Di Matteo M, Berardi E, Goveia J, Ghesquière B, Roskams T, Soenen S, Voets T, Manshian B, Fendt SM, Carmeliet P, Garg AD, DasGupta R, Topal B, Mazzone M | Nature cancer | 38844817 | Nat Cancer | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38844817 |
| Deficiency of the lipid flippase ATP10A causes diet-induced dyslipidemia in female mice. | Norris AC, Yazlovitskaya EM, Zhu L, Rose BS, May JC, Gibson-Corley KN, McLean JA, Stafford JM, Graham TR | bioRxiv : the preprint server for biology | 37398141 | bioRxiv | 2023 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/37398141 |
| Lactate-dependent transcriptional regulation controls mammalian eye morphogenesis. | Takata N, Miska JM, Morgan MA, Patel P, Billingham LK, Joshi N, Schipma MJ, Dumar ZJ, Joshi NR, Misharin AV, Embry RB, Fiore L, Gao P, Diebold LP, McElroy GS, Shilatifard A, Chandel NS, Oliver G | Nature communications | 37452018 | Nat Commun | 2023 Jul 14 | https://www.ncbi.nlm.nih.gov/pubmed/37452018 |
| Lipidomic Analysis Reveals Differences in the Extent of Remyelination in the Brain and Spinal Cord. | De Silva Mohotti N, Kobayashi H, Williams JM, Binjawadagi R, Evertsen MP, Christ EG, Hartley MD | Journal of proteome research | 38018851 | J Proteome Res | 2024 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/38018851 |
| Gut microbiota and metabolites in estrus cycle and their changes in a menopausal transition rat model with typical neuroendocrine aging. | Dai R, Huang J, Cui L, Sun R, Qiu X, Wang Y, Sun Y | Frontiers in endocrinology | 38161977 | Front Endocrinol (Lausanne) | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/38161977 |
| IL-1β-mediated adaptive reprogramming of endogenous human cardiac fibroblasts to cells with immune features during fibrotic remodeling. | Siamwala JH, Pagano FS, Dubielecka PM, Ivey MJ, Guirao-Abad JP, Zhao A, Chen S, Granston H, Jeong JY, Rounds S, Kanisicak O, Sadayappan S, Gilbert RJ | Communications biology | 38001239 | Commun Biol | 2023 Nov 25 | https://www.ncbi.nlm.nih.gov/pubmed/38001239 |
| Proteomic and metabolomic analyses of the human adult myocardium reveal ventricle-specific regulation in end-stage cardiomyopathies. | Hunter B, Li M, Parker BL, Koay YC, Harney DJ, Pearson E, Cao J, Chen GT, Guneratne O, Smyth GK, Larance M, O'Sullivan JF, Lal S | Communications biology | 39702518 | Commun Biol | 2024 Dec 19 | https://www.ncbi.nlm.nih.gov/pubmed/39702518 |
| Taurine from tumour niche drives glycolysis to promote leukaemogenesis. | Sharma S, Rodems BJ, Baker CD, Kaszuba CM, Franco EI, Smith BR, Ito T, Swovick K, Welle K, Zhang Y, Rock P, Chaves FA, Ghaemmaghami S, Calvi LM, Ganguly A, Burack WR, Becker MW, Liesveld JL, Brookes PS, Munger JC, Jordan CT, Ashton JM, Bajaj J | Nature | 40369079 | Nature | 2025 Aug | https://www.ncbi.nlm.nih.gov/pubmed/40369079 |
| Human adenovirus serotype 5 infection dysregulates cysteine, purine, and unsaturated fatty acid metabolism in fibroblasts. | Sanchez BC, Ortiz RM, Grasis JA | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 40052831 | FASEB J | 2025 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/40052831 |
| Mitochondrial complex I promotes kidney cancer metastasis. | Bezwada D, Perelli L, Lesner NP, Cai L, Brooks B, Wu Z, Vu HS, Sondhi V, Cassidy DL, Kasitinon S, Kelekar S, Cai F, Aurora AB, Patrick M, Leach A, Ghandour R, Zhang Y, Do D, McDaniel P, Sudderth J, Dumesnil D, House S, Rosales T, Poole AM, Lotan Y, Woldu S, Bagrodia A, Meng X, Cadeddu JA, Mishra P, Garcia-Bermudez J, Pedrosa I, Kapur P, Courtney KD, Malloy CR, Genovese G, Margulis V, DeBerardinis RJ | Nature | 39143213 | Nature | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/39143213 |
| Phosphate availability conditions caspofungin tolerance, capsule attachment and titan cell formation in Cryptococcus neoformans. | Qu X, Bhalla K, Horianopoulos LC, Hu G, Alcázar Magaña A, Foster LJ, Roque da Silva LB, Kretschmer M, Kronstad JW | Frontiers in fungal biology | 39206133 | Front Fungal Biol | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/39206133 |
| Histidine decarboxylase inhibition attenuates cancer-associated muscle wasting. | Dasgupta A, Schmitt RE, Kono T, Lee CC, Zoberi MI, Epstein SA, Schneider JZ, Hernandez A, Grandgenett PM, Caffrey TC, DiMaio DJ, Hollingsworth MA, Doles JD | The Journal of experimental medicine | 40600951 | J Exp Med | 2025 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/40600951 |
| Integrated Multiomics Analyses of the Molecular Landscape of Sarcopenia in Alcohol-Related Liver Disease. | Welch N, Kannan P, Mishra S, Bellar A, Agrawal V, Kidd G, Benson E, Musich R, Tabbalat R, Li L, Brown JM, Willard B, Esser KA, Nagy LE, Dasarathy S | Journal of cachexia, sarcopenia and muscle | 40308032 | J Cachexia Sarcopenia Muscle | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/40308032 |
| Severe Cognitive Decline in Long-term Care Is Related to Gut Microbiome Production of Metabolites Involved in Neurotransmission, Immunomodulation, and Autophagy. | Shoubridge AP, Carpenter L, Flynn E, Papanicolas LE, Collins J, Gordon D, Lynn DJ, Whitehead C, Leong LEX, Cations M, De Souza DP, Narayana VK, Choo JM, Wesselingh SL, Crotty M, Inacio MC, Ivey K, Taylor SL, Rogers GB | The journals of gerontology. Series A, Biological sciences and medical sciences | 40166866 | J Gerontol A Biol Sci Med Sci | 2025 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/40166866 |
| Left ventricular myocardial molecular profile of human diabetic ischaemic cardiomyopathy. | Hunter B, Zhang Y, Harney D, McEwen H, Koay YC, Pan M, Malecki C, Khor J, Hume RD, Guglielmi G, Walker A, Dutta S, Rajagopal V, Don A, Larance M, O'Sullivan JF, Yang JYH, Lal S | EMBO molecular medicine | 40759793 | EMBO Mol Med | 2025 Sep | https://www.ncbi.nlm.nih.gov/pubmed/40759793 |
| Synergistic action of specialized metabolites from divergent biosynthesis in the human oral microbiome. | Loop Yao M, Zill NA, Barber CC, Du Y, Lin P, Zhai R, Yoon E, Al Marzooqi D, Zhang W | Proceedings of the National Academy of Sciences of the United States of America | 40828023 | Proc Natl Acad Sci U S A | 2025 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/40828023 |
| IGF2BP3 redirects glycolytic flux to promote one-carbon metabolism and RNA methylation. | Sharma G, Gutierrez M, Jones AE, Kapoor S, Jaiswal AK, Neeb ZT, Rios A, Dorairaj P, Thaxton ML, Lin TL, Tran TM, Kabbani LES, Ritter AJ, Scherer GM, Sorrentino JP, Stiles L, Hoeve JT, Damoiseaux RD, Garg NK, Divakaruni AS, Sanford JR, Rao DS | Cell reports | 41015030 | Cell Rep | 2025 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/41015030 |
| Multi-omic profiling of squamous cell lung cancer identifies metabolites and related genes associated with squamous cell carcinoma. | Staaf J, Ehinger D, Brunnström H, Jönsson M, Rosengren F, Kotevska M, Karlsson A, Aine M, Frezza C, Planck M, Arbajian E | Molecular oncology | 40903981 | Mol Oncol | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/40903981 |
| Metabolome analysis as a potential source of endometriosis biomarkers with the use of multiomics approach in its diagnosis. | Wojtyła C, Kupcewicz B, Tołwiński I, Samborowska E, Radkiewicz M, Jaźwiec R, Sakowicz A, Rubel T, Goszczynska A, Winogradska B, Laudański P | Scientific reports | 41193662 | Sci Rep | 2025 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/41193662 |
| Surface acoustic wave hemolysis assay for evaluating stored red blood cells. | Song M, Anderson CC, Sridhar N, Reisz JA, Akh L, Gao Y, D'Alessandro A, Ding X | Lab on a chip | 41251214 | Lab Chip | 2026 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/41251214 |
| LPLAT11/MBOAT7-driven phosphatidylinositol remodeling ensures radial glial cell integrity in developing neocortex. | Ishino Y, Kishi Y, Iwama T, Kuwayama N, Arai H, Gotoh Y, Aoki J, Kono N | iScience | 41488780 | iScience | 2026 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/41488780 |
| Histone deacetylase SIRT6 regulates tryptophan catabolism and prevents metabolite imbalance associated with neurodegeneration. | Kaluski-Kopatch S, Stein D, Venzor AG, Ferreira Campos AM, Planque M, Goldstein B, De Allende-Becerra E, Smirnov D, Zaretsky A, Eremenko E, Portillo M, Einav M, Krejci AB, Abdu U, Khrameeva E, Gitler D, Fendt SM, Toiber D | Nature communications | 41345108 | Nat Commun | 2025 Dec 4 | https://www.ncbi.nlm.nih.gov/pubmed/41345108 |
| Interactions with bacteria shape diatom adaptation to carbon concentration changes. | Li C, Yin W, Pan Y, Hu H | Nature communications | 41455737 | Nat Commun | 2025 Dec 27 | https://www.ncbi.nlm.nih.gov/pubmed/41455737 |
| Kupffer cells control neonatal hepatic metabolism via Igf1 signaling. | Makdissi N, Hirschmann DJ, Frolov A, Sado I, Bennühr B, Nikolka F, Cheng J, Blank-Stein N, Viola MF, Yaghmour M, Arnold P, Bonaguro L, Becker M, Thiele C, Meissner F, Hiller K, Beyer MD, Mass E | Development (Cambridge, England) | 41459815 | Development | 2026 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/41459815 |
| AADAT-Driven Metabolic Control of Malate and CoQ(10) Shapes Immune Evasion in Triple-Negative Breast Cancer. | Chatterjee M, Gu F, Samanta S, Rasaily U, Thota SM, Varghese D, Qiu Y, Fordwuo LEE, Villanueva H, McKenna MK, Park JH, Zhang W, Tian L, Yu L, Piyarathna B, Gao Y, Simons BW, Jung SY, Karanam B, Putluri V, Chandandeep N, Mohamed N, Asirvatham JR, Jebakumar D, Rao A, Gutierrez C, Omilian AR, Morrison C, Das GM, Ambrosone C, Seeley EH, Kaipparettu BA, Kurland IJ, Putluri N, Elkhanany A, Davis AA, Zhu Q, Zhang XH, Sreekumar A | bioRxiv : the preprint server for biology | 41659489 | bioRxiv | 2026 Jan 30 | https://www.ncbi.nlm.nih.gov/pubmed/41659489 |
| Pan-African genome demonstrates how population-specific genome graphs improve high-throughput sequencing data analysis. | Tetikol HS, Turgut D, Narci K, Budak G, Kalay O, Arslan E, Demirkaya-Budak S, Dolgoborodov A, Kabakci-Zorlu D, Semenyuk V, Jain A, Davis-Dusenbery BN | Nature communications | 35927245 | Nat Commun | 2022 Aug 4 | https://www.ncbi.nlm.nih.gov/pubmed/35927245 |
| Homo Sapiens Chromosomal Location Ontology: A Framework for Genomic Data in Biomedical Knowledge Graphs. | Mohseni Ahooyi T, Stear B, Simmons JA, Nemarich CM, Silverstein JC, Taylor DM | Scientific data | 39799122 | Sci Data | 2025 Jan 11 | https://www.ncbi.nlm.nih.gov/pubmed/39799122 |
| RNAget: an API to securely retrieve RNA quantifications. | Upchurch S, Palumbo E, Adams J, Bujold D, Bourque G, Nedzel J, Graham K, Kagda MS, Assis P, Hitz B, Righi E, Guigó R, Wold BJ, GA4GH RNA-Seq Task Team | Bioinformatics (Oxford, England) | 36897015 | Bioinformatics | 2023 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/36897015 |
| Making Common Fund data more findable: catalyzing a data ecosystem. | Charbonneau AL, Brady A, Czajkowski K, Aluvathingal J, Canchi S, Carter R, Chard K, Clarke DJB, Crabtree J, Creasy HH, D'Arcy M, Felix V, Giglio M, Gingrich A, Harris RM, Hodges TK, Ifeonu O, Jeon M, Kropiwnicki E, Lim MCW, Liming RL, Lumian J, Mahurkar AA, Mandal M, Munro JB, Nadendla S, Richter R, Romano C, Rocca-Serra P, Schor M, Schuler RE, Tangmunarunkit H, Waldrop A, Williams C, Word K, Sansone SA, Ma'ayan A, Wagner R, Foster I, Kesselman C, Brown CT, White O | GigaScience | 36409836 | Gigascience | 2022 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/36409836 |
| PrismEXP: gene annotation prediction from stratified gene-gene co-expression matrices. | Lachmann A, Rizzo KA, Bartal A, Jeon M, Clarke DJB, Ma'ayan A | PeerJ | 36874981 | PeerJ | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/36874981 |
| Enrichr-KG: bridging enrichment analysis across multiple libraries. | Evangelista JE, Xie Z, Marino GB, Nguyen N, Clarke DJB, Ma'ayan A | Nucleic acids research | 37166973 | Nucleic Acids Res | 2023 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/37166973 |
| Appyters: Turning Jupyter Notebooks into data-driven web apps. | Clarke DJB, Jeon M, Stein DJ, Moiseyev N, Kropiwnicki E, Dai C, Xie Z, Wojciechowicz ML, Litz S, Hom J, Evangelista JE, Goldman L, Zhang S, Yoon C, Ahamed T, Bhuiyan S, Cheng M, Karam J, Jagodnik KM, Shu I, Lachmann A, Ayling S, Jenkins SL, Ma'ayan A | Patterns (New York, N.Y.) | 33748796 | Patterns (N Y) | 2021 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/33748796 |
| lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs. | Marino GB, Wojciechowicz ML, Clarke DJB, Kuleshov MV, Xie Z, Jeon M, Lachmann A, Ma'ayan A | Database : the journal of biological databases and curation | 36869839 | Database (Oxford) | 2023 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/36869839 |
| Computational screen to identify potential targets for immunotherapeutic identification and removal of senescence cells. | Deng EZ, Fleishman RH, Xie Z, Marino GB, Clarke DJB, Ma'ayan A | Aging cell | 37082798 | Aging Cell | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37082798 |
| blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation. | Lachmann A, Xie Z, Ma'ayan A | Bioinformatics (Oxford, England) | 35143610 | Bioinformatics | 2022 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/35143610 |
| Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomics. | Deng EZ, Marino GB, Clarke DJB, Diamant I, Resnick AC, Ma W, Wang P, Ma'ayan A | Cell reports methods | 39127042 | Cell Rep Methods | 2024 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/39127042 |
| Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning. | Kropiwnicki E, Evangelista JE, Stein DJ, Clarke DJB, Lachmann A, Kuleshov MV, Jeon M, Jagodnik KM, Ma'ayan A | Database : the journal of biological databases and curation | 33787872 | Database (Oxford) | 2021 Mar 31 | https://www.ncbi.nlm.nih.gov/pubmed/33787872 |
| Transforming L1000 profiles to RNA-seq-like profiles with deep learning. | Jeon M, Xie Z, Evangelista JE, Wojciechowicz ML, Clarke DJB, Ma'ayan A | BMC bioinformatics | 36100892 | BMC Bioinformatics | 2022 Sep 13 | https://www.ncbi.nlm.nih.gov/pubmed/36100892 |
| Getting Started with LINCS Datasets and Tools. | Xie Z, Kropiwnicki E, Wojciechowicz ML, Jagodnik KM, Shu I, Bailey A, Clarke DJB, Jeon M, Evangelista JE, V Kuleshov M, Lachmann A, Parigi AA, Sanchez JM, Jenkins SL, Ma'ayan A | Current protocols | 35876555 | Curr Protoc | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35876555 |
| SigCom LINCS: data and metadata search engine for a million gene expression signatures. | Evangelista JE, Clarke DJB, Xie Z, Lachmann A, Jeon M, Chen K, Jagodnik KM, Jenkins SL, Kuleshov MV, Wojciechowicz ML, Schürer SC, Medvedovic M, Ma'ayan A | Nucleic acids research | 35524556 | Nucleic Acids Res | 2022 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/35524556 |
| GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery. | Marino GB, Ngai M, Clarke DJB, Fleishman RH, Deng EZ, Xie Z, Ahmed N, Ma'ayan A | Nucleic acids research | 37166966 | Nucleic Acids Res | 2023 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/37166966 |
| Systems immunology-based drug repurposing framework to target inflammation in atherosclerosis. | Amadori L, Calcagno C, Fernandez DM, Koplev S, Fernandez N, Kaur R, Mury P, Khan NS, Sajja S, Shamailova R, Cyr Y, Jeon M, Hill CA, Chong PS, Naidu S, Sakurai K, Ghotbi AA, Soler R, Eberhardt N, Rahman A, Faries P, Moore KJ, Fayad ZA, Ma'ayan A, Giannarelli C | Nature cardiovascular research | 37771373 | Nat Cardiovasc Res | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37771373 |
