Common Fund Data Ecosystem (CFDE)
Common Fund Data Ecosystem (CFDE)
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 |
| 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 |
| 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, Desai H, Hausler R, Naqvi AS, 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 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/39974082 |
| 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 |
| 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 |
| 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 |
| WIMOAD: Weighted Integration of Multi-Omics data for Alzheimer's Disease (AD) Diagnosis. | Xiao H, Wang J, Wan S | bioRxiv : the preprint server for biology | 39386613 | bioRxiv | 2024 Sep 27 | https://www.ncbi.nlm.nih.gov/pubmed/39386613 |
| 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 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/40060540 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | 2024 Aug 27 | https://www.ncbi.nlm.nih.gov/pubmed/39190705 |
| 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 |
| 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 | bioRxiv : the preprint server for biology | 38712147 | bioRxiv | 2024 Jun 26 | https://www.ncbi.nlm.nih.gov/pubmed/38712147 |
| Characterization of aberrant splicing in pediatric central nervous system tumors reveals CLK1 as a candidate oncogenic dependency. | Naqvi AS, Corbett RJ, Seghal P, Conkrite KL, Rathi KS, Ennis BM, Hayer KE, Zhang B, Brown MA, Miller DP, 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 Feb 26 | https://www.ncbi.nlm.nih.gov/pubmed/39149264 |
| Neuronal cell adhesion molecule (NRCAM) variant defined by microexon skipping is an essential, antigenically distinct, and targetable proteoform in high-grade glioma. | 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, DeRaedt T, Powell DJ, Thomas-Tikhonenko A | bioRxiv : the preprint server for biology | 39868324 | bioRxiv | 2025 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/39868324 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | 2024 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/39572737 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/40021805 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
| 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 |
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| 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 |
| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 Jan 11 | https://www.ncbi.nlm.nih.gov/pubmed/40133794 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
