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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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 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
NRCAM variant defined by microexon skipping is an essential, antigenically distinct, and targetable 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, DeRaedt T, Powell DJ, Thomas-Tikhonenko A bioRxiv : the preprint server for biology 39868324 bioRxiv 2025 Jun 8 https://www.ncbi.nlm.nih.gov/pubmed/39868324
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 Bioinformatics (Oxford, England) 38796686 Bioinformatics 2024 Jun 3 https://www.ncbi.nlm.nih.gov/pubmed/38796686
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 Feb 28 https://www.ncbi.nlm.nih.gov/pubmed/40021805
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
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
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
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
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
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
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
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
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 May 27 https://www.ncbi.nlm.nih.gov/pubmed/40421888
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
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
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
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
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
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
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
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
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
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
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
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
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
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 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
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
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
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
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
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
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
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
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
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
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
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
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 Cancer reports (Hoboken, N.J.) 37533331 Cancer Rep (Hoboken) 2023 Sep https://www.ncbi.nlm.nih.gov/pubmed/37533331
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
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
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 Aug 1 https://www.ncbi.nlm.nih.gov/pubmed/40133794
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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OGDHL regulates nucleotide metabolism, tumor growth, and neuroendocrine marker expression in prostate cancer. Bernard MJ, Ruiz A, Diaz JA, Nunley NM, Dove RN, Heering KY, Bopardikar S, Gallardo A, Hashimoto T, Agrawal R, Smith CM, Wilde BR, Matulionis N, Richards HM, Sharifi MN, Lang JM, Zhao SG, Haffner MC, Boutros PC, Christofk HR, Goldstein AS bioRxiv : the preprint server for biology 40502162 bioRxiv 2025 Jun 1 https://www.ncbi.nlm.nih.gov/pubmed/40502162
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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
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

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