Program Publications
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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 |
---|---|---|---|---|---|
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
Flash entropy search to query all mass spectral libraries in real time. | Li Y, Fiehn O | Nature methods | 37735567 | Nat Methods | 2023 Oct |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
MetGENE: gene-centric metabolomics information retrieval tool. | Srinivasan S, Maurya MR, Ramachandran S, Fahy E, Subramaniam S | GigaScience | 37983749 | Gigascience | 2022 Dec 28 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |