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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
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
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
Deep learning enabled multi-organ segmentation of mouse embryos. Rolfe SM, Whikehart SM, Maga AM Biology open 36802342 Biol Open 2023 Feb 15
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
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A photothermal driven chemotherapy for the treatment of metastatic melanoma. Bhatt HN, Diwan R, Borrego EA, Pérez CAM, Varela-Ramirez A, Kumar R, Aguilera RJ, Nurunnabi M Journal of controlled release : official journal of the Controlled Release Society 37562554 J Control Release 2023 Sep
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Cadherin-11 targeted cell-specific liposomes enabled skin fibrosis treatment by inducing apoptosis. Bhatt HN, Diwan R, Estevao IL, Dong R, Smith J, Xiao C, Agarwal SK, Nurunnabi M Journal of controlled release : official journal of the Controlled Release Society 38648957 J Control Release 2024 Jun
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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
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
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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
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
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
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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
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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
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
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
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Evaluating cancer cell line and patient-derived xenograft recapitulation of tumor and non-diseased tissue gene expression profiles in silico. Williams AS, Wilk EJ, Fisher JL, Lasseigne BN bioRxiv : the preprint server for biology 37090499 bioRxiv 2023 Jun 15
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
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
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
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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
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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
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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
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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
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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
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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
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