Illuminating the Druggable Genome (IDG)
Illuminating the Druggable Genome (IDG)
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 |
|---|---|---|---|---|---|
| Systemic QSAR and phenotypic virtual screening: chasing butterflies in drug discovery. | Cruz-Monteagudo M, Schürer S, Tejera E, Pérez-Castillo Y, Medina-Franco JL, Sánchez-Rodríguez A, Borges F | Drug discovery today | 28274840 | Drug Discov Today | 2017 Jul |
| Proteomic analysis defines kinase taxonomies specific for subtypes of breast cancer. | Collins KAL, Stuhlmiller TJ, Zawistowski JS, East MP, Pham TT, Hall CR, Goulet DR, Bevill SM, Angus SP, Velarde SH, Sciaky N, Oprea TI, Graves LM, Johnson GL, Gomez SM | Oncotarget | 29643987 | Oncotarget | 2018 Mar 20 |
| From flamingo dance to (desirable) drug discovery: a nature-inspired approach. | Sánchez-Rodríguez A, Pérez-Castillo Y, Schürer SC, Nicolotti O, Mangiatordi GF, Borges F, Cordeiro MNDS, Tejera E, Medina-Franco JL, Cruz-Monteagudo M | Drug discovery today | 28624633 | Drug Discov Today | 2017 Oct |
| Noribogaine is a G-protein biased κ-opioid receptor agonist. | Maillet EL, Milon N, Heghinian MD, Fishback J, Schürer SC, Garamszegi N, Mash DC | Neuropharmacology | 26302653 | Neuropharmacology | 2015 Dec |
| CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision. | Junge A, Jensen LJ | Bioinformatics (Oxford, England) | 31199464 | Bioinformatics | 2020 Jan 1 |
| SmartGraph: a network pharmacology investigation platform. | Zahoránszky-Kőhalmi G, Sheils T, Oprea TI | Journal of cheminformatics | 33430980 | J Cheminform | 2020 Jan 21 |
| The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods. | Zdrazil B, Felix E, Hunter F, Manners EJ, Blackshaw J, Corbett S, de Veij M, Ioannidis H, Lopez DM, Mosquera JF, Magarinos MP, Bosc N, Arcila R, Kizilören T, Gaulton A, Bento AP, Adasme MF, Monecke P, Landrum GA, Leach AR | Nucleic acids research | 37933841 | Nucleic Acids Res | 2024 Jan 5 |
| Computational and Practical Aspects of Drug Repositioning. | Oprea TI, Overington JP | Assay and drug development technologies | 26241209 | Assay Drug Dev Technol | 2015 Jul-Aug |
| HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases. | Palleja A, Jensen LJ | PeerJ | 26157625 | PeerJ | 2015 |
| BDDCS, the Rule of 5 and drugability. | Benet LZ, Hosey CM, Ursu O, Oprea TI | Advanced drug delivery reviews | 27182629 | Adv Drug Deliv Rev | 2016 Jun 1 |
| Drug target ontology to classify and integrate drug discovery data. | Lin Y, Mehta S, Küçük-McGinty H, Turner JP, Vidovic D, Forlin M, Koleti A, Nguyen DT, Jensen LJ, Guha R, Mathias SL, Ursu O, Stathias V, Duan J, Nabizadeh N, Chung C, Mader C, Visser U, Yang JJ, Bologa CG, Oprea TI, Schürer SC | Journal of biomedical semantics | 29122012 | J Biomed Semantics | 2017 Nov 9 |
| Exploring the dark genome: implications for precision medicine. | Oprea TI | Mammalian genome : official journal of the International Mammalian Genome Society | 31270560 | Mamm Genome | 2019 Aug |
| How to Develop a Drug Target Ontology: KNowledge Acquisition and Representation Methodology (KNARM). | Küçük McGinty H, Visser U, Schürer S | Methods in molecular biology (Clifton, N.J.) | 30848456 | Methods Mol Biol | 2019 |
| DrugCentral: online drug compendium. | Ursu O, Holmes J, Knockel J, Bologa CG, Yang JJ, Mathias SL, Nelson SJ, Oprea TI | Nucleic acids research | 27789690 | Nucleic Acids Res | 2017 Jan 4 |
| Polypharmacology or Promiscuity? Structural Interactions of Resveratrol With Its Bandwagon of Targets. | Saqib U, Kelley TT, Panguluri SK, Liu D, Savai R, Baig MS, Schürer SC | Frontiers in pharmacology | 30405416 | Front Pharmacol | 2018 |
| The ChEMBL database in 2017. | Gaulton A, Hersey A, Nowotka M, Bento AP, Chambers J, Mendez D, Mutowo P, Atkinson F, Bellis LJ, Cibrián-Uhalte E, Davies M, Dedman N, Karlsson A, Magariños MP, Overington JP, Papadatos G, Smit I, Leach AR | Nucleic acids research | 27899562 | Nucleic Acids Res | 2017 Jan 4 |
| High quality, small molecule-activity datasets for kinase research. | Sharma R, Schürer SC, Muskal SM | F1000Research | 27429748 | F1000Res | 2016 |
| TIGA: target illumination GWAS analytics. | Yang JJ, Grissa D, Lambert CG, Bologa CG, Mathias SL, Waller A, Wild DJ, Jensen LJ, Oprea TI | Bioinformatics (Oxford, England) | 34086846 | Bioinformatics | 2021 Nov 5 |
| A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. | Zahoránszky-Kőhalmi G, Siramshetty VB, Kumar P, Gurumurthy M, Grillo B, Mathew B, Metaxatos D, Backus M, Mierzwa T, Simon R, Grishagin I, Brovold L, Mathé EA, Hall MD, Michael SG, Godfrey AG, Mestres J, Jensen LJ, Oprea TI | bioRxiv : the preprint server for biology | 33173863 | bioRxiv | 2020 Nov 5 |
| Badapple: promiscuity patterns from noisy evidence. | Yang JJ, Ursu O, Lipinski CA, Sklar LA, Oprea TI, Bologa CG | Journal of cheminformatics | 27239230 | J Cheminform | 2016 |
| Identification of hyper-rewired genomic stress non-oncogene addiction genes across 15 cancer types. | Hjaltelin JX, Izarzugaza JMG, Jensen LJ, Russo F, Westergaard D, Brunak S | NPJ systems biology and applications | 31396397 | NPJ Syst Biol Appl | 2019 |
| Unexplored therapeutic opportunities in the human genome. | Oprea TI, Bologa CG, Brunak S, Campbell A, Gan GN, Gaulton A, Gomez SM, Guha R, Hersey A, Holmes J, Jadhav A, Jensen LJ, Johnson GL, Karlson A, Leach AR, Ma'ayan A, Malovannaya A, Mani S, Mathias SL, McManus MT, Meehan TF, von Mering C, Muthas D, Nguyen DT, Overington JP, Papadatos G, Qin J, Reich C, Roth BL, Schürer SC, Simeonov A, Sklar LA, Southall N, Tomita S, Tudose I, Ursu O, Vidovic D, Waller A, Westergaard D, Yang JJ, Zahoránszky-Köhalmi G | Nature reviews. Drug discovery | 29567993 | Nat Rev Drug Discov | 2018 May |
| Unexplored therapeutic opportunities in the human genome. | Oprea TI, Bologa CG, Brunak S, Campbell A, Gan GN, Gaulton A, Gomez SM, Guha R, Hersey A, Holmes J, Jadhav A, Jensen LJ, Johnson GL, Karlson A, Leach AR, Ma'ayan A, Malovannaya A, Mani S, Mathias SL, McManus MT, Meehan TF, von Mering C, Muthas D, Nguyen DT, Overington JP, Papadatos G, Qin J, Reich C, Roth BL, Schürer SC, Simeonov A, Sklar LA, Southall N, Tomita S, Tudose I, Ursu O, Vidovic D, Waller A, Westergaard D, Yang JJ, Zahoránszky-Köhalmi G | Nature reviews. Drug discovery | 29472638 | Nat Rev Drug Discov | 2018 May |
| Comprehensive comparison of large-scale tissue expression datasets. | Santos A, Tsafou K, Stolte C, Pletscher-Frankild S, O'Donoghue SI, Jensen LJ | PeerJ | 26157623 | PeerJ | 2015 |
| Pharos: Collating protein information to shed light on the druggable genome. | Nguyen DT, Mathias S, Bologa C, Brunak S, Fernandez N, Gaulton A, Hersey A, Holmes J, Jensen LJ, Karlsson A, Liu G, Ma'ayan A, Mandava G, Mani S, Mehta S, Overington J, Patel J, Rouillard AD, Schürer S, Sheils T, Simeonov A, Sklar LA, Southall N, Ursu O, Vidovic D, Waller A, Yang J, Jadhav A, Oprea TI, Guha R | Nucleic acids research | 27903890 | Nucleic Acids Res | 2017 Jan 4 |
| Illuminating the druggable genome through patent bioactivity data. | Magariños MP, Gaulton A, Félix E, Kiziloren T, Arcila R, Oprea TI, Leach AR | PeerJ | 37151295 | PeerJ | 2023 |
| Discovery of a specific inhibitor of human GLUT5 by virtual screening and in vitro transport evaluation. | George Thompson AM, Ursu O, Babkin P, Iancu CV, Whang A, Oprea TI, Choe JY | Scientific reports | 27074918 | Sci Rep | 2016 Apr 14 |
| Drug and disease signature integration identifies synergistic combinations in glioblastoma. | Stathias V, Jermakowicz AM, Maloof ME, Forlin M, Walters W, Suter RK, Durante MA, Williams SL, Harbour JW, Volmar CH, Lyons NJ, Wahlestedt C, Graham RM, Ivan ME, Komotar RJ, Sarkaria JN, Subramanian A, Golub TR, Schürer SC, Ayad NG | Nature communications | 30552330 | Nat Commun | 2018 Dec 14 |
| Formalizing drug indications on the road to therapeutic intent. | Nelson SJ, Oprea TI, Ursu O, Bologa CG, Zaveri A, Holmes J, Yang JJ, Mathias SL, Mani S, Tuttle MS, Dumontier M | Journal of the American Medical Informatics Association : JAMIA | 29016968 | J Am Med Inform Assoc | 2017 Nov 1 |
| Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000. | Sinha S, Eisenhaber B, Jensen LJ, Kalbuaji B, Eisenhaber F | Proteomics | 30265449 | Proteomics | 2018 Nov |
| TIN-X: target importance and novelty explorer. | Cannon DC, Yang JJ, Mathias SL, Ursu O, Mani S, Waller A, Schürer SC, Jensen LJ, Sklar LA, Bologa CG, Oprea TI | Bioinformatics (Oxford, England) | 28398460 | Bioinformatics | 2017 Aug 15 |
| Estimation of Maximum Recommended Therapeutic Dose Using Predicted Promiscuity and Potency. | Liu T, Oprea T, Ursu O, Hasselgren C, Altman RB | Clinical and translational science | 27736015 | Clin Transl Sci | 2016 Dec |
| Protein biomarker druggability profiling. | Mani S, Cannon D, Ohls R, Oprea T, Mathias S, Ballard K, Ursu O, Bologa C | Journal of biomedical informatics | 28131723 | J Biomed Inform | 2017 Feb |
| A comprehensive map of molecular drug targets. | Santos R, Ursu O, Gaulton A, Bento AP, Donadi RS, Bologa CG, Karlsson A, Al-Lazikani B, Hersey A, Oprea TI, Overington JP | Nature reviews. Drug discovery | 27910877 | Nat Rev Drug Discov | 2017 Jan |
| A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. | Zahoránszky-Kőhalmi G, Siramshetty VB, Kumar P, Gurumurthy M, Grillo B, Mathew B, Metaxatos D, Backus M, Mierzwa T, Simon R, Grishagin I, Brovold L, Mathé EA, Hall MD, Michael SG, Godfrey AG, Mestres J, Jensen LJ, Oprea TI | Journal of chemical information and modeling | 35057621 | J Chem Inf Model | 2022 Feb 14 |
| Molecular systems evaluation of oligomerogenic APP(E693Q) and fibrillogenic APP(KM670/671NL)/PSEN1(Δexon9) mouse models identifies shared features with human Alzheimer's brain molecular pathology. | Readhead B, Haure-Mirande JV, Zhang B, Haroutunian V, Gandy S, Schadt EE, Dudley JT, Ehrlich ME | Molecular psychiatry | 26552589 | Mol Psychiatry | 2016 Aug |
| Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration. | von Schimmelmann M, Feinberg PA, Sullivan JM, Ku SM, Badimon A, Duff MK, Wang Z, Lachmann A, Dewell S, Ma'ayan A, Han MH, Tarakhovsky A, Schaefer A | Nature neuroscience | 27526204 | Nat Neurosci | 2016 Oct |
| Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. | Shameer K, Glicksberg BS, Hodos R, Johnson KW, Badgeley MA, Readhead B, Tomlinson MS, O'Connor T, Miotto R, Kidd BA, Chen R, Ma'ayan A, Dudley JT | Briefings in bioinformatics | 28200013 | Brief Bioinform | 2018 Jul 20 |
| Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition. | Koplev S, Lin K, Dohlman AB, Ma'ayan A | PLoS computational biology | 29293502 | PLoS Comput Biol | 2018 Jan |
| BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud. | Torre D, Lachmann A, Ma'ayan A | Cell systems | 30447998 | Cell Syst | 2018 Nov 28 |
| 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 |
| EXPLORING THE REPRODUCIBILITY OF PROBABILISTIC CAUSAL MOLECULAR NETWORK MODELS. | Cohain A, Divaraniya AA, Zhu K, Scarpa JR, Kasarskis A, Zhu J, Chang R, Dudley JT, Schadt EE | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 27896968 | Pac Symp Biocomput | 2017 |
| Integrative radiogenomic analysis for multicentric radiophenotype in glioblastoma. | Kong DS, Kim J, Lee IH, Kim ST, Seol HJ, Lee JI, Park WY, Ryu G, Wang Z, Ma'ayan A, Nam DH | Oncotarget | 26863628 | Oncotarget | 2016 Mar 8 |
| In silico methods for drug repurposing and pharmacology. | Hodos RA, Kidd BA, Shameer K, Readhead BP, Dudley JT | Wiley interdisciplinary reviews. Systems biology and medicine | 27080087 | Wiley Interdiscip Rev Syst Biol Med | 2016 May |
| Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks. | Glicksberg BS, Li L, Badgeley MA, Shameer K, Kosoy R, Beckmann ND, Pho N, Hakenberg J, Ma M, Ayers KL, Hoffman GE, Dan Li S, Schadt EE, Patel CJ, Chen R, Dudley JT | Bioinformatics (Oxford, England) | 27307606 | Bioinformatics | 2016 Jun 15 |
| Evaluation of direct-to-consumer low-volume lab tests in healthy adults. | Kidd BA, Hoffman G, Zimmerman N, Li L, Morgan JW, Glowe PK, Botwin GJ, Parekh S, Babic N, Doust MW, Stock GB, Schadt EE, Dudley JT | The Journal of clinical investigation | 27018593 | J Clin Invest | 2016 May 2 |
| Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions. | Xu K, Schadt EE, Pollard KS, Roussos P, Dudley JT | Molecular biology and evolution | 25681384 | Mol Biol Evol | 2015 May |
| An Integrated Transcriptome Atlas of Embryonic Hair Follicle Progenitors, Their Niche, and the Developing Skin. | Sennett R, Wang Z, Rezza A, Grisanti L, Roitershtein N, Sicchio C, Mok KW, Heitman NJ, Clavel C, Ma'ayan A, Rendl M | Developmental cell | 26256211 | Dev Cell | 2015 Sep 14 |
| An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions. | Sevilla A, Papatsenko D, Mazloom AR, Xu H, Vasileva A, Unwin RD, LeRoy G, Chen EY, Garrett-Bakelman FE, Lee DF, Trinite B, Webb RL, Wang Z, Su J, Gingold J, Melnick A, Garcia BA, Whetton AD, MacArthur BD, Ma'ayan A, Lemischka IR | Frontiers in cell and developmental biology | 33816475 | Front Cell Dev Biol | 2021 |
| Deep learning for healthcare: review, opportunities and challenges. | Miotto R, Wang F, Wang S, Jiang X, Dudley JT | Briefings in bioinformatics | 28481991 | Brief Bioinform | 2018 Nov 27 |
| A blueprint of cell identity. | Ma'ayan A, Duan Q | Nature biotechnology | 25299921 | Nat Biotechnol | 2014 Oct |
| Histone H3.3 and its proteolytically processed form drive a cellular senescence programme. | Duarte LF, Young AR, Wang Z, Wu HA, Panda T, Kou Y, Kapoor A, Hasson D, Mills NR, Ma'ayan A, Narita M, Bernstein E | Nature communications | 25394905 | Nat Commun | 2014 Nov 14 |
| Morphine Regulated Synaptic Networks Revealed by Integrated Proteomics and Network Analysis. | Stockton SD Jr, Gomes I, Liu T, Moraje C, Hipólito L, Jones MR, Ma'ayan A, Morón JA, Li H, Devi LA | Molecular & cellular proteomics : MCP | 26149443 | Mol Cell Proteomics | 2015 Oct |
| Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction. | Rouillard AD, Wang Z, Ma'ayan A | Computational biology and chemistry | 26101093 | Comput Biol Chem | 2015 Oct |
| Genome-wide significant loci: how important are they? Systems genetics to understand heritability of coronary artery disease and other common complex disorders. | Björkegren JLM, Kovacic JC, Dudley JT, Schadt EE | Journal of the American College of Cardiology | 25720628 | J Am Coll Cardiol | 2015 Mar 3 |
| Integrative network modeling approaches to personalized cancer medicine. | Kidd BA, Readhead BP, Eden C, Parekh S, Dudley JT | Personalized medicine | 27019658 | Per Med | 2015 Jun 1 |
| Cognitive Machine-Learning Algorithm for Cardiac Imaging: A Pilot Study for Differentiating Constrictive Pericarditis From Restrictive Cardiomyopathy. | Sengupta PP, Huang YM, Bansal M, Ashrafi A, Fisher M, Shameer K, Gall W, Dudley JT | Circulation. Cardiovascular imaging | 27266599 | Circ Cardiovasc Imaging | 2016 Jun |
| Krüppel-Like Factor 15 Mediates Glucocorticoid-Induced Restoration of Podocyte Differentiation Markers. | Mallipattu SK, Guo Y, Revelo MP, Roa-Peña L, Miller T, Ling J, Shankland SJ, Bialkowska AB, Ly V, Estrada C, Jain MK, Lu Y, Ma'ayan A, Mehrotra A, Yacoub R, Nord EP, Woroniecki RP, Yang VW, He JC | Journal of the American Society of Nephrology : JASN | 27288011 | J Am Soc Nephrol | 2017 Jan |
| L1000FWD: fireworks visualization of drug-induced transcriptomic signatures. | Wang Z, Lachmann A, Keenan AB, Ma'ayan A | Bioinformatics (Oxford, England) | 29420694 | Bioinformatics | 2018 Jun 15 |
| Automated cell type discovery and classification through knowledge transfer. | Lee HC, Kosoy R, Becker CE, Dudley JT, Kidd BA | Bioinformatics (Oxford, England) | 28158442 | Bioinformatics | 2017 Jun 1 |
| Fetal liver hematopoietic stem cell niches associate with portal vessels. | Khan JA, Mendelson A, Kunisaki Y, Birbrair A, Kou Y, Arnal-Estapé A, Pinho S, Ciero P, Nakahara F, Ma'ayan A, Bergman A, Merad M, Frenette PS | Science (New York, N.Y.) | 26634440 | Science | 2016 Jan 8 |
| An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study. | Wang Z, Ma'ayan A | F1000Research | 27583132 | F1000Res | 2016 |
| L1000CDS(2): LINCS L1000 characteristic direction signatures search engine. | Duan Q, Reid SP, Clark NR, Wang Z, Fernandez NF, Rouillard AD, Readhead B, Tritsch SR, Hodos R, Hafner M, Niepel M, Sorger PK, Dudley JT, Bavari S, Panchal RG, Ma'ayan A | NPJ systems biology and applications | 28413689 | NPJ Syst Biol Appl | 2016 |
| Intracoronary Imaging, Cholesterol Efflux, and Transcriptomics after Intensive Statin Treatment in Diabetes. | Chamaria S, Johnson KW, Vengrenyuk Y, Baber U, Shameer K, Divaraniya AA, Glicksberg BS, Li L, Bhatheja S, Moreno P, Maehara A, Mehran R, Dudley JT, Narula J, Sharma SK, Kini AS | Scientific reports | 28765529 | Sci Rep | 2017 Aug 1 |
| Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach. | Li L, Greene I, Readhead B, Menon MC, Kidd BA, Uzilov AV, Wei C, Philippe N, Schroppel B, He JC, Chen R, Dudley JT, Murphy B | Scientific reports | 28051114 | Sci Rep | 2017 Jan 4 |
| Replicating Cardiovascular Condition-Birth Month Associations. | Li L, Boland MR, Miotto R, Tatonetti NP, Dudley JT | Scientific reports | 27624541 | Sci Rep | 2016 Sep 14 |
| GEN3VA: aggregation and analysis of gene expression signatures from related studies. | Gundersen GW, Jagodnik KM, Woodland H, Fernandez NF, Sani K, Dohlman AB, Ung PM, Monteiro CD, Schlessinger A, Ma'ayan A | BMC bioinformatics | 27846806 | BMC Bioinformatics | 2016 Nov 15 |
| Signaling Networks among Stem Cell Precursors, Transit-Amplifying Progenitors, and their Niche in Developing Hair Follicles. | Rezza A, Wang Z, Sennett R, Qiao W, Wang D, Heitman N, Mok KW, Clavel C, Yi R, Zandstra P, Ma'ayan A, Rendl M | Cell reports | 27009580 | Cell Rep | 2016 Mar 29 |
| Drug-induced adverse events prediction with the LINCS L1000 data. | Wang Z, Clark NR, Ma'ayan A | Bioinformatics (Oxford, England) | 27153606 | Bioinformatics | 2016 Aug 1 |
| Systems Medicine Approaches to Improving Understanding, Treatment, and Clinical Management of Neuroendocrine Prostate Cancer. | Yadav KK, Shameer K, Readhead B, Yadav SS, Li L, Kasarskis A, Tewari AK, Dudley JT | Current pharmaceutical design | 27174811 | Curr Pharm Des | 2016 |
| Critical period plasticity-related transcriptional aberrations in schizophrenia and bipolar disorder. | Smith MR, Readhead B, Dudley JT, Morishita H | Schizophrenia research | 30442475 | Schizophr Res | 2019 May |
| Integrative bioinformatics identifies postnatal lead (Pb) exposure disrupts developmental cortical plasticity. | Smith MR, Yevoo P, Sadahiro M, Austin C, Amarasiriwardena C, Awawda M, Arora M, Dudley JT, Morishita H | Scientific reports | 30401819 | Sci Rep | 2018 Nov 6 |
| Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool. | Clark NR, Szymkiewicz M, Wang Z, Monteiro CD, Jones MR, Ma'ayan A | Proceedings. IEEE International Conference on Bioinformatics and Biomedicine | 26848405 | Proceedings (IEEE Int Conf Bioinformatics Biomed) | 2015 Nov |
| Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data. | Fernandez NF, Gundersen GW, Rahman A, Grimes ML, Rikova K, Hornbeck P, Ma'ayan A | Scientific data | 28994825 | Sci Data | 2017 Oct 10 |
| Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling. | Niepel M, Hafner M, Duan Q, Wang Z, Paull EO, Chung M, Lu X, Stuart JM, Golub TR, Subramanian A, Ma'ayan A, Sorger PK | Nature communications | 29084964 | Nat Commun | 2017 Oct 30 |
| Systematic Analysis of Environmental Chemicals That Dysregulate Critical Period Plasticity-Related Gene Expression Reveals Common Pathways That Mimic Immune Response to Pathogen. | Smith MR, Yevoo P, Sadahiro M, Readhead B, Kidd B, Dudley JT, Morishita H | Neural plasticity | 32454811 | Neural Plast | 2020 |
| The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. | Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma'ayan A | Database : the journal of biological databases and curation | 27374120 | Database (Oxford) | 2016 |
| Polygenic overlap between schizophrenia risk and antipsychotic response: a genomic medicine approach. | Ruderfer DM, Charney AW, Readhead B, Kidd BA, Kähler AK, Kenny PJ, Keiser MJ, Moran JL, Hultman CM, Scott SA, Sullivan PF, Purcell SM, Dudley JT, Sklar P | The lancet. Psychiatry | 26915512 | Lancet Psychiatry | 2016 Apr |
| Genomic Analysis of Kidney Allograft Injury Identifies Hematopoietic Cell Kinase as a Key Driver of Renal Fibrosis. | Wei C, Li L, Menon MC, Zhang W, Fu J, Kidd B, Keung KL, Woytovich C, Greene I, Xiao W, Salem F, Yi Z, He JC, Dudley JT, Murphy B | Journal of the American Society of Nephrology : JASN | 27927780 | J Am Soc Nephrol | 2017 May |
| Mapping the effects of drugs on the immune system. | Kidd BA, Wroblewska A, Boland MR, Agudo J, Merad M, Tatonetti NP, Brown BD, Dudley JT | Nature biotechnology | 26619012 | Nat Biotechnol | 2016 Jan |
| Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams. | Shameer K, Badgeley MA, Miotto R, Glicksberg BS, Morgan JW, Dudley JT | Briefings in bioinformatics | 26876889 | Brief Bioinform | 2017 Jan |
| 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 |
| Massive mining of publicly available RNA-seq data from human and mouse. | Lachmann A, Torre D, Keenan AB, Jagodnik KM, Lee HJ, Wang L, Silverstein MC, Ma'ayan A | Nature communications | 29636450 | Nat Commun | 2018 Apr 10 |
| Machine learning in cardiovascular medicine: are we there yet? | Shameer K, Johnson KW, Glicksberg BS, Dudley JT, Sengupta PP | Heart (British Cardiac Society) | 29352006 | Heart | 2018 Jul |
| Dynamics of the discovery process of protein-protein interactions from low content studies. | Wang Z, Clark NR, Ma'ayan A | BMC systems biology | 26048415 | BMC Syst Biol | 2015 Jun 6 |
| Integrative Analysis of Disease Signatures Shows Inflammation Disrupts Juvenile Experience-Dependent Cortical Plasticity. | Smith MR, Burman P, Sadahiro M, Kidd BA, Dudley JT, Morishita H | eNeuro | 28101530 | eNeuro | 2016 Nov-Dec |
| EXPLORING BRAIN TRANSCRIPTOMIC PATTERNS: A TOPOLOGICAL ANALYSIS USING SPATIAL EXPRESSION NETWORKS. | Kuncheva Z, Krishnan ML, Montana G | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 27896963 | Pac Symp Biocomput | 2017 |
| Gold Nanoparticle Reprograms Pancreatic Tumor Microenvironment and Inhibits Tumor Growth. | Saha S, Xiong X, Chakraborty PK, Shameer K, Arvizo RR, Kudgus RA, Dwivedi SK, Hossen MN, Gillies EM, Robertson JD, Dudley JT, Urrutia RA, Postier RG, Bhattacharya R, Mukherjee P | ACS nano | 27758098 | ACS Nano | 2016 Dec 27 |
| GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions. | Gundersen GW, Jones MR, Rouillard AD, Kou Y, Monteiro CD, Feldmann AS, Hu KS, Ma'ayan A | Bioinformatics (Oxford, England) | 25971742 | Bioinformatics | 2015 Sep 15 |
| Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets. | Duan Q, Wang Z, Fernandez NF, Rouillard AD, Tan CM, Benes CH, Ma'ayan A | Bioinformatics (Oxford, England) | 25100688 | Bioinformatics | 2014 Nov 15 |
| Lean Big Data integration in systems biology and systems pharmacology. | Ma'ayan A, Rouillard AD, Clark NR, Wang Z, Duan Q, Kou Y | Trends in pharmacological sciences | 25109570 | Trends Pharmacol Sci | 2014 Sep |
| REDD1 functions at the crossroads between the therapeutic and adverse effects of topical glucocorticoids. | Baida G, Bhalla P, Kirsanov K, Lesovaya E, Yakubovskaya M, Yuen K, Guo S, Lavker RM, Readhead B, Dudley JT, Budunova I | EMBO molecular medicine | 25504525 | EMBO Mol Med | 2015 Jan |
| Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses. | Torre D, Krawczuk P, Jagodnik KM, Lachmann A, Wang Z, Wang L, Kuleshov MV, Ma'ayan A | Scientific data | 29485625 | Sci Data | 2018 Feb 27 |
| Podocyte-Specific Induction of Krüppel-Like Factor 15 Restores Differentiation Markers and Attenuates Kidney Injury in Proteinuric Kidney Disease. | Guo Y, Pace J, Li Z, Ma'ayan A, Wang Z, Revelo MP, Chen E, Gu X, Attalah A, Yang Y, Estrada C, Yang VW, He JC, Mallipattu SK | Journal of the American Society of Nephrology : JASN | 30143559 | J Am Soc Nephrol | 2018 Oct |
| Cell-specific prediction and application of drug-induced gene expression profiles. | Hodos R, Zhang P, Lee HC, Duan Q, Wang Z, Clark NR, Ma'ayan A, Wang F, Kidd B, Hu J, Sontag D, Dudley J | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 29218867 | Pac Symp Biocomput | 2018 |
| Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age. | Wang Z, Li L, Glicksberg BS, Israel A, Dudley JT, Ma'ayan A | Journal of biomedical informatics | 29113935 | J Biomed Inform | 2017 Dec |
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| Deep Patient: An Unsupervised Representation to Predict the Future of Patients from the Electronic Health Records. | Miotto R, Li L, Kidd BA, Dudley JT | Scientific reports | 27185194 | Sci Rep | 2016 May 17 |
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| Complex systems biology. | Ma'ayan A | Journal of the Royal Society, Interface | 28931638 | J R Soc Interface | 2017 Sep |
| How to Illuminate the Druggable Genome Using Pharos. | Sheils T, Mathias SL, Siramshetty VB, Bocci G, Bologa CG, Yang JJ, Waller A, Southall N, Nguyen DT, Oprea TI | Current protocols in bioinformatics | 31898878 | Curr Protoc Bioinformatics | 2020 Mar |
| Machine and deep learning approaches for cancer drug repurposing. | Issa NT, Stathias V, Schürer S, Dakshanamurthy S | Seminars in cancer biology | 31904426 | Semin Cancer Biol | 2021 Jan |
| Improving the Utility of the Tox21 Dataset by Deep Metadata Annotations and Constructing Reusable Benchmarked Chemical Reference Signatures. | Cooper DJ, Schürer S | Molecules (Basel, Switzerland) | 31018579 | Molecules | 2019 Apr 23 |
| A critical overview of computational approaches employed for COVID-19 drug discovery. | Muratov EN , Amaro R , Andrade CH , Brown N , Ekins S , Fourches D , Isayev O , Kozakov D , Medina-Franco JL , Merz KM , Oprea TI , Poroikov V , Schneider G , Todd MH , Varnek A , Winkler DA , Zakharov AV , Cherkasov A , Tropsha A | Chemical Society reviews | 34212944 | Chem Soc Rev | 2021 Aug 21 |
| OSCI: standardized stem cell ontology representation and use cases for stem cell investigation. | He Y, Duncan WD, Cooper DJ, Hansen J, Iyengar R, Ong E, Walker K, Tibi O, Smith S, Serra LM, Zheng J, Sarntivijai S, Schürer S, O'Shea KS, Diehl AD | BMC bioinformatics | 31272389 | BMC Bioinformatics | 2019 Apr 25 |
| Machine learning prediction and tau-based screening identifies potential Alzheimer's disease genes relevant to immunity. | Binder J, Ursu O, Bologa C, Jiang S, Maphis N, Dadras S, Chisholm D, Weick J, Myers O, Kumar P, Yang JJ, Bhaskar K, Oprea TI | Communications biology | 35149761 | Commun Biol | 2022 Feb 11 |
| Crowdsourced mapping of unexplored target space of kinase inhibitors. | Cichońska A, Ravikumar B, Allaway RJ, Wan F, Park S, Isayev O, Li S, Mason M, Lamb A, Tanoli Z, Jeon M, Kim S, Popova M, Capuzzi S, Zeng J, Dang K, Koytiger G, Kang J, Wells CI, Willson TM, IDG-DREAM Drug-Kinase Binding Prediction Challenge Consortium, Oprea TI, Schlessinger A, Drewry DH, Stolovitzky G, Wennerberg K, Guinney J, Aittokallio T | Nature communications | 34083538 | Nat Commun | 2021 Jun 3 |
| Reversal of Lactate and PD-1-mediated Macrophage Immunosuppression Controls Growth of PTEN/p53-deficient Prostate Cancer. | Chaudagar K, Hieromnimon HM, Khurana R, Labadie B, Hirz T, Mei S, Hasan R, Shafran J, Kelley A, Apostolov E, Al-Eryani G, Harvey K, Rameshbabu S, Loyd M, Bynoe K, Drovetsky C, Solanki A, Markiewicz E, Zamora M, Fan X, Schürer S, Swarbrick A, Sykes DB, Patnaik A | Clinical cancer research : an official journal of the American Association for Cancer Research | 36862086 | Clin Cancer Res | 2023 May 15 |
| AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK. | Essegian DJ, Chavez V, Khurshid R, Merchan JR, Schürer SC | PLoS computational biology | 37235579 | PLoS Comput Biol | 2023 May |
| 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 |
| DrugCentral 2018: an update. | Ursu O, Holmes J, Bologa CG, Yang JJ, Mathias SL, Stathias V, Nguyen DT, Schürer S, Oprea T | Nucleic acids research | 30371892 | Nucleic Acids Res | 2019 Jan 8 |
| The Clinical Kinase Index: A Method to Prioritize Understudied Kinases as Drug Targets for the Treatment of Cancer. | Essegian D, Khurana R, Stathias V, Schürer SC | Cell reports. Medicine | 33205077 | Cell Rep Med | 2020 Oct 20 |
| Deciphering the Plasma Proteome of Type 2 Diabetes. | Elhadad MA, Jonasson C, Huth C, Wilson R, Gieger C, Matias P, Grallert H, Graumann J, Gailus-Durner V, Rathmann W, von Toerne C, Hauck SM, Koenig W, Sinner MF, Oprea TI, Suhre K, Thorand B, Hveem K, Peters A, Waldenberger M | Diabetes | 32928870 | Diabetes | 2020 Dec |
| TCRD and Pharos 2021: mining the human proteome for disease biology. | Sheils TK, Mathias SL, Kelleher KJ, Siramshetty VB, Nguyen DT, Bologa CG, Jensen LJ, Vidović D, Koleti A, Schürer SC, Waller A, Yang JJ, Holmes J, Bocci G, Southall N, Dharkar P, Mathé E, Simeonov A, Oprea TI | Nucleic acids research | 33156327 | Nucleic Acids Res | 2021 Jan 8 |
| LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. | Stathias V, Turner J, Koleti A, Vidovic D, Cooper D, Fazel-Najafabadi M, Pilarczyk M, Terryn R, Chung C, Umeano A, Clarke DJB, Lachmann A, Evangelista JE, Ma'ayan A, Medvedovic M, Schürer SC | Nucleic acids research | 31701147 | Nucleic Acids Res | 2020 Jan 8 |
| Identification of DOT1L inhibitors by structure-based virtual screening adapted from a nucleoside-focused library. | Gibbons GS, Chakraborty A, Grigsby SM, Umeano AC, Liao C, Moukha-Chafiq O, Pathak V, Mathew B, Lee YT, Dou Y, Schürer SC, Reynolds RC, Snowden TS, Nikolovska-Coleska Z | European journal of medicinal chemistry | 31978781 | Eur J Med Chem | 2020 Mar 1 |
| How many rare diseases are there? | Haendel M, Vasilevsky N, Unni D, Bologa C, Harris N, Rehm H, Hamosh A, Baynam G, Groza T, McMurry J, Dawkins H, Rath A, Thaxton C, Bocci G, Joachimiak MP, Köhler S, Robinson PN, Mungall C, Oprea TI | Nature reviews. Drug discovery | 32020066 | Nat Rev Drug Discov | 2020 Feb |
| Can BDDCS illuminate targets in drug design? | Bocci G, Benet LZ, Oprea TI | Drug discovery today | 31585170 | Drug Discov Today | 2019 Dec |
| Kinome-Wide Virtual Screening by Multi-Task Deep Learning. | Hu J, Allen BK, Stathias V, Ayad NG, Schürer SC | International journal of molecular sciences | 38473785 | Int J Mol Sci | 2024 Feb 22 |
| Best practices for managing and disseminating resources and outreach and evaluating the impact of the IDG Consortium. | Vidović D, Waller A, Holmes J, Sklar LA, Schürer SC | Drug discovery today | 38508231 | Drug Discov Today | 2024 May |
| The human endogenous metabolome as a pharmacology baseline for drug discovery. | Bofill A, Jalencas X, Oprea TI, Mestres J | Drug discovery today | 31226432 | Drug Discov Today | 2019 Sep |
| Research Techniques Made Simple: Molecular Docking in Dermatology - A Foray into In Silico Drug Discovery. | Issa NT, Badiavas EV, Schürer S | The Journal of investigative dermatology | 31753122 | J Invest Dermatol | 2019 Dec |
| Molecular Dynamics Simulations Identify Tractable Lead-like Phenyl-Piperazine Scaffolds as eIF4A1 ATP-competitive Inhibitors. | Essegian DJ, Cunningham TA, Zerio CJ, Chapman E, Schatz J, Schürer SC | ACS omega | 34604625 | ACS Omega | 2021 Sep 28 |
| CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding. | Ackloo S, Al-Awar R, Amaro RE, Arrowsmith CH, Azevedo H, Batey RA, Bengio Y, Betz UAK, Bologa CG, Chodera JD, Cornell WD, Dunham I, Ecker GF, Edfeldt K, Edwards AM, Gilson MK, Gordijo CR, Hessler G, Hillisch A, Hogner A, Irwin JJ, Jansen JM, Kuhn D, Leach AR, Lee AA, Lessel U, Morgan MR, Moult J, Muegge I, Oprea TI, Perry BG, Riley P, Rousseaux SAL, Saikatendu KS, Santhakumar V, Schapira M, Scholten C, Todd MH, Vedadi M, Volkamer A, Willson TM | Nature reviews. Chemistry | 35783295 | Nat Rev Chem | 2022 Apr |
| Pharos 2023: an integrated resource for the understudied human proteome. | Kelleher KJ, Sheils TK, Mathias SL, Yang JJ, Metzger VT, Siramshetty VB, Nguyen DT, Jensen LJ, Vidović D, Schürer SC, Holmes J, Sharma KR, Pillai A, Bologa CG, Edwards JS, Mathé EA, Oprea TI | Nucleic acids research | 36624666 | Nucleic Acids Res | 2023 Jan 6 |
| Cellular and molecular effects of PNCK, a non-canonical kinase target in renal cell carcinoma. | Essegian DJ, Chavez V, Bustamante F, Schürer SC, Merchan JR | iScience | 36465101 | iScience | 2022 Dec 22 |
| Far away from the lamppost. | Oprea TI, Jan L, Johnson GL, Roth BL, Ma'ayan A, Schürer S, Shoichet BK, Sklar LA, McManus MT | PLoS biology | 30532236 | PLoS Biol | 2018 Dec |
| TMEM16C is involved in thermoregulation and protects rodent pups from febrile seizures. | Wang TA, Chen C, Huang F, Feng S, Tien J, Braz JM, Basbaum AI, Jan YN, Jan LY | Proceedings of the National Academy of Sciences of the United States of America | 33972431 | Proc Natl Acad Sci U S A | 2021 May 18 |
| Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients. | Kaur N, Oskotsky B, Butte AJ, Hu Z | Genome biology | 35012625 | Genome Biol | 2022 Jan 10 |
| Leveraging Big Data to Transform Drug Discovery. | Glicksberg BS, Li L, Chen R, Dudley J, Chen B | Methods in molecular biology (Clifton, N.J.) | 30848458 | Methods Mol Biol | 2019 |
| SARS-CoV-2 ORF3A interacts with the Clic-like chloride channel-1 (CLCC1) and triggers an unfolded protein response. | Gruner HN, Zhang Y, Shariati K, Yiv N, Hu Z, Wang Y, Hejtmancik JF, McManus MT, Tharp K, Ku G | PeerJ | 37033725 | PeerJ | 2023 |
| GSK2801, a BAZ2/BRD9 Bromodomain Inhibitor, Synergizes with BET Inhibitors to Induce Apoptosis in Triple-Negative Breast Cancer. | Bevill SM, Olivares-Quintero JF, Sciaky N, Golitz BT, Singh D, Beltran AS, Rashid NU, Stuhlmiller TJ, Hale A, Moorman NJ, Santos CM, Angus SP, Zawistowski JS, Johnson GL | Molecular cancer research : MCR | 31000582 | Mol Cancer Res | 2019 Jul |
| A Chemical Probe for Dark Kinase STK17B Derives Its Potency and High Selectivity through a Unique P-Loop Conformation. | Picado A, Chaikuad A, Wells CI, Shrestha S, Zuercher WJ, Pickett JE, Kwarcinski FE, Sinha P, de Silva CS, Zutshi R, Liu S, Kannan N, Knapp S, Drewry DH, Willson TM | Journal of medicinal chemistry | 33215924 | J Med Chem | 2020 Dec 10 |
| In Depth Analysis of Kinase Cross Screening Data to Identify CAMKK2 Inhibitory Scaffolds. | O'Byrne SN, Scott JW, Pilotte JR, Santiago ADS, Langendorf CG, Oakhill JS, Eduful BJ, Couñago RM, Wells CI, Zuercher WJ, Willson TM, Drewry DH | Molecules (Basel, Switzerland) | 31941153 | Molecules | 2020 Jan 13 |
| Characterizing the role of the dark kinome in neurodegenerative disease - A mini review. | Axtman AD | Biochimica et biophysica acta. General subjects | 34547390 | Biochim Biophys Acta Gen Subj | 2021 Dec |
| Open source fraction collector/MALDI spotter for proteomics. | Ficarro SB, Max Alexander W, Tavares I, Marto JA | HardwareX | 35518277 | HardwareX | 2022 Apr |
| Competitive Kinase Enrichment Proteomics Reveals that Abemaciclib Inhibits GSK3β and Activates WNT Signaling. | Cousins EM, Goldfarb D, Yan F, Roques J, Darr D, Johnson GL, Major MB | Molecular cancer research : MCR | 29133594 | Mol Cancer Res | 2018 Feb |
| Recombination drives the evolution of mutational robustness. | Singhal S, Gomez SM, Burch CL | Current opinion in systems biology | 31572829 | Curr Opin Syst Biol | 2019 Feb |
| A Perspective on Extreme Open Science: Companies Sharing Compounds without Restriction. | Drewry DH, Wells CI, Zuercher WJ, Willson TM | SLAS discovery : advancing life sciences R & D | 31034310 | SLAS Discov | 2019 Jun |
| The Kinase Chemogenomic Set (KCGS): An Open Science Resource for Kinase Vulnerability Identification. | Wells CI, Al-Ali H, Andrews DM, Asquith CRM, Axtman AD, Dikic I, Ebner D, Ettmayer P, Fischer C, Frederiksen M, Futrell RE, Gray NS, Hatch SB, Knapp S, Lücking U, Michaelides M, Mills CE, Müller S, Owen D, Picado A, Saikatendu KS, Schröder M, Stolz A, Tellechea M, Turunen BJ, Vilar S, Wang J, Zuercher WJ, Willson TM, Drewry DH | International journal of molecular sciences | 33429995 | Int J Mol Sci | 2021 Jan 8 |
| Quantifying CDK inhibitor selectivity in live cells. | Wells CI, Vasta JD, Corona CR, Wilkinson J, Zimprich CA, Ingold MR, Pickett JE, Drewry DH, Pugh KM, Schwinn MK, Hwang BB, Zegzouti H, Huber KVM, Cong M, Meisenheimer PL, Willson TM, Robers MB | Nature communications | 32488087 | Nat Commun | 2020 Jun 2 |
| Temozolomide-induced guanine mutations create exploitable vulnerabilities of guanine-rich DNA and RNA regions in drug-resistant gliomas. | Tiek DM, Erdogdu B, Razaghi R, Jin L, Sadowski N, Alamillo-Ferrer C, Hogg JR, Haddad BR, Drewry DH, Wells CI, Pickett JE, Song X, Goenka A, Hu B, Goldlust SA, Zuercher WJ, Pertea M, Timp W, Cheng SY, Riggins RB | Science advances | 35731869 | Sci Adv | 2022 Jun 24 |
| Numb-associated kinases are required for SARS-CoV-2 infection and are cellular targets for antiviral strategies. | Karim M, Saul S, Ghita L, Sahoo MK, Ye C, Bhalla N, Lo CW, Jin J, Park JG, Martinez-Gualda B, East MP, Johnson GL, Pinsky BA, Martinez-Sobrido L, Asquith CRM, Narayanan A, De Jonghe S, Einav S | Antiviral research | 35738348 | Antiviral Res | 2022 Aug |
| Host Kinase CSNK2 is a Target for Inhibition of Pathogenic SARS-like β-Coronaviruses. | Yang X, Dickmander RJ, Bayati A, Taft-Benz SA, Smith JL, Wells CI, Madden EA, Brown JW, Lenarcic EM, Yount BL Jr, Chang E, Axtman AD, Baric RS, Heise MT, McPherson PS, Moorman NJ, Willson TM | ACS chemical biology | 35723434 | ACS Chem Biol | 2022 Jul 15 |
| Template-assisted covalent modification of DCAF16 underlies activity of BRD4 molecular glue degraders. | Li YD, Ma MW, Hassan MM, Hunkeler M, Teng M, Puvar K, Lumpkin R, Sandoval B, Jin CY, Ficarro SB, Wang MY, Xu S, Groendyke BJ, Sigua LH, Tavares I, Zou C, Tsai JM, Park PMC, Yoon H, Majewski FC, Marto JA, Qi J, Nowak RP, Donovan KA, Słabicki M, Gray NS, Fischer ES, Ebert BL | bioRxiv : the preprint server for biology | 36824856 | bioRxiv | 2023 Feb 15 |
| Proteomic approaches to study ubiquitinomics. | Sahu I, Zhu H, Buhrlage SJ, Marto JA | Biochimica et biophysica acta. Gene regulatory mechanisms | 37121501 | Biochim Biophys Acta Gene Regul Mech | 2023 Jun |
| Discovery of a Potent and Selective Naphthyridine-Based Chemical Probe for Casein Kinase 2. | Davis-Gilbert ZW, Krämer A, Dunford JE, Howell S, Senbabaoglu F, Wells CI, Bashore FM, Havener TM, Smith JL, Hossain MA, Oppermann U, Drewry DH, Axtman AD | ACS medicinal chemistry letters | 37077385 | ACS Med Chem Lett | 2023 Apr 13 |
| Targeted Proteomic Quantitation of NRF2 Signaling and Predictive Biomarkers in HNSCC. | Wamsley NT, Wilkerson EM, Guan L, LaPak KM, Schrank TP, Holmes BJ, Sprung RW, Gilmore PE, Gerndt SP, Jackson RS, Paniello RC, Pipkorn P, Puram SV, Rich JT, Townsend RR, Zevallos JP, Zolkind P, Le QT, Goldfarb D, Major MB | Molecular & cellular proteomics : MCP | 37716475 | Mol Cell Proteomics | 2023 Nov |
| Discovery and Characterization of a Chemical Probe for Cyclin-Dependent Kinase-Like 2. | Bashore FM, Min SM, Chen X, Howell S, Rinderle CH, Morel G, Silvaroli JA, Wells CI, Bunnell BA, Drewry DH, Pabla NS, Ultanir SK, Bullock AN, Axtman AD | bioRxiv : the preprint server for biology | 38798634 | bioRxiv | 2024 May 14 |
| Optimization of 3-Cyano-7-cyclopropylamino-pyrazolo[1,5-a]pyrimidines Toward the Development of an In Vivo Chemical Probe for CSNK2A. | Yang X, Ong HW, Dickmander RJ, Smith JL, Brown JW, Tao W, Chang E, Moorman NJ, Axtman AD, Willson TM | bioRxiv : the preprint server for biology | 37292607 | bioRxiv | 2023 Jul 23 |
| Modulation of tau tubulin kinases (TTBK1 and TTBK2) impacts ciliogenesis. | Bashore FM, Marquez AB, Chaikuad A, Howell S, Dunn AS, Beltran AA, Smith JL, Drewry DH, Beltran AS, Axtman AD | Scientific reports | 37059819 | Sci Rep | 2023 Apr 14 |
| WNT Activates the AAK1 Kinase to Promote Clathrin-Mediated Endocytosis of LRP6 and Establish a Negative Feedback Loop. | Agajanian MJ, Walker MP, Axtman AD, Ruela-de-Sousa RR, Serafin DS, Rabinowitz AD, Graham DM, Ryan MB, Tamir T, Nakamichi Y, Gammons MV, Bennett JM, Couñago RM, Drewry DH, Elkins JM, Gileadi C, Gileadi O, Godoi PH, Kapadia N, Müller S, Santiago AS, Sorrell FJ, Wells CI, Fedorov O, Willson TM, Zuercher WJ, Major MB | Cell reports | 30605688 | Cell Rep | 2019 Jan 2 |
| Kinome profiling of non-Hodgkin lymphoma identifies Tyro3 as a therapeutic target in primary effusion lymphoma. | Wong JP, Stuhlmiller TJ, Giffin LC, Lin C, Bigi R, Zhao J, Zhang W, Bravo Cruz AG, Park SI, Earp HS, Dittmer DP, Frye SV, Wang X, Johnson GL, Damania B | Proceedings of the National Academy of Sciences of the United States of America | 31346082 | Proc Natl Acad Sci U S A | 2019 Aug 13 |
| Discovery of Covalent CDK14 Inhibitors with Pan-TAIRE Family Specificity. | Ferguson FM, Doctor ZM, Ficarro SB, Browne CM, Marto JA, Johnson JL, Yaron TM, Cantley LC, Kim ND, Sim T, Berberich MJ, Kalocsay M, Sorger PK, Gray NS | Cell chemical biology | 30930164 | Cell Chem Biol | 2019 Jun 20 |
| Covalent inhibitors of EGFR family protein kinases induce degradation of human Tribbles 2 (TRIB2) pseudokinase in cancer cells. | Foulkes DM, Byrne DP, Yeung W, Shrestha S, Bailey FP, Ferries S, Eyers CE, Keeshan K, Wells C, Drewry DH, Zuercher WJ, Kannan N, Eyers PA | Science signaling | 30254057 | Sci Signal | 2018 Sep 25 |
| Identification of Pyrimidine-Based Lead Compounds for Understudied Kinases Implicated in Driving Neurodegeneration. | Drewry DH, Annor-Gyamfi JK, Wells CI, Pickett JE, Dederer V, Preuss F, Mathea S, Axtman AD | Journal of medicinal chemistry | 34333981 | J Med Chem | 2022 Jan 27 |
| EMBER: multi-label prediction of kinase-substrate phosphorylation events through deep learning. | Kirchoff KE, Gomez SM | Bioinformatics (Oxford, England) | 35157015 | Bioinformatics | 2022 Apr 12 |
| E2F1 proteolysis via SCF-cyclin F underlies synthetic lethality between cyclin F loss and Chk1 inhibition. | Burdova K, Yang H, Faedda R, Hume S, Chauhan J, Ebner D, Kessler BM, Vendrell I, Drewry DH, Wells CI, Hatch SB, Dianov GL, Buffa FM, D'Angiolella V | The EMBO journal | 31424118 | EMBO J | 2019 Oct 15 |
| Towards a RIOK2 chemical probe: cellular potency improvement of a selective 2-(acylamino)pyridine series. | Wang CB, Lorente-Macías Á, Wells C, Pickett JE, Picado A, Zuercher WJ, Axtman AD | RSC medicinal chemistry | 34046605 | RSC Med Chem | 2021 Jan 1 |
| Mapping the Degradable Kinome Provides a Resource for Expedited Degrader Development. | Donovan KA, Ferguson FM, Bushman JW, Eleuteri NA, Bhunia D, Ryu S, Tan L, Shi K, Yue H, Liu X, Dobrovolsky D, Jiang B, Wang J, Hao M, You I, Teng M, Liang Y, Hatcher J, Li Z, Manz TD, Groendyke B, Hu W, Nam Y, Sengupta S, Cho H, Shin I, Agius MP, Ghobrial IM, Ma MW, Che J, Buhrlage SJ, Sim T, Gray NS, Fischer ES | Cell | 33275901 | Cell | 2020 Dec 10 |
| Defining the Neural Kinome: Strategies and Opportunities for Small Molecule Drug Discovery to Target Neurodegenerative Diseases. | Krahn AI, Wells C, Drewry DH, Beitel LK, Durcan TM, Axtman AD | ACS chemical neuroscience | 32464049 | ACS Chem Neurosci | 2020 Jul 1 |
| The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases. | Berginski ME, Moret N, Liu C, Goldfarb D, Sorger PK, Gomez SM | Nucleic acids research | 33079988 | Nucleic Acids Res | 2021 Jan 8 |
| Editorial: The next generation of tools and technologies for studying human neurons in a dish. | Durcan TM, Axtman AD | Frontiers in cellular neuroscience | 37124399 | Front Cell Neurosci | 2023 |
| Development of a potent and selective chemical probe for the pleiotropic kinase CK2. | Wells CI, Drewry DH, Pickett JE, Tjaden A, Krämer A, Müller S, Gyenis L, Menyhart D, Litchfield DW, Knapp S, Axtman AD | Cell chemical biology | 33484635 | Cell Chem Biol | 2021 Apr 15 |
| On-Chip Preconcentration Microchip Capillary Electrophoresis Based CE-PRM-LIVE for High-Throughput Selectivity Profiling of Deubiquitinase Inhibitors. | Zhu H, Mellors JS, Chan WC, Thompson JW, Ficarro SB, Tavares I, Bratt AS, Decker J, Krause M, Kruppa G, Buhrlage SJ, Marto JA | Analytical chemistry | 35729701 | Anal Chem | 2022 Jul 12 |
| SGC-CAMKK2-1: A Chemical Probe for CAMKK2. | Wells C, Liang Y, Pulliam TL, Lin C, Awad D, Eduful B, O'Byrne S, Hossain MA, Catta-Preta CMC, Ramos PZ, Gileadi O, Gileadi C, Couñago RM, Stork B, Langendorf CG, Nay K, Oakhill JS, Mukherjee D, Racioppi L, Means AR, York B, McDonnell DP, Scott JW, Frigo DE, Drewry DH | Cells | 36672221 | Cells | 2023 Jan 11 |
| Combined kinome inhibition states are predictive of cancer cell line sensitivity to kinase inhibitor combination therapies. | Joisa CU, Chen KA, Beville S, Stuhlmiller T, Berginski ME, Okumu D, Golitz BT, East MP, Johnson GL, Gomez SM | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 38160286 | Pac Symp Biocomput | 2024 |
| Illuminating function of the understudied druggable kinome. | Gomez SM, Axtman AD, Willson TM, Major MB, Townsend RR, Sorger PK, Johnson GL | Drug discovery today | 38218213 | Drug Discov Today | 2024 Mar |
| Identification of 4-(6-((2-methoxyphenyl)amino)pyrazin-2-yl)benzoic acids as CSNK2A inhibitors with antiviral activity and improved selectivity over PIM3. | Galal KA, Krämer A, Strickland BG, Smith JL, Dickmander RJ, Moorman NJ, Willson TM | bioRxiv : the preprint server for biology | 38106118 | bioRxiv | 2023 Dec 5 |
| Combined kinome inhibition states are predictive of cancer cell line sensitivity to kinase inhibitor combination therapies. | Joisa CU, Chen KA, Beville S, Stuhlmiller T, Berginski ME, Okumu D, Golitz BT, Johnson GL, Gomez SM | bioRxiv : the preprint server for biology | 37577663 | bioRxiv | 2023 Aug 3 |
| Identification and Utilization of a Chemical Probe to Interrogate the Roles of PIKfyve in the Lifecycle of β-Coronaviruses. | Drewry DH, Potjewyd FM, Bayati A, Smith JL, Dickmander RJ, Howell S, Taft-Benz S, Min SM, Hossain MA, Heise M, McPherson PS, Moorman NJ, Axtman AD | Journal of medicinal chemistry | 36111834 | J Med Chem | 2022 Oct 13 |
| Epitope editing enables targeted immunotherapy of acute myeloid leukaemia. | Casirati G, Cosentino A, Mucci A, Salah Mahmoud M, Ugarte Zabala I, Zeng J, Ficarro SB, Klatt D, Brendel C, Rambaldi A, Ritz J, Marto JA, Pellin D, Bauer DE, Armstrong SA, Genovese P | Nature | 37648862 | Nature | 2023 Sep |
| Covalent Stapling of the Cereblon Sensor Loop Histidine Using Sulfur-Heterocycle Exchange. | Cruite JT, Nowak RP, Donovan KA, Ficarro SB, Huang H, Liu H, Liu Y, Marto JA, Metivier RJ, Fischer ES, Jones LH | ACS medicinal chemistry letters | 37974938 | ACS Med Chem Lett | 2023 Nov 9 |
| A small molecule exerts selective antiviral activity by targeting the human cytomegalovirus nuclear egress complex. | Chen H, Lye MF, Gorgulla C, Ficarro SB, Cuny GD, Scott DA, Wu F, Rothlauf PW, Wang X, Fernandez R, Pesola JM, Draga S, Marto JA, Hogle JM, Arthanari H, Coen DM | PLoS pathogens | 37976321 | PLoS Pathog | 2023 Nov |
| Discovery and optimization of narrow spectrum inhibitors of Tousled like kinase 2 (TLK2) using quantitative structure activity relationships. | Asquith CRM, East MP, Laitinen T, Alamillo-Ferrer C, Hartikainen E, Wells CI, Axtman AD, Drewry DH, Tizzard GJ, Poso A, Willson TM, Johnson GL | European journal of medicinal chemistry | 38636130 | Eur J Med Chem | 2024 May 5 |
| Tumor-Intrinsic Kinome Landscape of Pancreatic Cancer Reveals New Therapeutic Approaches. | Xu Y, Peng XL, East MP, McCabe IC, Stroman GC, Jenner MR, Chan PS, Morrison AB, Shen EC, Hererra SG, Joisa CU, Rashid NU, Iuga AC, Gomez SM, Miller-Phillips L, Boeck S, Heinemann V, Haas M, Ormanns S, Johnson GL, Yeh JJ | Cancer discovery | 39632628 | Cancer Discov | 2025 Feb 7 |
| Strategic Fluorination to Achieve a Potent, Selective, Metabolically Stable, and Orally Bioavailable Inhibitor of CSNK2. | Ong HW, Yang X, Smith JL, Taft-Benz S, Howell S, Dickmander RJ, Havener TM, Sanders MK, Brown JW, Couñago RM, Chang E, Krämer A, Moorman NJ, Heise M, Axtman AD, Drewry DH, Willson TM | Molecules (Basel, Switzerland) | 39275006 | Molecules | 2024 Sep 2 |
| Non-canonical role of Hippo tumor suppressor serine/threonine kinase 3 STK3 in prostate cancer. | Schirmer AU, Driver LM, Zhao MT, Wells CI, Pickett JE, O'Bryne SN, Eduful BJ, Yang X, Howard L, You S, Devi GR, DiGiovanni J, Freedland SJ, Chi JT, Drewry DH, Macias E | Molecular therapy : the journal of the American Society of Gene Therapy | 34450249 | Mol Ther | 2022 Jan 5 |
| Host kinase CSNK2 is a target for inhibition of pathogenic β-coronaviruses including SARS-CoV-2. | Yang X, Dickmander RJ, Bayati A, Taft-Benz SA, Smith JL, Wells CI, Madden EA, Brown JW, Lenarcic EM, Yount BL Jr, Chang E, Axtman AD, Baric RS, Heise MT, McPherson PS, Moorman NJ, Willson TM | bioRxiv : the preprint server for biology | 35018375 | bioRxiv | 2022 Jan 26 |
| Adaptive chromatin remodeling and transcriptional changes of the functional kinome in tumor cells in response to targeted kinase inhibition. | East MP, Johnson GL | The Journal of biological chemistry | 34958800 | J Biol Chem | 2022 Feb |
| PRM-LIVE with Trapped Ion Mobility Spectrometry and Its Application in Selectivity Profiling of Kinase Inhibitors. | Zhu H, Ficarro SB, Alexander WM, Fleming LE, Adelmant G, Zhang T, Willetts M, Decker J, Brehmer S, Krause M, East MP, Gray NS, Johnson GL, Kruppa G, Marto JA | Analytical chemistry | 34606255 | Anal Chem | 2021 Oct 19 |
| CDK16: the pick of the understudied PCTAIRE kinases. | Axtman A, Drewry D, Wells C | Nature reviews. Drug discovery | 31267068 | Nat Rev Drug Discov | 2019 Jul |
| Cheminformatics Tools for Analyzing and Designing Optimized Small-Molecule Collections and Libraries. | Moret N, Clark NA, Hafner M, Wang Y, Lounkine E, Medvedovic M, Wang J, Gray N, Jenkins J, Sorger PK | Cell chemical biology | 30956147 | Cell Chem Biol | 2019 May 16 |
| Discrete Adaptive Responses to MEK Inhibitor in Subpopulations of Triple-Negative Breast Cancer. | Goulet DR, Foster JP 2nd, Zawistowski JS, Bevill SM, Noël MP, Olivares-Quintero JF, Sciaky N, Singh D, Santos C, Pattenden SG, Davis IJ, Johnson GL | Molecular cancer research : MCR | 32753473 | Mol Cancer Res | 2020 Nov |
| Chemical Biology Toolkit for DCLK1 Reveals Connection to RNA Processing. | Liu Y, Ferguson FM, Li L, Kuljanin M, Mills CE, Subramanian K, Harshbarger W, Gondi S, Wang J, Sorger PK, Mancias JD, Gray NS, Westover KD | Cell chemical biology | 32755567 | Cell Chem Biol | 2020 Oct 15 |
| PKIS deep dive yields a chemical starting point for dark kinases and a cell active BRSK2 inhibitor. | Tamir TY, Drewry DH, Wells C, Major MB, Axtman AD | Scientific reports | 32985588 | Sci Rep | 2020 Sep 28 |
| Concise, gram-scale synthesis of furo[2,3-b]pyridines with functional handles for chemoselective cross-coupling. | O'Byrne SN, Eduful BJ, Willson TM, Drewry DH | Tetrahedron letters | 33012852 | Tetrahedron Lett | 2020 Sep 17 |
| Machine learning identifies candidates for drug repurposing in Alzheimer's disease. | Rodriguez S, Hug C, Todorov P, Moret N, Boswell SA, Evans K, Zhou G, Johnson NT, Hyman BT, Sorger PK, Albers MW, Sokolov A | Nature communications | 33589615 | Nat Commun | 2021 Feb 15 |
| Quantitative, Wide-Spectrum Kinase Profiling in Live Cells for Assessing the Effect of Cellular ATP on Target Engagement. | Vasta JD, Corona CR, Wilkinson J, Zimprich CA, Hartnett JR, Ingold MR, Zimmerman K, Machleidt T, Kirkland TA, Huwiler KG, Ohana RF, Slater M, Otto P, Cong M, Wells CI, Berger BT, Hanke T, Glas C, Ding K, Drewry DH, Huber KVM, Willson TM, Knapp S, Müller S, Meisenheimer PL, Fan F, Wood KV, Robers MB | Cell chemical biology | 29174542 | Cell Chem Biol | 2018 Feb 15 |
| Discovery and resistance mechanism of a selective CDK12 degrader. | Jiang B, Gao Y, Che J, Lu W, Kaltheuner IH, Dries R, Kalocsay M, Berberich MJ, Jiang J, You I, Kwiatkowski N, Riching KM, Daniels DL, Sorger PK, Geyer M, Zhang T, Gray NS | Nature chemical biology | 33753926 | Nat Chem Biol | 2021 Jun |
| Hinge Binder Scaffold Hopping Identifies Potent Calcium/Calmodulin-Dependent Protein Kinase Kinase 2 (CAMKK2) Inhibitor Chemotypes. | Eduful BJ, O'Byrne SN, Temme L, Asquith CRM, Liang Y, Picado A, Pilotte JR, Hossain MA, Wells CI, Zuercher WJ, Catta-Preta CMC, Zonzini Ramos P, Santiago AS, Couñago RM, Langendorf CG, Nay K, Oakhill JS, Pulliam TL, Lin C, Awad D, Willson TM, Frigo DE, Scott JW, Drewry DH | Journal of medicinal chemistry | 34264658 | J Med Chem | 2021 Aug 12 |
| FOXA1 and adaptive response determinants to HER2 targeted therapy in TBCRC 036. | Angus SP, Stuhlmiller TJ, Mehta G, Bevill SM, Goulet DR, Olivares-Quintero JF, East MP, Tanioka M, Zawistowski JS, Singh D, Sciaky N, Chen X, He X, Rashid NU, Chollet-Hinton L, Fan C, Soloway MG, Spears PA, Jefferys S, Parker JS, Gallagher KK, Forero-Torres A, Krop IE, Thompson AM, Murthy R, Gatza ML, Perou CM, Earp HS, Carey LA, Johnson GL | NPJ breast cancer | 33980863 | NPJ Breast Cancer | 2021 May 12 |
| Progress towards a public chemogenomic set for protein kinases and a call for contributions. | Drewry DH, Wells CI, Andrews DM, Angell R, Al-Ali H, Axtman AD, Capuzzi SJ, Elkins JM, Ettmayer P, Frederiksen M, Gileadi O, Gray N, Hooper A, Knapp S, Laufer S, Luecking U, Michaelides M, Müller S, Muratov E, Denny RA, Saikatendu KS, Treiber DK, Zuercher WJ, Willson TM | PloS one | 28767711 | PLoS One | 2017 |
| ADCK3/COQ8A: the choice target of the UbiB protein kinase-like family. | Asquith CRM, Murray NH, Pagliarini DJ | Nature reviews. Drug discovery | 31673128 | Nat Rev Drug Discov | 2019 Oct |
| SGC-GAK-1: A Chemical Probe for Cyclin G Associated Kinase (GAK). | Asquith CRM, Berger BT, Wan J, Bennett JM, Capuzzi SJ, Crona DJ, Drewry DH, East MP, Elkins JM, Fedorov O, Godoi PH, Hunter DM, Knapp S, Müller S, Torrice CD, Wells CI, Earp HS, Willson TM, Zuercher WJ | Journal of medicinal chemistry | 30768268 | J Med Chem | 2019 Mar 14 |
| Synthesis of 5-Benzylamino and 5-Alkylamino-Substituted Pyrimido[4,5-c]quinoline Derivatives as CSNK2A Inhibitors with Antiviral Activity. | Asressu KH, Smith JL, Dickmander RJ, Moorman NJ, Wellnitz J, Popov KI, Axtman AD, Willson TM | Pharmaceuticals (Basel, Switzerland) | 38543092 | Pharmaceuticals (Basel) | 2024 Feb 27 |
| More than an Amide Bioisostere: Discovery of 1,2,4-Triazole-containing Pyrazolo[1,5-a]pyrimidine Host CSNK2 Inhibitors for Combatting β-Coronavirus Replication. | Ong HW, Yang X, Smith JL, Dickmander RJ, Brown JW, Havener TM, Taft-Benz S, Howell S, Sanders MK, Capener JL, Couñago RM, Chang E, Krämer A, Moorman NJ, Heise M, Axtman AD, Drewry DH, Willson TM | Journal of medicinal chemistry | 38959455 | J Med Chem | 2024 Jul 25 |
| Discovery of a Potent and Selective CDKL5/GSK3 Chemical Probe That Is Neuroprotective. | Ong HW, Liang Y, Richardson W, Lowry ER, Wells CI, Chen X, Silvestre M, Dempster K, Silvaroli JA, Smith JL, Wichterle H, Pabla NS, Ultanir SK, Bullock AN, Drewry DH, Axtman AD | ACS chemical neuroscience | 37084253 | ACS Chem Neurosci | 2023 May 3 |
| Evaluation of a Selective Chemical Probe Validates That CK2 Mediates Neuroinflammation in a Human Induced Pluripotent Stem Cell-Derived Microglial Model. | Mishra S, Kinoshita C, Axtman AD, Young JE | Frontiers in molecular neuroscience | 35774866 | Front Mol Neurosci | 2022 |
| An atlas of substrate specificities for the human serine/threonine kinome. | Johnson JL, Yaron TM, Huntsman EM, Kerelsky A, Song J, Regev A, Lin TY, Liberatore K, Cizin DM, Cohen BM, Vasan N, Ma Y, Krismer K, Robles JT, van de Kooij B, van Vlimmeren AE, Andrée-Busch N, Käufer NF, Dorovkov MV, Ryazanov AG, Takagi Y, Kastenhuber ER, Goncalves MD, Hopkins BD, Elemento O, Taatjes DJ, Maucuer A, Yamashita A, Degterev A, Uduman M, Lu J, Landry SD, Zhang B, Cossentino I, Linding R, Blenis J, Hornbeck PV, Turk BE, Yaffe MB, Cantley LC | Nature | 36631611 | Nature | 2023 Jan |
| Optimization of 3-Cyano-7-cyclopropylamino-pyrazolo[1,5-a]pyrimidines toward the Development of an In Vivo Chemical Probe for CSNK2A. | Yang X, Ong HW, Dickmander RJ, Smith JL, Brown JW, Tao W, Chang E, Moorman NJ, Axtman AD, Willson TM | ACS omega | 37901516 | ACS Omega | 2023 Oct 24 |
| Discovery and characterization of a specific inhibitor of serine-threonine kinase cyclin-dependent kinase-like 5 (CDKL5) demonstrates role in hippocampal CA1 physiology. | Castano A, Silvestre M, Wells CI, Sanderson JL, Ferrer CA, Ong HW, Lang Y, Richardson W, Silvaroli JA, Bashore FM, Smith JL, Genereux IM, Dempster K, Drewry DH, Pabla NS, Bullock AN, Benke TA, Ultanir SK, Axtman AD | eLife | 37490324 | Elife | 2023 Jul 25 |
| Investigation of the Host Kinome Response to Coronavirus Infection Reveals PI3K/mTOR Inhibitors as Betacoronavirus Antivirals. | Fritch EJ, Mordant AL, Gilbert TSK, Wells CI, Yang X, Barker NK, Madden EA, Dinnon KH 3rd, Hou YJ, Tse LV, Castillo IN, Sims AC, Moorman NJ, Lakshmanane P, Willson TM, Herring LE, Graves LM, Baric RS | Journal of proteome research | 37634194 | J Proteome Res | 2023 Oct 6 |
| How many kinases are druggable? A review of our current understanding. | Anderson B, Rosston P, Ong HW, Hossain MA, Davis-Gilbert ZW, Drewry DH | The Biochemical journal | 37642371 | Biochem J | 2023 Aug 30 |
| SGC-CLK-1: A chemical probe for the Cdc2-like kinases CLK1, CLK2, and CLK4. | Tiek D, Wells CI, Schröder M, Song X, Alamillo-Ferrer C, Goenka A, Iglesia R, Lu M, Hu B, Kwarcinski F, Sintha P, de Silva C, Hossain MA, Picado A, Zuercher W, Zutshi R, Knapp S, Riggins RB, Cheng SY, Drewry DH | Current research in chemical biology | 38009092 | Curr Res Chem Biol | 2023 |
| A Semi-automated and Scalable 3D Spheroid Assay to Study Neuroblast Migration. | Ducker M, Millar V, Ebner D, Szele FG | Stem cell reports | 32763162 | Stem Cell Reports | 2020 Sep 8 |
| Gain-of-function genetic screen of the kinome reveals BRSK2 as an inhibitor of the NRF2 transcription factor. | Tamir TY, Bowman BM, Agajanian MJ, Goldfarb D, Schrank TP, Stohrer T, Hale AE, Siesser PF, Weir SJ, Murphy RM, LaPak KM, Weissman BE, Moorman NJ, Major MB | Journal of cell science | 32546533 | J Cell Sci | 2020 Jul 15 |
| Identification and Optimization of 4-Anilinoquinolines as Inhibitors of Cyclin G Associated Kinase. | Asquith CRM, Laitinen T, Bennett JM, Godoi PH, East MP, Tizzard GJ, Graves LM, Johnson GL, Dornsife RE, Wells CI, Elkins JM, Willson TM, Zuercher WJ | ChemMedChem | 29072804 | ChemMedChem | 2018 Jan 8 |
| Coral: Clear and Customizable Visualization of Human Kinome Data. | Metz KS, Deoudes EM, Berginski ME, Jimenez-Ruiz I, Aksoy BA, Hammerbacher J, Gomez SM, Phanstiel DH | Cell systems | 30172842 | Cell Syst | 2018 Sep 26 |
| Application of Integrated Drug Screening/Kinome Analysis to Identify Inhibitors of Gemcitabine-Resistant Pancreatic Cancer Cell Growth. | Krulikas LJ, McDonald IM, Lee B, Okumu DO, East MP, Gilbert TSK, Herring LE, Golitz BT, Wells CI, Axtman AD, Zuercher WJ, Willson TM, Kireev D, Yeh JJ, Johnson GL, Baines AT, Graves LM | SLAS discovery : advancing life sciences R & D | 29742358 | SLAS Discov | 2018 Sep |
| Mass Spectrometry-Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers. | Mundt F, Rajput S, Li S, Ruggles KV, Mooradian AD, Mertins P, Gillette MA, Krug K, Guo Z, Hoog J, Erdmann-Gilmore P, Primeau T, Huang S, Edwards DP, Wang X, Wang X, Kawaler E, Mani DR, Clauser KR, Gao F, Luo J, Davies SR, Johnson GL, Huang KL, Yoon CJ, Ding L, Fenyö D, Ellis MJ, Townsend RR, Held JM, Carr SA, Ma CX | Cancer research | 29472518 | Cancer Res | 2018 May 15 |
| Identification of 4-Anilinoquin(az)oline as a Cell-Active Protein Kinase Novel 3 (PKN3) Inhibitor Chemotype. | Asquith CRM, Temme L, East MP, Laitinen T, Pickett J, Kwarcinski FE, Sinha P, Wells CI, Johnson GL, Zutshi R, Drewry DH | ChemMedChem | 35403825 | ChemMedChem | 2022 Jun 20 |
| Protein proximity networks and functional evaluation of the casein kinase 1 gamma family reveal unique roles for CK1γ3 in WNT signaling. | Agajanian MJ, Potjewyd FM, Bowman BM, Solomon S, LaPak KM, Bhatt DP, Smith JL, Goldfarb D, Axtman AD, Major MB | The Journal of biological chemistry | 35487243 | J Biol Chem | 2022 Jun |
| A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules. | Liu C, Kutchukian P, Nguyen ND, AlQuraishi M, Sorger PK | Journal of chemical information and modeling | 37595065 | J Chem Inf Model | 2023 Sep 11 |
| Multiplexed and reproducible high content screening of live and fixed cells using Dye Drop. | Mills CE, Subramanian K, Hafner M, Niepel M, Gerosa L, Chung M, Victor C, Gaudio B, Yapp C, Nirmal AJ, Clark N, Sorger PK | Nature communications | 36376301 | Nat Commun | 2022 Nov 14 |
| Accelerating inhibitor discovery for deubiquitinating enzymes. | Chan WC, Liu X, Magin RS, Girardi NM, Ficarro SB, Hu W, Tarazona Guzman MI, Starnbach CA, Felix A, Adelmant G, Varca AC, Hu B, Bratt AS, DaSilva E, Schauer NJ, Jaen Maisonet I, Dolen EK, Ayala AX, Marto JA, Buhrlage SJ | Nature communications | 36754960 | Nat Commun | 2023 Feb 8 |
| Development of Cell Permeable NanoBRET Probes for the Measurement of PLK1 Target Engagement in Live Cells. | Yang X, Smith JL, Beck MT, Wilkinson JM, Michaud A, Vasta JD, Robers MB, Willson TM | Molecules (Basel, Switzerland) | 37049713 | Molecules | 2023 Mar 25 |
| Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma. | Flint AC, Mitchell DK, Angus SP, Smith AE, Bessler W, Jiang L, Mang H, Li X, Lu Q, Rodriguez B, Sandusky GE, Masters AR, Zhang C, Dang P, Koenig J, Johnson GL, Shen W, Liu J, Aggarwal A, Donoho GP, Willard MD, Bhagwat SV, Clapp DW, Rhodes SD | Clinical cancer research : an official journal of the American Association for Cancer Research | 37406085 | Clin Cancer Res | 2023 Sep 1 |
| A Potent and Selective CDKL5/GSK3 Chemical Probe is Neuroprotective. | Ong HW, Liang Y, Richardson W, Lowry ER, Wells CI, Chen X, Silvestre M, Dempster K, Silvaroli JA, Smith JL, Wichterle H, Pabla NS, Ultanir SK, Bullock AN, Drewry DH, Axtman AD | bioRxiv : the preprint server for biology | 36798313 | bioRxiv | 2023 Feb 10 |
| Kinome inhibition states and multiomics data enable prediction of cell viability in diverse cancer types. | Berginski ME, Joisa CU, Golitz BT, Gomez SM | PLoS computational biology | 36809237 | PLoS Comput Biol | 2023 Feb |
| Integrated single-dose kinome profiling data is predictive of cancer cell line sensitivity to kinase inhibitors. | Joisa CU, Chen KA, Berginski ME, Golitz BT, Jenner MR, Herrera Loeza G, Yeh JJ, Gomez SM | PeerJ | 38025707 | PeerJ | 2023 |
| PIP4K2C inhibition reverses autophagic flux impairment induced by SARS-CoV-2. | Karim M, Mishra M, Lo CW, Saul S, Cagirici HB, Tran DHN, Agrawal A, Ghita L, Ojha A, East MP, Gammeltoft KA, Sahoo MK, Johnson GL, Das S, Jochmans D, Cohen CA, Gottwein J, Dye J, Neff N, Pinsky BA, Laitinen T, Pantsar T, Poso A, Zanini F, Jonghe S, Asquith CRM, Einav S | bioRxiv : the preprint server for biology | 38659941 | bioRxiv | 2024 Apr 17 |
| Utilizing Low-Dimensional Molecular Embeddings for Rapid Chemical Similarity Search. | Kirchoff KE, Wellnitz J, Hochuli JE, Maxfield T, Popov KI, Gomez S, Tropsha A | Advances in information retrieval : ... European Conference on IR Research, ECIR ... proceedings. European Conference on IR Research | 38585224 | Adv Inf Retr | 2024 Mar |
| Development of a covalent cereblon-based PROTAC employing a fluorosulfate warhead. | Nowak RP, Ragosta L, Huerta F, Liu H, Ficarro SB, Cruite JT, Metivier RJ, Donovan KA, Marto JA, Fischer ES, Zerfas BL, Jones LH | RSC chemical biology | 37920397 | RSC Chem Biol | 2023 Nov 1 |
| Discovery and Characterization of a Chemical Probe for Cyclin-Dependent Kinase-Like 2. | Bashore FM, Min SM, Chen X, Howell S, Rinderle CH, Morel G, Silvaroli JA, Wells CI, Bunnell BA, Drewry DH, Pabla NS, Ultanir SK, Bullock AN, Axtman AD | ACS medicinal chemistry letters | 39140040 | ACS Med Chem Lett | 2024 Aug 8 |
| Template-assisted covalent modification underlies activity of covalent molecular glues. | Li YD, Ma MW, Hassan MM, Hunkeler M, Teng M, Puvar K, Rutter JC, Lumpkin RJ, Sandoval B, Jin CY, Schmoker AM, Ficarro SB, Cheong H, Metivier RJ, Wang MY, Xu S, Byun WS, Groendyke BJ, You I, Sigua LH, Tavares I, Zou C, Tsai JM, Park PMC, Yoon H, Majewski FC, Sperling HT, Marto JA, Qi J, Nowak RP, Donovan KA, Słabicki M, Gray NS, Fischer ES, Ebert BL | Nature chemical biology | 39075252 | Nat Chem Biol | 2024 Dec |
| Report and Application of a Tool Compound Data Set. | Butler KV, MacDonald IA, Hathaway NA, Jin J | Journal of chemical information and modeling | 29035535 | J Chem Inf Model | 2017 Nov 27 |
| DREADD Agonist 21 Is an Effective Agonist for Muscarinic-Based DREADDs in Vitro and in Vivo. | Thompson KJ, Khajehali E, Bradley SJ, Navarrete JS, Huang XP, Slocum S, Jin J, Liu J, Xiong Y, Olsen RHJ, Diberto JF, Boyt KM, Pina MM, Pati D, Molloy C, Bundgaard C, Sexton PM, Kash TL, Krashes MJ, Christopoulos A, Roth BL, Tobin AB | ACS pharmacology & translational science | 30868140 | ACS Pharmacol Transl Sci | 2018 Sep 14 |
| TRUPATH, an open-source biosensor platform for interrogating the GPCR transducerome. | Olsen RHJ, DiBerto JF, English JG, Glaudin AM, Krumm BE, Slocum ST, Che T, Gavin AC, McCorvy JD, Roth BL, Strachan RT | Nature chemical biology | 32367019 | Nat Chem Biol | 2020 Aug |
| Biased signaling of the proton-sensing receptor OGR1 by benzodiazepines. | Pera T, Deshpande DA, Ippolito M, Wang B, Gavrila A, Michael JV, Nayak AP, Tompkins E, Farrell E, Kroeze WK, Roth BL, Panettieri RA Jr, Benovic JL, An SS, Dulin NO, Penn RB | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 29042451 | FASEB J | 2018 Feb |
| How Ligands Illuminate GPCR Molecular Pharmacology. | Wacker D, Stevens RC, Roth BL | Cell | 28753422 | Cell | 2017 Jul 27 |
| XFEL structures of the human MT(2) melatonin receptor reveal the basis of subtype selectivity. | Johansson LC, Stauch B, McCorvy JD, Han GW, Patel N, Huang XP, Batyuk A, Gati C, Slocum ST, Li C, Grandner JM, Hao S, Olsen RHJ, Tribo AR, Zaare S, Zhu L, Zatsepin NA, Weierstall U, Yous S, Stevens RC, Liu W, Roth BL, Katritch V, Cherezov V | Nature | 31019305 | Nature | 2019 May |
| Molecular pharmacology of metabotropic receptors targeted by neuropsychiatric drugs. | Roth BL | Nature structural & molecular biology | 31270468 | Nat Struct Mol Biol | 2019 Jul |
| Publisher Correction: Structural basis of ligand recognition at the human MT(1) melatonin receptor. | Stauch B, Johansson LC, McCorvy JD, Patel N, Han GW, Huang XP, Gati C, Batyuk A, Slocum ST, Ishchenko A, Brehm W, White TA, Michaelian N, Madsen C, Zhu L, Grant TD, Grandner JM, Shiriaeva A, Olsen RHJ, Tribo AR, Yous S, Stevens RC, Weierstall U, Katritch V, Roth BL, Liu W, Cherezov V | Nature | 31048811 | Nature | 2019 May |
| Inactive and active state structures template selective tools for the human 5-HT(5A) receptor. | Zhang S, Chen H, Zhang C, Yang Y, Popov P, Liu J, Krumm BE, Cao C, Kim K, Xiong Y, Katritch V, Shoichet BK, Jin J, Fay JF, Roth BL | Nature structural & molecular biology | 35835867 | Nat Struct Mol Biol | 2022 Jul |
| MRGPRX4 mediates phospho-drug-associated pruritus in a humanized mouse model. | Chien DC, Limjunyawong N, Cao C, Meixiong J, Peng Q, Ho CY, Fay JF, Roth BL, Dong X | Science translational medicine | 38718132 | Sci Transl Med | 2024 May 8 |
| Design, Synthesis, and Characterization of Ogerin-Based Positive Allosteric Modulators for G Protein-Coupled Receptor 68 (GPR68). | Yu X, Huang XP, Kenakin TP, Slocum ST, Chen X, Martini ML, Liu J, Jin J | Journal of medicinal chemistry | 31298539 | J Med Chem | 2019 Aug 22 |
| In silico design of novel probes for the atypical opioid receptor MRGPRX2. | Lansu K, Karpiak J, Liu J, Huang XP, McCorvy JD, Kroeze WK, Che T, Nagase H, Carroll FI, Jin J, Shoichet BK, Roth BL | Nature chemical biology | 28288109 | Nat Chem Biol | 2017 May |
| Defining Structure-Functional Selectivity Relationships (SFSR) for a Class of Non-Catechol Dopamine D(1) Receptor Agonists. | Martini ML, Liu J, Ray C, Yu X, Huang XP, Urs A, Urs N, McCorvy JD, Caron MG, Roth BL, Jin J | Journal of medicinal chemistry | 30875219 | J Med Chem | 2019 Apr 11 |
| Discovery of new GPCR ligands to illuminate new biology. | Roth BL, Irwin JJ, Shoichet BK | Nature chemical biology | 29045379 | Nat Chem Biol | 2017 Nov |
| Agonist and antagonist TRUPATH assays for G protein-coupled receptors. | DiBerto JF, Smart K, Olsen RHJ, Roth BL | STAR protocols | 35403009 | STAR Protoc | 2022 Jun 17 |
| Nanobody-enabled monitoring of kappa opioid receptor states. | Che T, English J, Krumm BE, Kim K, Pardon E, Olsen RHJ, Wang S, Zhang S, Diberto JF, Sciaky N, Carroll FI, Steyaert J, Wacker D, Roth BL | Nature communications | 32123179 | Nat Commun | 2020 Mar 2 |
| Structure-Based Design of a Chemical Probe Set for the 5-HT(5A) Serotonin Receptor. | Levit Kaplan A, Strachan RT, Braz JM, Craik V, Slocum S, Mangano T, Amabo V, O'Donnell H, Lak P, Basbaum AI, Roth BL, Shoichet BK | Journal of medicinal chemistry | 35195401 | J Med Chem | 2022 Mar 10 |
| Virtual discovery of melatonin receptor ligands to modulate circadian rhythms. | Stein RM, Kang HJ, McCorvy JD, Glatfelter GC, Jones AJ, Che T, Slocum S, Huang XP, Savych O, Moroz YS, Stauch B, Johansson LC, Cherezov V, Kenakin T, Irwin JJ, Shoichet BK, Roth BL, Dubocovich ML | Nature | 32040955 | Nature | 2020 Mar |
| Deschloroclozapine, a potent and selective chemogenetic actuator enables rapid neuronal and behavioral modulations in mice and monkeys. | Nagai Y, Miyakawa N, Takuwa H, Hori Y, Oyama K, Ji B, Takahashi M, Huang XP, Slocum ST, DiBerto JF, Xiong Y, Urushihata T, Hirabayashi T, Fujimoto A, Mimura K, English JG, Liu J, Inoue KI, Kumata K, Seki C, Ono M, Shimojo M, Zhang MR, Tomita Y, Nakahara J, Suhara T, Takada M, Higuchi M, Jin J, Roth BL, Minamimoto T | Nature neuroscience | 32632286 | Nat Neurosci | 2020 Sep |
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| The structure, function, and pharmacology of MRGPRs. | Cao C, Roth BL | Trends in pharmacological sciences | 36870785 | Trends Pharmacol Sci | 2023 Apr |
| TRUPATH: An Open-Source Biosensor Platform for Interrogating the GPCR Transducerome. | DiBerto JF, Olsen RHJ, Roth BL | Methods in molecular biology (Clifton, N.J.) | 35836068 | Methods Mol Biol | 2022 |
| Molecular basis for selective activation of DREADD-based chemogenetics. | Zhang S, Gumpper RH, Huang XP, Liu Y, Krumm BE, Cao C, Fay JF, Roth BL | Nature | 36450989 | Nature | 2022 Dec |
| Structural basis of ligand recognition at the human MT(1) melatonin receptor. | Stauch B, Johansson LC, McCorvy JD, Patel N, Han GW, Huang XP, Gati C, Batyuk A, Slocum ST, Ishchenko A, Brehm W, White TA, Michaelian N, Madsen C, Zhu L, Grant TD, Grandner JM, Shiriaeva A, Olsen RHJ, Tribo AR, Yous S, Stevens RC, Weierstall U, Katritch V, Roth BL, Liu W, Cherezov V | Nature | 31019306 | Nature | 2019 May |
| VEGAS as a Platform for Facile Directed Evolution in Mammalian Cells. | English JG, Olsen RHJ, Lansu K, Patel M, White K, Cockrell AS, Singh D, Strachan RT, Wacker D, Roth BL | Cell | 31280962 | Cell | 2019 Jul 25 |
| VEGAS as a Platform for Facile Directed Evolution in Mammalian Cells. | English JG, Olsen RHJ, Lansu K, Patel M, White K, Cockrell AS, Singh D, Strachan RT, Wacker D, Roth BL | Cell | 31398329 | Cell | 2019 Aug 8 |
| How structure informs and transforms chemogenetics. | Roth BL | Current opinion in structural biology | 30818201 | Curr Opin Struct Biol | 2019 Aug |
| Ultra-large library docking for discovering new chemotypes. | Lyu J, Wang S, Balius TE, Singh I, Levit A, Moroz YS, O'Meara MJ, Che T, Algaa E, Tolmachova K, Tolmachev AA, Shoichet BK, Roth BL, Irwin JJ | Nature | 30728502 | Nature | 2019 Feb |
| Gut Microbial β-Glucuronidase Inhibition via Catalytic Cycle Interception. | Pellock SJ, Creekmore BC, Walton WG, Mehta N, Biernat KA, Cesmat AP, Ariyarathna Y, Dunn ZD, Li B, Jin J, James LI, Redinbo MR | ACS central science | 30062115 | ACS Cent Sci | 2018 Jul 25 |
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| D(2) Dopamine Receptor G Protein-Biased Partial Agonists Based on Cariprazine. | Shen Y, McCorvy JD, Martini ML, Rodriguiz RM, Pogorelov VM, Ward KM, Wetsel WC, Liu J, Roth BL, Jin J | Journal of medicinal chemistry | 30964661 | J Med Chem | 2019 May 9 |
| Alternative splicing of latrophilin-3 controls synapse formation. | Wang S, DeLeon C, Sun W, Quake SR, Roth BL, Südhof TC | Nature | 38233523 | Nature | 2024 Feb |
| Structure-inspired design of β-arrestin-biased ligands for aminergic GPCRs. | McCorvy JD, Butler KV, Kelly B, Rechsteiner K, Karpiak J, Betz RM, Kormos BL, Shoichet BK, Dror RO, Jin J, Roth BL | Nature chemical biology | 29227473 | Nat Chem Biol | 2018 Feb |
| Protamine is an antagonist of apelin receptor, and its activity is reversed by heparin. | Le Gonidec S, Chaves-Almagro C, Bai Y, Kang HJ, Smith A, Wanecq E, Huang XP, Prats H, Knibiehler B, Roth BL, Barak LS, Caron MG, Valet P, Audigier Y, Masri B | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 28242772 | FASEB J | 2017 Jun |
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| Bioinformatic analysis of human ZPR1 gene pathogenic exome mutations. | Abok JI, Garver WS, Edwards JS | bioRxiv : the preprint server for biology | 38464185 | bioRxiv | 2024 Mar 1 |
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| Highly Accurate Chip-Based Resequencing of SARS-CoV-2 Clinical Samples. | Hoff K, Ding X, Carter L, Duque J, Lin JY, Dung S, Singh P, Sun J, Crnogorac F, Swaminathan R, Alden EN, Zhu X, Shimada R, Posavi M, Hull N, Dinwiddie D, Halasz AM, McGall G, Zhou W, Edwards JS | Langmuir : the ACS journal of surfaces and colloids | 33848173 | Langmuir | 2021 Apr 27 |
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| Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer. | Ravanmehr V, Blau H, Cappelletti L, Fontana T, Carmody L, Coleman B, George J, Reese J, Joachimiak M, Bocci G, Hansen P, Bult C, Rueter J, Casiraghi E, Valentini G, Mungall C, Oprea TI, Robinson PN | NAR genomics and bioinformatics | 34888523 | NAR Genom Bioinform | 2021 Dec |
| State of the Art and Uses for the Biopharmaceutics Drug Disposition Classification System (BDDCS): New Additions, Revisions, and Citation References. | Bocci G, Oprea TI, Benet LZ | The AAPS journal | 35199251 | AAPS J | 2022 Feb 23 |
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| Exploring DrugCentral: from molecular structures to clinical effects. | Halip L, Avram S, Curpan R, Borota A, Bora A, Bologa C, Oprea TI | Journal of computer-aided molecular design | 37707619 | J Comput Aided Mol Des | 2023 Dec |
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| The COVID-19 Gene and Drug Set Library. | Kuleshov MV, Clarke DJB, Kropiwnicki E, Jagodnik KM, Bartal A, Evangelista JE, Zhou A, Ferguson LB, Lachmann A, Ma'ayan A | Research square | 32702729 | Res Sq | 2020 May 13 |
| 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 |
| 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 |
| Predicting Lyme Disease From Patients' Peripheral Blood Mononuclear Cells Profiled With RNA-Sequencing. | Clarke DJB, Rebman AW, Bailey A, Wojciechowicz ML, Jenkins SL, Evangelista JE, Danieletto M, Fan J, Eshoo MW, Mosel MR, Robinson W, Ramadoss N, Bobe J, Soloski MJ, Aucott JN, Ma'ayan A | Frontiers in immunology | 33763080 | Front Immunol | 2021 |
| Gene Set Knowledge Discovery with Enrichr. | Xie Z, Bailey A, Kuleshov MV, Clarke DJB, Evangelista JE, Jenkins SL, Lachmann A, Wojciechowicz ML, Kropiwnicki E, Jagodnik KM, Jeon M, Ma'ayan A | Current protocols | 33780170 | Curr Protoc | 2021 Mar |
| Loss of proximal tubular transcription factor Krüppel-like factor 15 exacerbates kidney injury through loss of fatty acid oxidation. | Piret SE, Attallah AA, Gu X, Guo Y, Gujarati NA, Henein J, Zollman A, Hato T, Ma'ayan A, Revelo MP, Dickman KG, Chen CH, Shun CT, Rosenquist TA, He JC, Mallipattu SK | Kidney international | 34634362 | Kidney Int | 2021 Dec |
| Geneshot: search engine for ranking genes from arbitrary text queries. | Lachmann A, Schilder BM, Wojciechowicz ML, Torre D, Kuleshov MV, Keenan AB, Ma'ayan A | Nucleic acids research | 31114885 | Nucleic Acids Res | 2019 Jul 2 |
| ChEA3: transcription factor enrichment analysis by orthogonal omics integration. | Keenan AB, Torre D, Lachmann A, Leong AK, Wojciechowicz ML, Utti V, Jagodnik KM, Kropiwnicki E, Wang Z, Ma'ayan A | Nucleic acids research | 31114921 | Nucleic Acids Res | 2019 Jul 2 |
| 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 |
| 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 |
| 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 |
| Mining data and metadata from the gene expression omnibus. | Wang Z, Lachmann A, Ma'ayan A | Biophysical reviews | 30594974 | Biophys Rev | 2019 Feb |
| Dermal sheath contraction powers stem cell niche relocation during hair cycle regression. | Heitman N, Sennett R, Mok KW, Saxena N, Srivastava D, Martino P, Grisanti L, Wang Z, Ma'ayan A, Rompolas P, Rendl M | Science (New York, N.Y.) | 31857493 | Science | 2020 Jan 10 |
| Single-cell immune landscape of human atherosclerotic plaques. | Fernandez DM, Rahman AH, Fernandez NF, Chudnovskiy A, Amir ED, Amadori L, Khan NS, Wong CK, Shamailova R, Hill CA, Wang Z, Remark R, Li JR, Pina C, Faries C, Awad AJ, Moss N, Bjorkegren JLM, Kim-Schulze S, Gnjatic S, Ma'ayan A, Mocco J, Faries P, Merad M, Giannarelli C | Nature medicine | 31591603 | Nat Med | 2019 Oct |
| 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 |
| Krüppel-like factor 6-mediated loss of BCAA catabolism contributes to kidney injury in mice and humans. | Piret SE, Guo Y, Attallah AA, Horne SJ, Zollman A, Owusu D, Henein J, Sidorenko VS, Revelo MP, Hato T, Ma'ayan A, He JC, Mallipattu SK | Proceedings of the National Academy of Sciences of the United States of America | 34074766 | Proc Natl Acad Sci U S A | 2021 Jun 8 |
| Systems Analysis Implicates WAVE2 Complex in the Pathogenesis of Developmental Left-Sided Obstructive Heart Defects. | Edwards JJ, Rouillard AD, Fernandez NF, Wang Z, Lachmann A, Shankaran SS, Bisgrove BW, Demarest B, Turan N, Srivastava D, Bernstein D, Deanfield J, Giardini A, Porter G, Kim R, Roberts AE, Newburger JW, Goldmuntz E, Brueckner M, Lifton RP, Seidman CE, Chung WK, Tristani-Firouzi M, Yost HJ, Ma'ayan A, Gelb BD | JACC. Basic to translational science | 32368696 | JACC Basic Transl Sci | 2020 Apr |
| The COVID-19 Drug and Gene Set Library. | Kuleshov MV, Stein DJ, Clarke DJB, Kropiwnicki E, Jagodnik KM, Bartal A, Evangelista JE, Hom J, Cheng M, Bailey A, Zhou A, Ferguson LB, Lachmann A, Ma'ayan A | Patterns (New York, N.Y.) | 32838343 | Patterns (N Y) | 2020 Sep 11 |
| 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 |
| 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 |
| modEnrichr: a suite of gene set enrichment analysis tools for model organisms. | Kuleshov MV, Diaz JEL, Flamholz ZN, Keenan AB, Lachmann A, Wojciechowicz ML, Cagan RL, Ma'ayan A | Nucleic acids research | 31069376 | Nucleic Acids Res | 2019 Jul 2 |
| Predicting opioid dependence from electronic health records with machine learning. | Ellis RJ, Wang Z, Genes N, Ma'ayan A | BioData mining | 30728857 | BioData Min | 2019 |
| Temporal proteomic profiling of postnatal human cortical development. | Breen MS, Ozcan S, Ramsey JM, Wang Z, Ma'ayan A, Rustogi N, Gottschalk MG, Webster MJ, Weickert CS, Buxbaum JD, Bahn S | Translational psychiatry | 30518843 | Transl Psychiatry | 2018 Dec 5 |
| Connectivity Mapping Identifies BI-2536 as a Potential Drug to Treat Diabetic Kidney Disease. | Zhang L, Wang Z, Liu R, Li Z, Lin J, Wojciechowicz ML, Huang J, Lee K, Ma'ayan A, He JC | Diabetes | 33067313 | Diabetes | 2021 Feb |
| Chemokine Signatures of Pathogen-Specific T Cells II: Memory T Cells in Acute and Chronic Infection. | Davenport B, Eberlein J, Nguyen TT, Victorino F, van der Heide V, Kuleshov M, Ma'ayan A, Kedl R, Homann D | Journal of immunology (Baltimore, Md. : 1950) | 32948682 | J Immunol | 2020 Oct 15 |
| Chemokine Signatures of Pathogen-Specific T Cells I: Effector T Cells. | Eberlein J, Davenport B, Nguyen TT, Victorino F, Jhun K, van der Heide V, Kuleshov M, Ma'ayan A, Kedl R, Homann D | Journal of immunology (Baltimore, Md. : 1950) | 32948687 | J Immunol | 2020 Oct 15 |
| Prioritizing Pain-Associated Targets with Machine Learning. | Jeon M, Jagodnik KM, Kropiwnicki E, Stein DJ, Ma'ayan A | Biochemistry | 33606503 | Biochemistry | 2021 May 11 |
| eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks. | Clarke DJB, Kuleshov MV, Schilder BM, Torre D, Duffy ME, Keenan AB, Lachmann A, Feldmann AS, Gundersen GW, Silverstein MC, Wang Z, Ma'ayan A | Nucleic acids research | 29800326 | Nucleic Acids Res | 2018 Jul 2 |
| Integration of protein phosphorylation, acetylation, and methylation data sets to outline lung cancer signaling networks. | Grimes M, Hall B, Foltz L, Levy T, Rikova K, Gaiser J, Cook W, Smirnova E, Wheeler T, Clark NR, Lachmann A, Zhang B, Hornbeck P, Ma'ayan A, Comb M | Science signaling | 29789295 | Sci Signal | 2018 May 22 |
| Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures. | Wang Z, He E, Sani K, Jagodnik KM, Silverstein MC, Ma'ayan A | Bioinformatics (Oxford, England) | 30169739 | Bioinformatics | 2019 Apr 1 |
| KEA3: improved kinase enrichment analysis via data integration. | Kuleshov MV, Xie Z, London ABK, Yang J, Evangelista JE, Lachmann A, Shu I, Torre D, Ma'ayan A | Nucleic acids research | 34019655 | Nucleic Acids Res | 2021 Jul 2 |
| Memory of Divisional History Directs the Continuous Process of Primitive Hematopoietic Lineage Commitment. | Bernitz JM, Rapp K, Daniel MG, Shcherbinin D, Yuan Y, Gomes A, Waghray A, Brosh R, Lachmann A, Ma'ayan A, Papatsenko D, Moore KA | Stem cell reports | 32243840 | Stem Cell Reports | 2020 Apr 14 |
| EnrichrBot: Twitter bot tracking tweets about human genes. | Bartal A, Lachmann A, Clarke DJB, Seiden AH, Jagodnik KM, Ma'ayan A | Bioinformatics (Oxford, England) | 32277816 | Bioinformatics | 2020 Jun 1 |
| Dex-Benchmark: datasets and code to evaluate algorithms for transcriptomics data analysis. | Xie Z, Chen C, Ma'ayan A | PeerJ | 37953774 | PeerJ | 2023 |
| Engineering a haematopoietic stem cell niche by revitalizing mesenchymal stromal cells. | Nakahara F, Borger DK, Wei Q, Pinho S, Maryanovich M, Zahalka AH, Suzuki M, Cruz CD, Wang Z, Xu C, Boulais PE, Ma'ayan A, Greally JM, Frenette PS | Nature cell biology | 30988422 | Nat Cell Biol | 2019 May |
| Dermal Condensate Niche Fate Specification Occurs Prior to Formation and Is Placode Progenitor Dependent. | Mok KW, Saxena N, Heitman N, Grisanti L, Srivastava D, Muraro MJ, Jacob T, Sennett R, Wang Z, Su Y, Yang LM, Ma'ayan A, Ornitz DM, Kasper M, Rendl M | Developmental cell | 30595537 | Dev Cell | 2019 Jan 7 |
| GPR84: an immune response dial? | Wojciechowicz ML, Ma'ayan A | Nature reviews. Drug discovery | 32494048 | Nat Rev Drug Discov | 2020 Jun |
| 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 |
| 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 |
| 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 |
| Pan-cancer proteogenomics characterization of tumor immunity. | Petralia F, Ma W, Yaron TM, Caruso FP, Tignor N, Wang JM, Charytonowicz D, Johnson JL, Huntsman EM, Marino GB, Calinawan A, Evangelista JE, Selvan ME, Chowdhury S, Rykunov D, Krek A, Song X, Turhan B, Christianson KE, Lewis DA, Deng EZ, Clarke DJB, Whiteaker JR, Kennedy JJ, Zhao L, Segura RL, Batra H, Raso MG, Parra ER, Soundararajan R, Tang X, Li Y, Yi X, Satpathy S, Wang Y, Wiznerowicz M, González-Robles TJ, Iavarone A, Gosline SJC, Reva B, Robles AI, Nesvizhskii AI, Mani DR, Gillette MA, Klein RJ, Cieslik M, Zhang B, Paulovich AG, Sebra R, Gümüş ZH, Hostetter G, Fenyö D, Omenn GS, Cantley LC, Ma'ayan A, Lazar AJ, Ceccarelli M, Wang P, Clinical Proteomic Tumor Analysis Consortium | Cell | 38359819 | Cell | 2024 Feb 29 |
| 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 |
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| A Whole-Genome RNA Interference Screen Reveals a Role for Spry2 in Insulin Transcription and the Unfolded Protein Response. | Pappalardo Z, Gambhir Chopra D, Hennings TG, Richards H, Choe J, Yang K, Baeyens L, Ang K, Chen S, Arkin M, German MS, McManus MT, Ku GM | Diabetes | 28246293 | Diabetes | 2017 Jun |
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| VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data. | Brunson T, Sanati N, Huffman A, Masci AM, Zheng J, Cooke MF, Conley P, He Y, Wu G | Frontiers in immunology | 37180100 | Front Immunol | 2023 |
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| Using the Reactome Database. | Rothfels K, Milacic M, Matthews L, Haw R, Sevilla C, Gillespie M, Stephan R, Gong C, Ragueneau E, May B, Shamovsky V, Wright A, Weiser J, Beavers D, Conley P, Tiwari K, Jassal B, Griss J, Senff-Ribeiro A, Brunson T, Petryszak R, Hermjakob H, D'Eustachio P, Wu G, Stein L | Current protocols | 37053306 | Curr Protoc | 2023 Apr |
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| Identification of Cellular Interactions in the Tumor Immune Microenvironment Underlying CD8 T Cell Exhaustion. | Klocke C, Moran A, Adey A, McWeeney S, Wu G | bioRxiv : the preprint server for biology | 38014233 | bioRxiv | 2023 Nov 13 |
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| The fatty acid omega hydroxylase genes (CYP4 family) in the progression of metabolic dysfunction-associated steatotic liver disease (MASLD): An RNA sequence database analysis and review. | Leahy C, Osborne N, Shirota L, Rote P, Lee YK, Song BJ, Yin L, Zhang Y, Garcia V, Hardwick JP | Biochemical pharmacology | 38697309 | Biochem Pharmacol | 2024 Oct |
| Nuclear phosphoinositide signaling promotes YAP/TAZ-TEAD transcriptional activity in breast cancer. | Jung O, Baek MJ, Wooldrik C, Johnson KR, Fisher KW, Lou J, Ricks TJ, Wen T, Best MD, Cryns VL, Anderson RA, Choi S | The EMBO journal | 38565949 | EMBO J | 2024 May |
| Loss of Brain Angiogenesis Inhibitor-3 (BAI3) G-Protein Coupled Receptor in Mice Regulates Adaptive Thermogenesis by Enhancing Energy Expenditure. | Alsharif H, Latimer MN, Perez KC, Alexander J, Rahman MM, Challa AK, Kim JA, Ramanadham S, Young M, Bhatnagar S | Metabolites | 37367869 | Metabolites | 2023 May 31 |
| Noncanonical Regulation of cAMP-Dependent Insulin Secretion and Its Implications in Type 2 Diabetes. | Ramanadham S, Turk J, Bhatnagar S | Comprehensive Physiology | 37358504 | Compr Physiol | 2023 Jun 26 |
| Generation and initial characterization of mice lacking full-length BAI3 (ADGRB3) expression. | Shiu FH, Wong JC, Bhattacharya D, Kuranaga Y, Parag RR, Alsharif HA, Bhatnagar S, Van Meir EG, Escayg A | Basic & clinical pharmacology & toxicology | 37337931 | Basic Clin Pharmacol Toxicol | 2023 Oct |
| To block or not to block: Targeting SK channels in diseased hearts. | Terentyev D, Belevych AE, Choi BR, Hamilton S | Journal of molecular and cellular cardiology | 37742783 | J Mol Cell Cardiol | 2023 Oct |
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| Kir6.1, a component of an ATP-sensitive potassium channel, regulates natural killer cell development. | Samper N, Hardardottir L, Depierreux DM, Song SC, Nakazawa A, Gando I, Nakamura TY, Sharkey AM, Nowosad CR, Feske S, Colucci F, Coetzee WA | Frontiers in immunology | 39687626 | Front Immunol | 2024 |
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| Sex and Racial Disparities in Peripheral Artery Disease. | Divakaran S, Krawisz AK, Secemsky EA, Kant S | Arteriosclerosis, thrombosis, and vascular biology | 37706319 | Arterioscler Thromb Vasc Biol | 2023 Nov |
| TNF-alpha promotes cilia elongation via mixed lineage kinases signaling in mouse fibroblasts and human RPE-1 cells. | Kumari A, Caliz AD, Yoo HJ, Kant S, Vertii A | Cytoskeleton (Hoboken, N.J.) | 38767050 | Cytoskeleton (Hoboken) | 2024 Nov |
| Pharmacological Activities, Therapeutic Effects, and Mechanistic Actions of Trigonelline. | Nguyen V, Taine EG, Meng D, Cui T, Tan W | International journal of molecular sciences | 38542359 | Int J Mol Sci | 2024 Mar 16 |
| Chlorogenic Acid: A Systematic Review on the Biological Functions, Mechanistic Actions, and Therapeutic Potentials. | Nguyen V, Taine EG, Meng D, Cui T, Tan W | Nutrients | 38612964 | Nutrients | 2024 Mar 23 |
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| Exploring the role of pyroptosis in the pathogenicity of heart disease. | Bhatti R, Sato PY | Frontiers in physiology | 38645692 | Front Physiol | 2024 |
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| SARS-CoV-2 replication in airway epithelia requires motile cilia and microvillar reprogramming. | Wu CT, Lidsky PV, Xiao Y, Cheng R, Lee IT, Nakayama T, Jiang S, He W, Demeter J, Knight MG, Turn RE, Rojas-Hernandez LS, Ye C, Chiem K, Shon J, Martinez-Sobrido L, Bertozzi CR, Nolan GP, Nayak JV, Milla C, Andino R, Jackson PK | Cell | 36580912 | Cell | 2023 Jan 5 |
| trans-Interacting Plasma Membrane Proteins and Binding Partner Identification. | Zhang S, Ma Z | Journal of proteome research | 38937710 | J Proteome Res | 2024 Aug 2 |
| Electrically silent KvS subunits associate with native Kv2 channels in brain and impact diverse properties of channel function. | Ferns M, van der List D, Vierra NC, Lacey T, Murray K, Kirmiz M, Stewart RG, Sack JT, Trimmer JS | bioRxiv : the preprint server for biology | 38328147 | bioRxiv | 2024 Jan 25 |
| A Kv2 inhibitor combination reveals native neuronal conductances consistent with Kv2/KvS heteromers. | Stewart RG, Marquis MJ, Jo S, Aberra A, Cook V, Whiddon Z, Ferns M, Sack JT | bioRxiv : the preprint server for biology | 38352561 | bioRxiv | 2024 May 14 |
| Drosophila tweety facilitates autophagy to regulate mitochondrial homeostasis and bioenergetics in Glia. | Leung HH, Mansour C, Rousseau M, Nakhla A, Kiselyov K, Venkatachalam K, Wong CO | Glia | 37870193 | Glia | 2024 Feb |
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| Group based prenatal care in a low-and high risk population in the Netherlands: a study protocol for a stepped wedge cluster randomized controlled trial. | van Zwicht BS, Crone MR, van Lith JM, Rijnders ME | BMC pregnancy and childbirth | 27846824 | BMC Pregnancy Childbirth | 2016 Nov 15 |
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| Biophysical characterization of chloride intracellular channel 6 (CLIC6). | Loyo-Celis V, Patel D, Sanghvi S, Kaur K, Ponnalagu D, Zheng Y, Bindra S, Bhachu HR, Deschenes I, Gururaja Rao S, Singh H | The Journal of biological chemistry | 37838179 | J Biol Chem | 2023 Nov |
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| Development of adenoviral vectors that transduce Purkinje cells and other cerebellar cell-types in the cerebellum of a humanized mouse model. | Kul E, Okoroafor U, Dougherty A, Palkovic L, Li H, Valiño-Ramos P, Aberman L, Young SM Jr | Molecular therapy. Methods & clinical development | 38605812 | Mol Ther Methods Clin Dev | 2024 Jun 13 |
| Confocal Imaging and 3D Reconstruction to Determine How Genetic Perturbations Impact Presynaptic Morphology at the Mouse Calyx of Held. | Keine C, Radulovic T, Al-Yaari M, Young SM Jr | Bio-protocol | 37849785 | Bio Protoc | 2023 Sep 5 |
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| Zinc finger protein 24-dependent transcription factor SOX9 up-regulation protects tubular epithelial cells during acute kidney injury. | Kim JY, Silvaroli JA, Martinez GV, Bisunke B, Luna Ramirez AV, Jayne LA, Feng MJHH, Girotra B, Acosta Martinez SM, Vermillion CR, Karel IZ, Ferrell N, Weisleder N, Chung S, Christman JW, Brooks CR, Madhavan SM, Hoyt KR, Cianciolo RE, Satoskar AA, Zepeda-Orozco D, Sullivan JC, Davidson AJ, Bajwa A, Pabla NS | Kidney international | 36921719 | Kidney Int | 2023 Jun |
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| NEK5 activity regulates the mesenchymal and migratory phenotype in breast cancer cells. | Matossian MD, Elliott S, Van Hoang T, Burks HE, Wright MK, Alzoubi MS, Yan T, Chang T, Wathieu H, Windsor GO, Hartono AB, Lee S, Zuercher WJ, Drewry DH, Wells C, Kapadia N, Buechlein A, Fang F, Nephew KP, Collins-Burow BM, Burow ME | Breast cancer research and treatment | 34196902 | Breast Cancer Res Treat | 2021 Aug |
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| Calcium/Calmodulin Dependent Protein Kinase Kinase 2 Regulates the Expansion of Tumor-Induced Myeloid-Derived Suppressor Cells. | Huang W, Liu Y, Luz A, Berrong M, Meyer JN, Zou Y, Swann E, Sundaramoorthy P, Kang Y, Jauhari S, Lento W, Chao N, Racioppi L | Frontiers in immunology | 34712241 | Front Immunol | 2021 |
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| Dissection of a Down syndrome-associated trisomy to separate the gene dosage-dependent and -independent effects of an extra chromosome. | Xing Z, Li Y, Cortes-Gomez E, Jiang X, Gao S, Pao A, Shan J, Song Y, Perez A, Yu T, Highsmith MR, Boadu F, Conroy JM, Singh PK, Bakin AV, Cheng J, Duan Z, Wang J, Liu S, Tycko B, Yu YE | Human molecular genetics | 37014740 | Hum Mol Genet | 2023 Jun 19 |
| VRK1 as a synthetic lethal target in VRK2 promoter-methylated cancers of the nervous system. | So J, Mabe NW, Englinger B, Chow KH, Moyer SM, Yerrum S, Trissal MC, Marques JG, Kwon JJ, Shim B, Pal S, Panditharatna E, Quinn T, Schaefer DA, Jeong D, Mayhew DL, Hwang J, Beroukhim R, Ligon KL, Stegmaier K, Filbin MG, Hahn WC | JCI insight | 36040810 | JCI Insight | 2022 Oct 10 |
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| The potassium channel auxiliary subunit Kvβ2 (Kcnab2) regulates Kv1 channels and dopamine neuron firing. | Yee JX, Rastani A, Soden ME | Journal of neurophysiology | 35788155 | J Neurophysiol | 2022 Jul 1 |
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| The ion channel CALHM6 controls bacterial infection-induced cellular cross-talk at the immunological synapse. | Danielli S, Ma Z, Pantazi E, Kumar A, Demarco B, Fischer FA, Paudel U, Weissenrieder J, Lee RJ, Joyce S, Foskett JK, Bezbradica JS | The EMBO journal | 36861806 | EMBO J | 2023 Apr 3 |
| A PKA inhibitor motif within SMOOTHENED controls Hedgehog signal transduction. | Happ JT, Arveseth CD, Bruystens J, Bertinetti D, Nelson IB, Olivieri C, Zhang J, Hedeen DS, Zhu JF, Capener JL, Bröckel JW, Vu L, King CC, Ruiz-Perez VL, Ge X, Veglia G, Herberg FW, Taylor SS, Myers BR | Nature structural & molecular biology | 36202993 | Nat Struct Mol Biol | 2022 Oct |
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| Tra2beta-Dependent Regulation of RIO Kinase 3 Splicing During Rift Valley Fever Virus Infection Underscores the Links Between Alternative Splicing and Innate Antiviral Immunity. | White LA, Bisom TC, Grimes HL, Hayashi M, Lanchy JM, Lodmell JS | Frontiers in cellular and infection microbiology | 35127560 | Front Cell Infect Microbiol | 2021 |
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| Mouse Adrenal Macrophages Are Associated with Pre- and Postsynaptic Neuronal Elements and Respond to Multiple Neuromodulators. | Whim MD | eNeuro | 39900506 | eNeuro | 2025 Feb |
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| CRISPR-addressable yeast strains with applications in human G protein-coupled receptor profiling and synthetic biology. | Rowe JB, Taghon GJ, Kapolka NJ, Morgan WM, Isom DG | The Journal of biological chemistry | 32358068 | J Biol Chem | 2020 Jun 12 |
| An acidic residue buried in the dimer interface of isocitrate dehydrogenase 1 (IDH1) helps regulate catalysis and pH sensitivity. | Luna LA, Lesecq Z, White KA, Hoang A, Scott DA, Zagnitko O, Bobkov AA, Barber DL, Schiffer JM, Isom DG, Sohl CD | The Biochemical journal | 32729927 | Biochem J | 2020 Aug 28 |
| Cavβ1 regulates T cell expansion and apoptosis independently of voltage-gated Ca(2+) channel function. | Erdogmus S, Concepcion AR, Yamashita M, Sidhu I, Tao AY, Li W, Rocha PP, Huang B, Garippa R, Lee B, Lee A, Hell JW, Lewis RS, Prakriya M, Feske S | Nature communications | 35440113 | Nat Commun | 2022 Apr 19 |
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| NeuriteNet: A convolutional neural network for assessing morphological parameters of neurite growth. | Vecchi JT, Mullan S, Lopez JA, Hansen MR, Sonka M, Lee A | Journal of neuroscience methods | 34480956 | J Neurosci Methods | 2021 Nov 1 |
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| Blockade of IL-22 signaling reverses erythroid dysfunction in stress-induced anemias. | Raundhal M, Ghosh S, Myers SA, Cuoco MS, Singer M, Carr SA, Waikar SS, Bonventre JV, Ritz J, Stone RM, Steensma DP, Regev A, Glimcher LH | Nature immunology | 33753942 | Nat Immunol | 2021 Apr |
| RIOK2 transcriptionally regulates TRiC and dyskerin complexes to prevent telomere shortening. | Ghosh S, Nguyen MT, Choi HE, Stahl M, Kühn AL, Van der Auwera S, Grabe HJ, Völzke H, Homuth G, Myers SA, Hogaboam CM, Noth I, Martinez FJ, Petsko GA, Glimcher LH | Nature communications | 39164231 | Nat Commun | 2024 Aug 20 |
| A Superfolder Green Fluorescent Protein-Based Biosensor Allows Monitoring of Chloride in the Endoplasmic Reticulum. | Shariati K, Zhang Y, Giubbolini S, Parra R, Liang S, Edwards A, Hejtmancik JF, Ratto GM, Arosio D, Ku G | ACS sensors | 35951356 | ACS Sens | 2022 Aug 26 |
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