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 |
|---|---|---|---|---|---|
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| SmartGraph: a network pharmacology investigation platform. | Zahoránszky-Kőhalmi G, Sheils T, Oprea TI | Journal of cheminformatics | 33430980 | J Cheminform | 2020 Jan 21 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Computational and Practical Aspects of Drug Repositioning. | Oprea TI, Overington JP | Assay and drug development technologies | 26241209 | Assay Drug Dev Technol | 2015 Jul-Aug |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases. | Palleja A, Jensen LJ | PeerJ | 26157625 | PeerJ | 2015 |
| 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 |
| High quality, small molecule-activity datasets for kinase research. | Sharma R, Schürer SC, Muskal SM | F1000Research | 27429748 | F1000Res | 2016 |
| 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 |
| 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 |
| Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd. | Wang Z, Monteiro CD, Jagodnik KM, Fernandez NF, Gundersen GW, Rouillard AD, Jenkins SL, Feldmann AS, Hu KS, McDermott MG, Duan Q, Clark NR, Jones MR, Kou Y, Goff T, Woodland H, Amaral FMR, Szeto GL, Fuchs O, Schüssler-Fiorenza Rose SM, Sharma S, Schwartz U, Bausela XB, Szymkiewicz M, Maroulis V, Salykin A, Barra CM, Kruth CD, Bongio NJ, Mathur V, Todoric RD, Rubin UE, Malatras A, Fulp CT, Galindo JA, Motiejunaite R, Jüschke C, Dishuck PC, Lahl K, Jafari M, Aibar S, Zaravinos A, Steenhuizen LH, Allison LR, Gamallo P, de Andres Segura F, Dae Devlin T, Pérez-García V, Ma'ayan A | Nature communications | 27667448 | Nat Commun | 2016 Sep 26 |
| 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 |
| 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 |
| 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 |
| A blueprint of cell identity. | Ma'ayan A, Duan Q | Nature biotechnology | 25299921 | Nat Biotechnol | 2014 Oct |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Complex systems biology. | Ma'ayan A | Journal of the Royal Society, Interface | 28931638 | J R Soc Interface | 2017 Sep |
| Artificial Intelligence in Cardiology. | Johnson KW, Torres Soto J, Glicksberg BS, Shameer K, Miotto R, Ali M, Ashley E, Dudley JT | Journal of the American College of Cardiology | 29880128 | J Am Coll Cardiol | 2018 Jun 12 |
| 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 |
| 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 |
| Reply: Deep Learning With Unsupervised Feature in Echocardiographic Imaging. | Narula S, Shameer K, Salem Omar AM, Dudley JT, Sengupta PP | Journal of the American College of Cardiology | 28427589 | J Am Coll Cardiol | 2017 Apr 25 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits. | Glicksberg BS, Amadori L, Akers NK, Sukhavasi K, Franzén O, Li L, Belbin GM, Ayers KL, Shameer K, Badgeley MA, Johnson KW, Readhead B, Darrow BJ, Kenny EE, Betsholtz C, Ermel R, Skogsberg J, Ruusalepp A, Schadt EE, Dudley JT, Ren H, Kovacic JC, Giannarelli C, Li SD, Björkegren JLM, Chen R | BMC medical genomics | 31345219 | BMC Med Genomics | 2019 Jul 25 |
| 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 |
| 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 |
| Activation of tumor suppressor protein PP2A inhibits KRAS-driven tumor growth. | Sangodkar J, Perl A, Tohme R, Kiselar J, Kastrinsky DB, Zaware N, Izadmehr S, Mazhar S, Wiredja DD, O'Connor CM, Hoon D, Dhawan NS, Schlatzer D, Yao S, Leonard D, Borczuk AC, Gokulrangan G, Wang L, Svenson E, Farrington CC, Yuan E, Avelar RA, Stachnik A, Smith B, Gidwani V, Giannini HM, McQuaid D, McClinch K, Wang Z, Levine AC, Sears RC, Chen EY, Duan Q, Datt M, Haider S, Ma'ayan A, DiFeo A, Sharma N, Galsky MD, Brautigan DL, Ioannou YA, Xu W, Chance MR, Ohlmeyer M, Narla G | The Journal of clinical investigation | 28504649 | J Clin Invest | 2017 Jun 1 |
| 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 |
| 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 |
| 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 |
| LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. | Duan Q, Flynn C, Niepel M, Hafner M, Muhlich JL, Fernandez NF, Rouillard AD, Tan CM, Chen EY, Golub TR, Sorger PK, Subramanian A, Ma'ayan A | Nucleic acids research | 24906883 | Nucleic Acids Res | 2014 Jul |
| 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 |
| 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 |
| Differential cytokine contributions of perivascular haematopoietic stem cell niches. | Asada N, Kunisaki Y, Pierce H, Wang Z, Fernandez NF, Birbrair A, Ma'ayan A, Frenette PS | Nature cell biology | 28218906 | Nat Cell Biol | 2017 Mar |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Identification of type 2 diabetes subgroups through topological analysis of patient similarity. | Li L, Cheng WY, Glicksberg BS, Gottesman O, Tamler R, Chen R, Bottinger EP, Dudley JT | Science translational medicine | 26511511 | Sci Transl Med | 2015 Oct 28 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
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| 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 |
| 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 |
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| 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 |
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| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| EMBER: multi-label prediction of kinase-substrate phosphorylation events through deep learning. | Kirchoff KE, Gomez SM | Bioinformatics (Oxford, England) | 35157015 | Bioinformatics | 2022 Apr 12 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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, East MP, Johnson GL, Gomez SM | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 38160286 | Pac Symp Biocomput | 2024 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 | ACS medicinal chemistry letters | 39140040 | ACS Med Chem Lett | 2024 Aug 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Open source fraction collector/MALDI spotter for proteomics. | Ficarro SB, Max Alexander W, Tavares I, Marto JA | HardwareX | 35518277 | HardwareX | 2022 Apr |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| How structure informs and transforms chemogenetics. | Roth BL | Current opinion in structural biology | 30818201 | Curr Opin Struct Biol | 2019 Aug |
| 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 |
| 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 |
| 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 |
| 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 |
| Structure-based discovery of potent and selective melatonin receptor agonists. | Patel N, Huang XP, Grandner JM, Johansson LC, Stauch B, McCorvy JD, Liu Y, Roth B, Katritch V | eLife | 32118583 | Elife | 2020 Mar 2 |
| 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 |
| Structure, function and pharmacology of human itch GPCRs. | Cao C, Kang HJ, Singh I, Chen H, Zhang C, Ye W, Hayes BW, Liu J, Gumpper RH, Bender BJ, Slocum ST, Krumm BE, Lansu K, McCorvy JD, Kroeze WK, English JG, DiBerto JF, Olsen RHJ, Huang XP, Zhang S, Liu Y, Kim K, Karpiak J, Jan LY, Abraham SN, Jin J, Shoichet BK, Fay JF, Roth BL | Nature | 34789874 | Nature | 2021 Dec |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| Mining data and metadata from the gene expression omnibus. | Wang Z, Lachmann A, Ma'ayan A | Biophysical reviews | 30594974 | Biophys Rev | 2019 Feb |
| 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 |
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| 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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| σ1 receptor ligands control a switch between passive and active threat responses. | Rennekamp AJ, Huang XP, Wang Y, Patel S, Lorello PJ, Cade L, Gonzales AP, Yeh JR, Caldarone BJ, Roth BL, Kokel D, Peterson RT | Nature chemical biology | 27239788 | Nat Chem Biol | 2016 Jul |
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| Transketolase (TKT) activity and nuclear localization promote hepatocellular carcinoma in a metabolic and a non-metabolic manner. | Qin Z, Xiang C, Zhong F, Liu Y, Dong Q, Li K, Shi W, Ding C, Qin L, He F | Journal of experimental & clinical cancer research : CR | 30971297 | J Exp Clin Cancer Res | 2019 Apr 11 |
| A proteomic landscape of diffuse-type gastric cancer. | Ge S, Xia X, Ding C, Zhen B, Zhou Q, Feng J, Yuan J, Chen R, Li Y, Ge Z, Ji J, Zhang L, Wang J, Li Z, Lai Y, Hu Y, Li Y, Li Y, Gao J, Chen L, Xu J, Zhang C, Jung SY, Choi JM, Jain A, Liu M, Song L, Liu W, Guo G, Gong T, Huang Y, Qiu Y, Huang W, Shi T, Zhu W, Wang Y, He F, Shen L, Qin J | Nature communications | 29520031 | Nat Commun | 2018 Mar 8 |
| Non-Substrate Based, Small Molecule Inhibitors of the Human Isoprenylcysteine Carboxyl Methyltransferase. | Butler KV, Bohn K, Hrycyna CA, Jin J | MedChemComm | 27547295 | Medchemcomm | 2016 May 1 |
| Inhibition of Lapatinib-Induced Kinome Reprogramming in ERBB2-Positive Breast Cancer by Targeting BET Family Bromodomains. | Stuhlmiller TJ, Miller SM, Zawistowski JS, Nakamura K, Beltran AS, Duncan JS, Angus SP, Collins KA, Granger DA, Reuther RA, Graves LM, Gomez SM, Kuan PF, Parker JS, Chen X, Sciaky N, Carey LA, Earp HS, Jin J, Johnson GL | Cell reports | 25865888 | Cell Rep | 2015 Apr 21 |
| Transcriptome-wide identification and study of cancer-specific splicing events across multiple tumors. | Tsai YS, Dominguez D, Gomez SM, Wang Z | Oncotarget | 25749525 | Oncotarget | 2015 Mar 30 |
| ABC transporters control ATP release through cholesterol-dependent volume-regulated anion channel activity. | Dunn PJ, Salm EJ, Tomita S | The Journal of biological chemistry | 31988241 | J Biol Chem | 2020 Apr 17 |
| GARLH Family Proteins Stabilize GABA(A) Receptors at Synapses. | Yamasaki T, Hoyos-Ramirez E, Martenson JS, Morimoto-Tomita M, Tomita S | Neuron | 28279354 | Neuron | 2017 Mar 8 |
| Zebrafish behavioural profiling identifies GABA and serotonin receptor ligands related to sedation and paradoxical excitation. | McCarroll MN, Gendelev L, Kinser R, Taylor J, Bruni G, Myers-Turnbull D, Helsell C, Carbajal A, Rinaldi C, Kang HJ, Gong JH, Sello JK, Tomita S, Peterson RT, Keiser MJ, Kokel D | Nature communications | 31501447 | Nat Commun | 2019 Sep 9 |
| TMEM163 Regulates ATP-Gated P2X Receptor and Behavior. | Salm EJ, Dunn PJ, Shan L, Yamasaki M, Malewicz NM, Miyazaki T, Park J, Sumioka A, Hamer RRL, He WW, Morimoto-Tomita M, LaMotte RH, Tomita S | Cell reports | 32492420 | Cell Rep | 2020 Jun 2 |
| Assembly rules for GABA(A) receptor complexes in the brain. | Martenson JS, Yamasaki T, Chaudhury NH, Albrecht D, Tomita S | eLife | 28816653 | Elife | 2017 Aug 17 |
| Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65. | Huang XP, Karpiak J, Kroeze WK, Zhu H, Chen X, Moy SS, Saddoris KA, Nikolova VD, Farrell MS, Wang S, Mangano TJ, Deshpande DA, Jiang A, Penn RB, Jin J, Koller BH, Kenakin T, Shoichet BK, Roth BL | Nature | 26550826 | Nature | 2015 Nov 26 |
| In Vitro and In Vivo Characterization of the Alkaloid Nuciferine. | Farrell MS, McCorvy JD, Huang XP, Urban DJ, White KL, Giguere PM, Doak AK, Bernstein AI, Stout KA, Park SM, Rodriguiz RM, Gray BW, Hyatt WS, Norwood AP, Webster KA, Gannon BM, Miller GW, Porter JH, Shoichet BK, Fantegrossi WE, Wetsel WC, Roth BL | PloS one | 26963248 | PLoS One | 2016 |
| D(4) dopamine receptor high-resolution structures enable the discovery of selective agonists. | Wang S, Wacker D, Levit A, Che T, Betz RM, McCorvy JD, Venkatakrishnan AJ, Huang XP, Dror RO, Shoichet BK, Roth BL | Science (New York, N.Y.) | 29051383 | Science | 2017 Oct 20 |
| Discovery and Characterization of Novel GPR39 Agonists Allosterically Modulated by Zinc. | Sato S, Huang XP, Kroeze WK, Roth BL | Molecular pharmacology | 27754899 | Mol Pharmacol | 2016 Dec |
| Structure-based discovery of opioid analgesics with reduced side effects. | Manglik A, Lin H, Aryal DK, McCorvy JD, Dengler D, Corder G, Levit A, Kling RC, Bernat V, Hübner H, Huang XP, Sassano MF, Giguère PM, Löber S, Da Duan, Scherrer G, Kobilka BK, Gmeiner P, Roth BL, Shoichet BK | Nature | 27533032 | Nature | 2016 Sep 8 |
| Identification of Novel Smoothened Ligands Using Structure-Based Docking. | Lacroix C, Fish I, Torosyan H, Parathaman P, Irwin JJ, Shoichet BK, Angers S | PloS one | 27490099 | PLoS One | 2016 |
| PRESTO-Tango as an open-source resource for interrogation of the druggable human GPCRome. | Kroeze WK, Sassano MF, Huang XP, Lansu K, McCorvy JD, Giguère PM, Sciaky N, Roth BL | Nature structural & molecular biology | 25895059 | Nat Struct Mol Biol | 2015 May |
| An African-specific haplotype in MRGPRX4 is associated with menthol cigarette smoking. | Kozlitina J, Risso D, Lansu K, Olsen RHJ, Sainz E, Luiselli D, Barik A, Frigerio-Domingues C, Pagani L, Wooding S, Kirchner T, Niaura R, Roth B, Drayna D | PLoS genetics | 30768591 | PLoS Genet | 2019 Feb |
| The organization of frontostriatal brain wiring in non-affective early psychosis compared with healthy subjects using a novel diffusion imaging fiber cluster analysis. | Levitt JJ, Zhang F, Vangel M, Nestor PG, Rathi Y, Cetin-Karayumak S, Kubicki M, Coleman MJ, Lewandowski KE, Holt DJ, Keshavan M, Bouix S, Öngür D, Breier A, Shenton ME, O'Donnell LJ | Molecular psychiatry | 37173451 | Mol Psychiatry | 2023 Jun |
| Docking Screens for Novel Ligands Conferring New Biology. | Irwin JJ, Shoichet BK | Journal of medicinal chemistry | 26913380 | J Med Chem | 2016 May 12 |
| Cre-dependent DREADD (Designer Receptors Exclusively Activated by Designer Drugs) mice. | Zhu H, Aryal DK, Olsen RH, Urban DJ, Swearingen A, Forbes S, Roth BL, Hochgeschwender U | Genesis (New York, N.Y. : 2000) | 27194399 | Genesis | 2016 Aug |
| Single Amino Acid Variation Underlies Species-Specific Sensitivity to Amphibian Skin-Derived Opioid-like Peptides. | Vardy E, Sassano MF, Rennekamp AJ, Kroeze WK, Mosier PD, Westkaemper RB, Stevens CW, Katritch V, Stevens RC, Peterson RT, Roth BL | Chemistry & biology | 26091169 | Chem Biol | 2015 Jun 18 |
| Integrated Approaches for Genome-wide Interrogation of the Druggable Non-olfactory G Protein-coupled Receptor Superfamily. | Roth BL, Kroeze WK | The Journal of biological chemistry | 26100629 | J Biol Chem | 2015 Aug 7 |
| Informatic challenges and advances in illuminating the druggable proteome. | Taujale R, Gravel N, Zhou Z, Yeung W, Kochut K, Kannan N | Drug discovery today | 38266979 | Drug Discov Today | 2024 Mar |
| Predicting protein and pathway associations for understudied dark kinases using pattern-constrained knowledge graph embedding. | Salcedo MV, Gravel N, Keshavarzi A, Huang LC, Kochut KJ, Kannan N | PeerJ | 37868056 | PeerJ | 2023 |
| A comprehensive exploration of the druggable conformational space of protein kinases using AI-predicted structures. | Herrington NB, Li YC, Stein D, Pandey G, Schlessinger A | PLoS computational biology | 39046952 | PLoS Comput Biol | 2024 Jul |
| Structural analysis of genomic and proteomic signatures reveal dynamic expression of intrinsically disordered regions in breast cancer. | Zatorski N, Sun Y, Elmas A, Dallago C, Karl T, Stein D, Rost B, Huang KL, Walsh M, Schlessinger A | iScience | 39310778 | iScience | 2024 Sep 20 |
| Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set. | Stein D, Kars ME, Wu Y, Bayrak ÇS, Stenson PD, Cooper DN, Schlessinger A, Itan Y | Genome medicine | 38037155 | Genome Med | 2023 Nov 30 |
| Low-frequency ERK and Akt activity dynamics are predictive of stochastic cell division events. | Bennett JJR, Stern AD, Zhang X, Birtwistle MR, Pandey G | NPJ systems biology and applications | 38834572 | NPJ Syst Biol Appl | 2024 Jun 4 |
| A web portal for exploring kinase-substrate interactions. | Sekar JAP, Li YC, Schlessinger A, Pandey G | NPJ systems biology and applications | 39362876 | NPJ Syst Biol Appl | 2024 Oct 3 |
| Pan-cancer proteogenomics expands the landscape of therapeutic targets. | Savage SR, Yi X, Lei JT, Wen B, Zhao H, Liao Y, Jaehnig EJ, Somes LK, Shafer PW, Lee TD, Fu Z, Dou Y, Shi Z, Gao D, Hoyos V, Gao Q, Zhang B | Cell | 38917788 | Cell | 2024 Aug 8 |
| Deciphering the dark cancer phosphoproteome using machine-learned co-regulation of phosphosites. | Jiang W, Jaehnig EJ, Liao Y, Shi Z, Yaron-Barir TM, Johnson JL, Cantley LC, Zhang B | Nature communications | 40113755 | Nat Commun | 2025 Mar 20 |
| Mapping the functional network of human cancer through machine learning and pan-cancer proteogenomics. | Shi Z, Lei JT, Elizarraras JM, Zhang B | Nature cancer | 39663389 | Nat Cancer | 2025 Jan |
| A proteogenomics data-driven knowledge base of human cancer. | Liao Y, Savage SR, Dou Y, Shi Z, Yi X, Jiang W, Lei JT, Zhang B | Cell systems | 37619559 | Cell Syst | 2023 Sep 20 |
| KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response. | Reese J, Unni D, Callahan TJ, Cappelletti L, Ravanmehr V, Carbon S, Fontana T, Blau H, Matentzoglu N, Harris NL, Munoz-Torres MC, Robinson PN, Joachimiak MP, Mungall CJ | bioRxiv : the preprint server for biology | 32839776 | bioRxiv | 2020 Aug 18 |
| GRAPE for fast and scalable graph processing and random-walk-based embedding. | Cappelletti L, Fontana T, Casiraghi E, Ravanmehr V, Callahan TJ, Cano C, Joachimiak MP, Mungall CJ, Robinson PN, Reese J, Valentini G | Nature computational science | 38177435 | Nat Comput Sci | 2023 Jun |
| KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response. | Reese JT, Unni D, Callahan TJ, Cappelletti L, Ravanmehr V, Carbon S, Shefchek KA, Good BM, Balhoff JP, Fontana T, Blau H, Matentzoglu N, Harris NL, Munoz-Torres MC, Haendel MA, Robinson PN, Joachimiak MP, Mungall CJ | Patterns (New York, N.Y.) | 33196056 | Patterns (N Y) | 2021 Jan 8 |
| KG-Hub-building and exchanging biological knowledge graphs. | Caufield JH, Putman T, Schaper K, Unni DR, Hegde H, Callahan TJ, Cappelletti L, Moxon SAT, Ravanmehr V, Carbon S, Chan LE, Cortes K, Shefchek KA, Elsarboukh G, Balhoff J, Fontana T, Matentzoglu N, Bruskiewich RM, Thessen AE, Harris NL, Munoz-Torres MC, Haendel MA, Robinson PN, Joachimiak MP, Mungall CJ, Reese JT | Bioinformatics (Oxford, England) | 37389415 | Bioinformatics | 2023 Jul 1 |
| The crystal structure of the protein kinase HIPK2 reveals a unique architecture of its CMGC-insert region. | Agnew C, Liu L, Liu S, Xu W, You L, Yeung W, Kannan N, Jablons D, Jura N | The Journal of biological chemistry | 31341017 | J Biol Chem | 2019 Sep 13 |
| mTORC2 controls the activity of PKC and Akt by phosphorylating a conserved TOR interaction motif. | Baffi TR, Lordén G, Wozniak JM, Feichtner A, Yeung W, Kornev AP, King CC, Del Rio JC, Limaye AJ, Bogomolovas J, Gould CM, Chen J, Kennedy EJ, Kannan N, Gonzalez DJ, Stefan E, Taylor SS, Newton AC | Science signaling | 33850054 | Sci Signal | 2021 Apr 13 |
| Quantitative Structure-Mutation-Activity Relationship Tests (QSMART) model for protein kinase inhibitor response prediction. | Huang LC, Yeung W, Wang Y, Cheng H, Venkat A, Li S, Ma P, Rasheed K, Kannan N | BMC bioinformatics | 33183223 | BMC Bioinformatics | 2020 Nov 12 |
| Nucleotide Binding, Evolutionary Insights, and Interaction Partners of the Pseudokinase Unc-51-like Kinase 4. | Preuss F, Chatterjee D, Mathea S, Shrestha S, St-Germain J, Saha M, Kannan N, Raught B, Rottapel R, Knapp S | Structure (London, England : 1993) | 32814032 | Structure | 2020 Nov 3 |
| PDBe-KB: a community-driven resource for structural and functional annotations. | PDBe-KB consortium | Nucleic acids research | 31584092 | Nucleic Acids Res | 2020 Jan 8 |
| Emerging roles of the αC-β4 loop in protein kinase structure, function, evolution, and disease. | Yeung W, Ruan Z, Kannan N | IUBMB life | 32101380 | IUBMB Life | 2020 Jun |
| Computational tools and resources for pseudokinase research. | O'Boyle B, Shrestha S, Kochut K, Eyers PA, Kannan N | Methods in enzymology | 35525549 | Methods Enzymol | 2022 |
| A peroxiredoxin-P38 MAPK scaffold increases MAPK activity by MAP3K-independent mechanisms. | Cao M, Day AM, Galler M, Latimer HR, Byrne DP, Foy TW, Dwyer E, Bennett E, Palmer J, Morgan BA, Eyers PA, Veal EA | Molecular cell | 37572670 | Mol Cell | 2023 Sep 7 |
| Cataloguing the dead: breathing new life into pseudokinase research. | Shrestha S, Byrne DP, Harris JA, Kannan N, Eyers PA | The FEBS journal | 32053275 | FEBS J | 2020 Oct |
| Analysis of human Tribbles 2 (TRIB2) pseudokinase. | Harris JA, Fairweather E, Byrne DP, Eyers PA | Methods in enzymology | 35525562 | Methods Enzymol | 2022 |
| Protein kinase inhibitor selectivity "hinges" on evolution. | Shrestha S, Bendzunas G, Kannan N | Structure (London, England : 1993) | 36459973 | Structure | 2022 Dec 1 |
| Evolutionary and cellular analysis of the 'dark' pseudokinase PSKH2. | Byrne DP, Shrestha S, Daly LA, Marensi V, Ramakrishnan K, Eyers CE, Kannan N, Eyers PA | The Biochemical journal | 36520605 | Biochem J | 2023 Jan 31 |
| KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. | Huang LC, Taujale R, Gravel N, Venkat A, Yeung W, Byrne DP, Eyers PA, Kannan N | BMC bioinformatics | 34537014 | BMC Bioinformatics | 2021 Sep 18 |
| Dark kinase annotation, mining, and visualization using the Protein Kinase Ontology. | Soleymani S, Gravel N, Huang LC, Yeung W, Bozorgi E, Bendzunas NG, Kochut KJ, Kannan N | PeerJ | 38077442 | PeerJ | 2023 |
| KSFinder-a knowledge graph model for link prediction of novel phosphorylated substrates of kinases. | Anandakrishnan M, Ross KE, Chen C, Shanker V, Cowart J, Wu CH | PeerJ | 37818330 | PeerJ | 2023 |
| Illuminating Dark Proteins using Reactome Pathways. | Brunson T, Sanati N, Matthews L, Haw R, Beavers D, Shorser S, Sevilla C, Viteri G, Conley P, Rothfels K, Hermjakob H, Stein L, D'Eustachio P, Wu G | bioRxiv : the preprint server for biology | 37333417 | bioRxiv | 2023 Jun 5 |
| ChatGPT usage in the Reactome curation process. | Tiwari K, Matthews L, May B, Shamovsky V, Orlic-Milacic M, Rothfels K, Ragueneau E, Gong C, Stephan R, Li N, Wu G, Stein L, D'Eustachio P, Hermjakob H | bioRxiv : the preprint server for biology | 37986970 | bioRxiv | 2023 Nov 8 |
| Detection of neoplastic-immune hybrid cells with metastatic properties in uveal melanoma. | Anderson AN, Conley P, Klocke CD, Sengupta SK, Pang A, Farley HC, Gillingham AR, Dawson AD, Fan Y, Jones JA, Gibbs SL, Skalet AH, Wu G, Wong MH | Research square | 38106024 | Res Sq | 2023 Dec 6 |
| ReactomeGSA: new features to simplify public data reuse. | Grentner A, Ragueneau E, Gong C, Prinz A, Gansberger S, Oyarzun I, Hermjakob H, Griss J | Bioinformatics (Oxford, England) | 38806182 | Bioinformatics | 2024 Jun 3 |
| Detection of neoplastic-immune hybrid cells with metastatic properties in uveal melanoma. | Anderson AN, Conley P, Klocke CD, Sengupta SK, Pang A, Farley HC, Gillingham AR, Dawson AD, Fan Y, Jones JA, Gibbs SL, Skalet AH, Wu G, Wong MH | Biomarker research | 39030653 | Biomark Res | 2024 Jul 20 |
| The reactome pathway knowledgebase 2022. | Gillespie M, Jassal B, Stephan R, Milacic M, Rothfels K, Senff-Ribeiro A, Griss J, Sevilla C, Matthews L, Gong C, Deng C, Varusai T, Ragueneau E, Haider Y, May B, Shamovsky V, Weiser J, Brunson T, Sanati N, Beckman L, Shao X, Fabregat A, Sidiropoulos K, Murillo J, Viteri G, Cook J, Shorser S, Bader G, Demir E, Sander C, Haw R, Wu G, Stein L, Hermjakob H, D'Eustachio P | Nucleic acids research | 34788843 | Nucleic Acids Res | 2022 Jan 7 |
| Leveraging biochemical reactions to unravel functional impacts of cancer somatic variants affecting protein interaction interfaces. | Raimondi F, Burkhart JG, Betts MJ, Russell RB, Wu G | F1000Research | 36569594 | F1000Res | 2021 |
| Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz. | Blucher AS, McWeeney SK, Stein L, Wu G | F1000Research | 31372215 | F1000Res | 2019 |
| 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 |
| 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 |
| Illuminate the Functions of Dark Proteins Using the Reactome-IDG Web Portal. | Beavers D, Brunson T, Sanati N, Matthews L, Haw R, Shorser S, Sevilla C, Viteri G, Conley P, Rothfels K, Hermjakob H, Stein L, D'Eustachio P, Wu G | Current protocols | 37467006 | Curr Protoc | 2023 Jul |
| 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 |
| The landscape of cancer-rewired GPCR signaling axes. | Arora C, Matic M, Bisceglia L, Di Chiaro P, De Oliveira Rosa N, Carli F, Clubb L, Nemati Fard LA, Kargas G, Diaferia GR, Vukotic R, Licata L, Wu G, Natoli G, Gutkind JS, Raimondi F | Cell genomics | 38723607 | Cell Genom | 2024 May 8 |
| The Reactome Pathway Knowledgebase 2024. | Milacic M, Beavers D, Conley P, Gong C, Gillespie M, Griss J, Haw R, Jassal B, Matthews L, May B, Petryszak R, Ragueneau E, Rothfels K, Sevilla C, Shamovsky V, Stephan R, Tiwari K, Varusai T, Weiser J, Wright A, Wu G, Stein L, Hermjakob H, D'Eustachio P | Nucleic acids research | 37941124 | Nucleic Acids Res | 2024 Jan 5 |
| Data Valuation with Gradient Similarity. | Evans NJ, Mills GB, Wu G, Song X, McWeeney S | ArXiv | 38800649 | ArXiv | 2024 May 13 |
| Phosphatidylinositol (4,5)-bisphosphate Impacts Ectosome Shedding from C. elegans Ciliated Sensory Neurons. | Elsayyid M, Semmel AE, Prova NS, Parekh KD, Tanis JE | bioRxiv : the preprint server for biology | 39975196 | bioRxiv | 2025 Feb 8 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Do K(ATP) channels have a role in immunity? | Feske S, Colucci F, Coetzee WA | Frontiers in immunology | 39669557 | Front Immunol | 2024 |
| 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 |
| Inflammatory stress-mediated chromatin changes underlie dysfunction in endothelial cells. | Liu H, Caliz AD, Learnard H, Koupenova M, Keaney JF, Kant S, Zhu LJ, Vertii A | bioRxiv : the preprint server for biology | 37905100 | bioRxiv | 2023 Oct 16 |
| 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 |
| 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 |
| Unheralded Adrenergic Receptor Signaling in Cellular Oxidative Stress and Death. | Underwood L, Jiang CS, Oh JY, Sato PY | Current opinion in physiology | 39070968 | Curr Opin Physiol | 2024 Aug |
| Exploring the role of pyroptosis in the pathogenicity of heart disease. | Bhatti R, Sato PY | Frontiers in physiology | 38645692 | Front Physiol | 2024 |
| 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 |
| Single-molecule imaging in the primary cilium. | Weiss LE, Love JF, Yoon J, Comerci CJ, Milenkovic L, Kanie T, Jackson PK, Stearns T, Gustavsson AK | Methods in cell biology | 37164543 | Methods Cell Biol | 2023 |
| trans-Interacting Plasma Membrane Proteins and Binding Partner Identification. | Zhang S, Ma Z | Journal of proteome research | 38937710 | J Proteome Res | 2024 Aug 2 |
| A Kv2 inhibitor combination reveals native neuronal conductances consistent with Kv2/KvS heteromers. | Stewart RG, Marquis MJ, Jo S, Harris B, Aberra A, Cook V, Whiddon Z, Yarov-Yarovoy V, Ferns M, Sack JT | bioRxiv : the preprint server for biology | 38352561 | bioRxiv | 2025 Apr 3 |
| 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 |
| The Electrically Silent Kv5.1 Subunit Forms Heteromeric Kv2 Channels in Cortical Neurons and Confers Distinct Functional Properties. | Ferns M, van der List D, Vierra NC, Lacey T, Murray K, Kirmiz M, Stewart RG, Sack JT, Trimmer JS | The Journal of neuroscience : the official journal of the Society for Neuroscience | 39933932 | J Neurosci | 2025 Mar 26 |
| Roles of sensory receptors in non-sensory organs: the kidney and beyond. | Xu J, Shepard BD, Pluznick JL | Nature reviews. Nephrology | 39753689 | Nat Rev Nephrol | 2025 Apr |
| 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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| 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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| 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 Atypical Kinase RIOK3 Limits RVFV Propagation and Is Regulated by Alternative Splicing. | Havranek KE, White LA, Bisom TC, Lanchy JM, Lodmell JS | Viruses | 33652597 | Viruses | 2021 Feb 26 |
| 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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| 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 |
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