Mount Sinai Center for Bioinformatics

Research output

Research output per year 2005 2008 2010 2011 2012 2013 2014 2016 2018 2019 2020 2021 2022 2023

• 25630 Citations
• 59 h-index
• 164 Article
• 18 Review article
• 8 Short survey
• 7 Conference contribution
• 14 More
  • 6 Comment/debate
  • 4 Chapter
  • 2 Letter
  • 1 Book
  • 1 Foreword/postscript

Research output per year

Research output per year

Search results

• 2023

  Computational screen to identify potential targets for immunotherapeutic identification and removal of senescence cells

  Deng, E. Z., Fleishman, R. H., Xie, Z., Marino, G. B., Clarke, D. J. B. & Ma'ayan, A., 2023, (Accepted/In press) In: Aging Cell.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Cellular Senescence 100%
  • Genes 36%
  • RNA-Seq 15%
  • Atlases 13%
  • Transcriptome 11%

• lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs

  Marino, G. B., Wojciechowicz, M. L., Clarke, D. J. B., Kuleshov, M. V., Xie, Z., Jeon, M., Lachmann, A. & Ma'ayan, A., 2023, In: Database : the journal of biological databases and curation. 2023, baad009.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Ribonucleic Acid 100%
  • RNA 94%
  • Databases 47%
  • mice 45%
  • Genes 45%

• PrismEXP: gene annotation prediction from stratified gene-gene co-expression matrices

  Lachmann, A., Rizzo, K. A., Bartal, A., Jeon, M., Clarke, D. J. B. & Ma’ayan, A., Feb 2023, In: PeerJ. 11, e14927.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Molecular Sequence Annotation 100%
  • prediction 51%
  • Gene Expression 45%
  • RNA-Seq 44%
  • Boidae 36%
  1 Scopus citations
• 2022

  Age alters the oncogenic trajectory toward luminal mammary tumors that activate unfolded proteins responses

  Jenkins, E. C., Chattopadhyay, M., Gomez, M., Torre, D., Ma'ayan, A., Torres-Martin, M., Sia, D. & Germain, D., Oct 2022, In: Aging Cell. 21, 10, e13665.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Unfolded Protein Response 100%
  • Estrogen Receptor alpha 93%
  • Breast Neoplasms 51%
  • Genes 12%
  • Endoplasmic Reticulum 9%

• A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses

  Gross, S. M., Dane, M. A., Smith, R. L., Devlin, K. L., McLean, I. C., Derrick, D. S., Mills, C. E., Subramanian, K., London, A. B., Torre, D., Evangelista, J. E., Clarke, D. J. B., Xie, Z., Erdem, C., Lyons, N., Natoli, T., Pessa, S., Lu, X., Mullahoo, J., Li, J., & 30 othersAdam, M., Wassie, B., Liu, M., Kilburn, D. F., Liby, T. A., Bucher, E., Sanchez-Aguila, C., Daily, K., Omberg, L., Wang, Y., Jacobson, C., Yapp, C., Chung, M., Vidovic, D., Lu, Y., Schurer, S., Lee, A., Pillai, A., Subramanian, A., Papanastasiou, M., Fraenkel, E., Feiler, H. S., Mills, G. B., Jaffe, J. D., Ma’ayan, A., Birtwistle, M. R., Sorger, P. K., Korkola, J. E., Gray, J. W. & Heiser, L. M., Dec 2022, In: Communications Biology. 5, 1, 1066.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • multiomics 100%
  • ligands 60%
  • computational methodology 58%
  • Datasets 52%
  • Ligands 46%
  1 Scopus citations

• BlitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation

  Lachmann, A., Xie, Z. & Ma'ayan, A., 15 Apr 2022, In: Bioinformatics. 38, 8, p. 2356-2357 2 p.

  Research output: Contribution to journal › Article › peer-review

  • Gamma distribution 100%
  • Gene 92%
  • Genes 90%
  • Set theory 60%
  • Differential Expression 58%
  1 Scopus citations

• Connecting omics signatures and revealing biological mechanisms with iLINCS

  Pilarczyk, M., Fazel-Najafabadi, M., Kouril, M., Shamsaei, B., Vasiliauskas, J., Niu, W., Mahi, N., Zhang, L., Clark, N. A., Ren, Y., White, S., Karim, R., Xu, H., Biesiada, J., Bennett, M. F., Davidson, S. E., Reichard, J. F., Roberts, K., Stathias, V., Koleti, A., & 6 othersVidovic, D., Clarke, D. J. B., Schürer, S. C., Ma’ayan, A., Meller, J. & Medvedovic, M., Dec 2022, In: Nature Communications. 13, 1, 4678.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Proteogenomics 100%
  • Drug Repositioning 82%
  • Mining 68%
  • Workflow 66%
  • Computational Biology 56%
  4 Scopus citations

• DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules

  Kropiwnicki, E., Lachmann, A., Clarke, D. J. B., Xie, Z., Jagodnik, K. M. & Ma’ayan, A., Dec 2022, In: BMC Bioinformatics. 23, 1, 76.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Drugs 100%
  • Molecules 95%
  • Term 52%
  • Drug 44%
  • Pharmaceutical Preparations 40%
  1 Scopus citations

• Gene and drug landing page aggregator

  Clarke, D. J. B., Kuleshov, M. V., Xie, Z., Evangelista, J. E., Meyers, M. R., Kropiwnicki, E., Jenkins, S. L. & Ma'ayan, A., 2022, In: Bioinformatics Advances. 2, 1, vbac013.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Landing 100%
  • Genes 95%
  • GS-5734 47%
  • Pharmaceutical Preparations 41%
  • Search Engine 14%

• Gene set predictor for post-treatment Lyme disease

  Clarke, D. J. B., Rebman, A. W., Fan, J., Soloski, M. J., Aucott, J. N. & Ma'ayan, A., 15 Nov 2022, In: Cell Reports Medicine. 3, 11, 100816.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Post-Lyme Disease Syndrome 100%
  • RNA Sequencing 94%
  • Lyme Disease 69%
  • Biological Marker 51%
  • Acute Disease 36%

• Getting Started with LINCS Datasets and Tools

  Xie, Z., Kropiwnicki, E., Wojciechowicz, M. L., Jagodnik, K. M., Shu, I., Bailey, A., Clarke, D. J. B., Jeon, M., Evangelista, J. E., V. Kuleshov, M., Lachmann, A., Parigi, A. A., Sanchez, J. M., Jenkins, S. L. & Ma'ayan, A., Jul 2022, In: Current Protocols. 2, 7, e487.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Libraries 100%
  • Datasets 89%
  • Knowledge Discovery 35%
  • Workflow 24%
  • Proteomics 20%

• Getting Started with the IDG KMC Datasets and Tools

  Kropiwnicki, E., Binder, J. L., Yang, J. J., Holmes, J., Lachmann, A., Clarke, D. J. B., Sheils, T., Kelleher, K. J., Metzger, V. T., Bologa, C. G., Oprea, T. I. & Ma'ayan, A., Jan 2022, In: Current Protocols. 2, 1, e355.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Datasets 100%
  • Genome 85%
  • Protein 52%
  • Machine Learning 47%
  • Proteins 38%
  4 Scopus citations

• Making Common Fund data more findable: catalyzing a data ecosystem

  Charbonneau, A. L., Brady, A., Czajkowski, K., Aluvathingal, J., Canchi, S., Carter, R., Chard, K., Clarke, D. J. B., Crabtree, J., Creasy, H. H., D'Arcy, M., Felix, V., Giglio, M., Gingrich, A., Harris, R. M., Hodges, T. K., Ifeonu, O., Jeon, M., Kropiwnicki, E., Lim, M. C. W., & 22 othersLiming, R. L., Lumian, J., Mahurkar, A. A., Mandal, M., Munro, J. B., Nadendla, S., Richter, R., Romano, C., Rocca-Serra, P., Schor, M., Schuler, R. E., Tangmunarunkit, H., Waldrop, A., Williams, C., Word, K., Sansone, S. A., Ma'ayan, A., Wagner, R., Foster, I., Kesselman, C., Brown, C. T. & White, O., 2022, In: GigaScience. 11, giac105.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Metadata 100%
  • Ecosystem 75%
  • Ecosystems 72%
  • Datasets 35%
  • Catalogs 28%
  1 Scopus citations

• PPARdelta activation induces metabolic and contractile maturation of human pluripotent stem cell-derived cardiomyocytes

  Wickramasinghe, N. M., Sachs, D., Shewale, B., Gonzalez, D. M., Dhanan-Krishnan, P., Torre, D., LaMarca, E., Raimo, S., Dariolli, R., Serasinghe, M. N., Mayourian, J., Sebra, R., Beaumont, K., Iyengar, S., French, D. L., Hansen, A., Eschenhagen, T., Chipuk, J. E., Sobie, E. A., Jacobs, A., & 6 othersAkbarian, S., Ischiropoulos, H., Ma'ayan, A., Houten, S. M., Costa, K. & Dubois, N. C., 7 Apr 2022, In: Cell Stem Cell. 29, 4, p. 559-576.e7

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • PPAR delta 100%
  • Metabolic Activation 80%
  • Pluripotent Stem Cells 77%
  • Cardiac Myocytes 61%
  • Fatty Acids 56%
  10 Scopus citations

• SigCom LINCS: data and metadata search engine for a million gene expression signatures

  Evangelista, J. E., Clarke, D. J. B., Xie, Z., Lachmann, A., Jeon, M., Chen, K., Jagodnik, K. M., Jenkins, S. L., Kuleshov, M. V., Wojciechowicz, M. L., Schürer, S. C., Medvedovic, M. & Ma'ayan, A., 5 Jul 2022, In: Nucleic Acids Research. 50, W1, p. W697-W709

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Metadata 100%
  • Search Engine 86%
  • Transcriptome 62%
  • Libraries 60%
  • Genes 15%
  8 Scopus citations

• Transcriptomic profiling of recessive dystrophic epidermolysis bullosa wounded skin highlights drug repurposing opportunities to improve wound healing

  Onoufriadis, A., Proudfoot, L. E., Ainali, C., Torre, D., Papanikolaou, M., Rayinda, T., Rashidghamat, E., Danarti, R., Mellerio, J. E., Ma’ayan, A. & McGrath, J. A., Mar 2022, In: Experimental Dermatology. 31, 3, p. 420-426 7 p.

  Research output: Contribution to journal › Article › peer-review

  • Epidermolysis Bullosa Dystrophica 100%
  • Drug Repositioning 91%
  • Wound Healing 58%
  • Methotrexate 41%
  • Skin 36%
  2 Scopus citations

• Transforming L1000 profiles to RNA-seq-like profiles with deep learning

  Jeon, M., Xie, Z., Evangelista, J. E., Wojciechowicz, M. L., Clarke, D. J. B. & Ma’ayan, A., Dec 2022, In: BMC Bioinformatics. 23, 1, 374.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Deep Learning 100%
  • RNA 87%
  • RNA-Seq 84%
  • Gene 71%
  • Genes 69%
  1 Scopus citations
• 2021

  An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions

  Sevilla, A., Papatsenko, D., Mazloom, A. R., Xu, H., Vasileva, A., Unwin, R. D., LeRoy, G., Chen, E. Y., Garrett-Bakelman, F. E., Lee, D. F., Trinite, B., Webb, R. L., Wang, Z., Su, J., Gingold, J., Melnick, A., Garcia, B. A., Whetton, A. D., MacArthur, B. D., Ma’ayan, A., & 1 othersLemischka, I. R., 19 Mar 2021, In: Frontiers in Cell and Developmental Biology. 9, 630067.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Estrogen Receptor beta 100%
  • Mouse Embryonic Stem Cells 64%
  • Chromatin Assembly and Disassembly 30%
  • DNA Methylation 25%
  • Transcription Factors 19%
  4 Scopus citations

• Appyters: Turning Jupyter Notebooks into data-driven web apps

  Clarke, D. J. B., Jeon, M., Stein, D. J., Moiseyev, N., Kropiwnicki, E., Dai, C., Xie, Z., Wojciechowicz, M. L., Litz, S., Hom, J., Evangelista, J. E., Goldman, L., Zhang, S., Yoon, C., Ahamed, T., Bhuiyan, S., Cheng, M., Karam, J., Jagodnik, K. M., Shu, I., & 4 othersLachmann, A., Ayling, S., Jenkins, S. L. & Ma'ayan, A., 12 Mar 2021, In: Patterns. 2, 3, 100213.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Bioinformatics 100%
  • Apps 77%
  • Web-based 65%
  • Machine Learning 30%
  • Visualization 24%
  34 Scopus citations

• Connectivity Mapping Identifies BI-2536 as a Potential Drug to Treat Diabetic Kidney Disease

  Zhang, L., Wang, Z., Liu, R., Li, Z., Lin, J., Wojciechowicz, M. L., Huang, J., Lee, K., Ma’ayan, A. & He, J. C., Feb 2021, In: Diabetes. 70, 2, p. 589-602 14 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • BI 2536 100%
  • Diabetic Nephropathies 57%
  • Mesangial Cells 32%
  • NF-kappa B 29%
  • Pharmaceutical Preparations 22%
  11 Scopus citations

• Drugmonizome and Drugmonizome-ML: Integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning

  Kropiwnicki, E., Evangelista, J. E., Stein, D. J., Clarke, D. J. B., Lachmann, A., Kuleshov, M. V., Jeon, M., Jagodnik, K. M. & Ma'ayan, A., 2021, In: Database : the journal of biological databases and curation. 2021, baab017.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • artificial intelligence 100%
  • Machine Learning 95%
  • Molecules 81%
  • Machine learning 61%
  • drugs 56%
  9 Scopus citations

• Gene Set Knowledge Discovery with Enrichr

  Xie, Z., Bailey, A., Kuleshov, M. V., Clarke, D. J. B., Evangelista, J. E., Jenkins, S. L., Lachmann, A., Wojciechowicz, M. L., Kropiwnicki, E., Jagodnik, K. M., Jeon, M. & Ma'ayan, A., Mar 2021, In: Current Protocols. 1, 3, e90.

  Research output: Contribution to journal › Article › peer-review

  • Knowledge Discovery 100%
  • Protein 26%
  • Genes 25%
  • Search Engine 16%
  • Metabolomics 13%
  588 Scopus citations

• KEA3: Improved kinase enrichment analysis via data integration

  Kuleshov, M. V., Xie, Z., London, A. B. K., Yang, J., Evangelista, J. E., Lachmann, A., Shu, I., Torre, D. & Ma'Ayan, A., 2 Jul 2021, In: Nucleic Acids Research. 49, W1, p. W304-W316

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Phosphotransferases 100%
  • Data Analysis 96%
  • Proteomics 16%
  • Benchmarking 9%
  • Protein Kinases 8%
  22 Scopus citations

• Krüppel-like factor 6-mediated loss of BCAA catabolism contributes to kidney injury in mice and humans

  Piret, S. E., Guo, Y., Attallah, A. A., Horne, S. J., Zollman, A., Owusu, D., Henein, J., Sidorenko, V. S., Revelo, M. P., Hato, T., Ma'ayan, A., He, J. C. & Mallipattu, S. K., 8 Jun 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 23, e2024414118.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Branched Chain Amino Acids 100%
  • Kidney 41%
  • Wounds and Injuries 37%
  • Acute Kidney Injury 32%
  • Fibrosis 19%
  14 Scopus citations

• Loss of proximal tubular transcription factor Krüppel-like factor 15 exacerbates kidney injury through loss of fatty acid oxidation

  Piret, S. E., Attallah, A. A., Gu, X., Guo, Y., Gujarati, N. A., Henein, J., Zollman, A., Hato, T., Ma'ayan, A., Revelo, M. P., Dickman, K. G., Chen, C. H., Shun, C. T., Rosenquist, T. A., He, J. C. & Mallipattu, S. K., Dec 2021, In: Kidney International. 100, 6, p. 1250-1267 18 p.

  Research output: Contribution to journal › Article › peer-review

  • aristolochic acid I 100%
  • Fatty Acids 76%
  • Transcription Factors 67%
  • Kidney 47%
  • Peroxisome Proliferator-Activated Receptors 46%
  11 Scopus citations

• Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses

  Broyde, J., Simpson, D. R., Murray, D., Paull, E. O., Chu, B. W., Tagore, S., Jones, S. J., Griffin, A. T., Giorgi, F. M., Lachmann, A., Jackson, P., Sweet-Cordero, E. A., Honig, B. & Califano, A., Feb 2021, In: Nature Biotechnology. 39, 2, p. 215-224 10 p.

  Research output: Contribution to journal › Article › peer-review

  • Molecular interactions 100%
  • Oncogene Proteins 74%
  • Proteins 61%
  • Tumorigenic 50%
  • Lethal 39%
  10 Scopus citations

• piNET: A versatile web platform for downstream analysis and visualization of proteomics data

  Shamsaei, B., Chojnacki, S., Pilarczyk, M., Najafabadi, M., Niu, W., Chen, C., Ross, K., Matlock, A., Muhlich, J., Chutipongtanate, S., Zheng, J., Turner, J., Vidović, D., Jaffe, J., MacCoss, M., Wu, C., Pillai, A., Ma'ayan, A., Schürer, S., Kouril, M., & 2 othersMedvedovic, M. & Meller, J., 2021, In: Nucleic Acids Research. 48, p. W85-W93

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Data Visualization 100%
  • Proteomics 63%
  • Peptide Mapping 60%
  • Workflow 50%
  • Enzymes 37%
  11 Scopus citations

• Predicting Lyme Disease From Patients' Peripheral Blood Mononuclear Cells Profiled With RNA-Sequencing

  Clarke, D. J. B., Rebman, A. W., Bailey, A., Wojciechowicz, M. L., Jenkins, S. L., Evangelista, J. E., Danieletto, M., Fan, J., Eshoo, M. W., Mosel, M. R., Robinson, W., Ramadoss, N., Bobe, J., Soloski, M. J., Aucott, J. N. & Ma'ayan, A., 8 Mar 2021, In: Frontiers in Immunology. 12, 636289.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Lyme Disease 100%
  • RNA Sequence Analysis 92%
  • Blood Cells 67%
  • RNA-Seq 19%
  • Machine Learning 18%
  6 Scopus citations

• Prioritizing pain-associated targets with machine learning

  Jeon, M., Jagodnik, K. M., Kropiwnicki, E., Stein, D. J. & Ma'ayan, A., 11 May 2021, In: Biochemistry. 60, 18, p. 1430-1446 17 p.

  Research output: Contribution to journal › Article › peer-review

  • Machine Learning 100%
  • Analgesic 99%
  • Pain 51%
  • Drug Target 50%
  • Statistical Ensemble 43%
  3 Scopus citations

• Transcriptome analysis of human dermal fibroblasts following red light phototherapy

  Austin, E., Koo, E., Merleev, A., Torre, D., Marusina, A., Luxardi, G., Mamalis, A., Isseroff, R. R., Ma’ayan, A., Maverakis, E. & Jagdeo, J., Dec 2021, In: Scientific Reports. 11, 1, 7315.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Phototherapy 100%
  • Gene Expression Profiling 86%
  • Fibroblasts 62%
  • Light 59%
  • Skin 45%
  6 Scopus citations
• 2020

  Chemokine signatures of pathogen-Specific T cells I: Effector T cells

  Eberlein, J., Davenport, B., Nguyen, T. T., Victorino, F., Jhun, K., van der Heide, V., Kuleshov, M., Ma’ayan, A., Kedl, R. & Homann, D., 15 Oct 2020, In: Journal of Immunology. 205, 8, p. 2169-2187 19 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Chemokines 100%
  • T-Lymphocytes 65%
  • Chemotaxis 14%
  • Allergy and Immunology 14%
  • Antigen-Antibody Complex 13%
  16 Scopus citations

• Chemokine signatures of pathogen-Specific T cells II: Memory T cells in acute and chronic infection

  Davenport, B., Eberlein, J., Nguyen, T. T., Victorino, F., van der Heide, V., Kuleshov, M., Ma’ayan, A., Kedl, R. & Homann, D., 15 Oct 2020, In: Journal of Immunology. 205, 8, p. 2188-2206 19 p.

  Research output: Contribution to journal › Article › peer-review

  • Chemokines 100%
  • T-Lymphocytes 65%
  • Infections 50%
  • Chemokine CCL1 24%
  • Allergy and Immunology 14%
  3 Scopus citations

• Dermal sheath contraction powers stem cell niche relocation during hair cycle regression

  Heitman, N., Sennett, R., Mok, K. W., Saxena, N., Srivastava, D., Martino, P., Grisanti, L., Wang, Z., Ma'ayan, A., Rompolas, P. & Rendl, M., 10 Jan 2020, In: Science. 367, 6474, p. 161-166 6 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Stem Cell Niche 100%
  • Hair 76%
  • Smooth Muscle 45%
  • Skin 42%
  • Homeostasis 37%
  44 Scopus citations

• EnrichrBot: Twitter bot tracking tweets about human genes

  Bartal, A., Lachmann, A., Clarke, D. J. B., Seiden, A. H., Jagodnik, K. M. & Ma'Ayan, A., 31 Mar 2020, In: Bioinformatics. 36, 12, p. 3932-3934 3 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Gene 100%
  • Genes 97%
  • Human 91%
  • Genome-Wide Association Study 30%
  • Blogging 22%
  2 Scopus citations

• Genetic driver mutations introduced in identical cell-of-origin in murine glioblastoma reveal distinct immune landscapes but similar response to checkpoint blockade

  Chen, Z., Herting, C. J., Ross, J. L., Gabanic, B., Puigdelloses Vallcorba, M., Szulzewsky, F., Wojciechowicz, M. L., Cimino, P. J., Ezhilarasan, R., Sulman, E. P., Ying, M., Ma'ayan, A., Read, R. D. & Hambardzumyan, D., 1 Oct 2020, In: GLIA. 68, 10, p. 2148-2166 19 p.

  Research output: Contribution to journal › Article › peer-review

  • Glioblastoma 100%
  • Mutation 56%
  • Myeloid Cells 34%
  • epidermal growth factor receptor VIII 27%
  • Proto-Oncogene Proteins c-sis 24%
  17 Scopus citations

• 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, D. J. B., Lachmann, A., Evangelista, J. E., Ma'Ayan, A., Medvedovic, M. & Schürer, S. C., 1 Jan 2020, In: Nucleic Acids Research. 48, D1, p. D431-D439

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Libraries 100%
  • Metadata 66%
  • Catalogs 28%
  • Datasets 17%
  • Genes 9%
  76 Scopus citations

• Memory of Divisional History Directs the Continuous Process of Primitive Hematopoietic Lineage Commitment

  Bernitz, J. M., Rapp, K., Daniel, M. G., Shcherbinin, D., Yuan, Y., Gomes, A., Waghray, A., Brosh, R., Lachmann, A., Ma'ayan, A., Papatsenko, D. & Moore, K. A., 14 Apr 2020, In: Stem Cell Reports. 14, 4, p. 561-574 14 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • RNA Sequencing 100%
  • Hematopoietic Stem Cells 59%
  • History 45%
  • Memory 43%
  • Polycomb Repressive Complex 2 36%
  7 Scopus citations

• Systems Analysis Implicates WAVE2 Complex in the Pathogenesis of Developmental Left-Sided Obstructive Heart Defects

  Edwards, J. J., Rouillard, A. D., Fernandez, N. F., Wang, Z., Lachmann, A., Shankaran, S. S., Bisgrove, B. W., Demarest, B., Turan, N., Srivastava, D., Bernstein, D., Deanfield, J., Giardini, A., Porter, G., Kim, R., Roberts, A. E., Newburger, J. W., Goldmuntz, E., Brueckner, M., Lifton, R. P., & 6 othersSeidman, C. E., Chung, W. K., Tristani-Firouzi, M., Yost, H. J., Ma'ayan, A. & Gelb, B. D., Apr 2020, In: JACC: Basic to Translational Science. 5, 4, p. 376-386 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Systems Analysis 100%
  • Heart Diseases 71%
  • Monomeric GTP-Binding Proteins 69%
  • Heart 57%
  • Wiskott-Aldrich Syndrome Protein Family 49%
  5 Scopus citations

• The COVID-19 Drug and Gene Set Library

  Kuleshov, M. V., Stein, D. J., Clarke, D. J. B., Kropiwnicki, E., Jagodnik, K. M., Bartal, A., Evangelista, J. E., Hom, J., Cheng, M., Bailey, A., Zhou, A., Ferguson, L. B., Lachmann, A. & Ma'ayan, A., 11 Sep 2020, In: Patterns. 1, 6, 100090.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Gene 100%
  • Drugs 93%
  • Machine Learning 29%
  • Vaccine 18%
  • Therapy 11%
  38 Scopus citations
• 2019

  A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines

  LINCS Consortium, 24 Jul 2019, In: Cell Systems. 9, 1, p. 35-48.e5

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Cell Line 100%
  • Pharmaceutical Preparations 69%
  60 Scopus citations

• ChEA3: transcription factor enrichment analysis by orthogonal omics integration

  Keenan, A. B., Torre, D., Lachmann, A., Leong, A. K., Wojciechowicz, M. L., Utti, V., Jagodnik, K. M., Kropiwnicki, E., Wang, Z. & Ma'ayan, A., 1 Jul 2019, In: Nucleic Acids Research. 47, W1, p. W212-W224

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Statistical Factor Analysis 100%
  • Transcription Factors 84%
  • Libraries 22%
  • General Transcription Factors 18%
  • Chromatin Immunoprecipitation Sequencing 16%
  236 Scopus citations

• Dermal Condensate Niche Fate Specification Occurs Prior to Formation and Is Placode Progenitor Dependent

  Mok, K. W., Saxena, N., Heitman, N., Grisanti, L., Srivastava, D., Muraro, M. J., Jacob, T., Sennett, R., Wang, Z., Su, Y., Yang, L. M., Ma'ayan, A., Ornitz, D. M., Kasper, M. & Rendl, M., 7 Jan 2019, In: Developmental Cell. 48, 1, p. 32-48.e5

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Signalling Molecule 100%
  • Hair Follicle 92%
  • Wave 73%
  • Transcription Factors 59%
  • Fibroblasts 59%
  47 Scopus citations

• Direct activation of PP2A for the treatment of tyrosine kinase inhibitor-resistant lung adenocarcinoma

  Tohmé, R., Izadmehr, S., Gandhe, S., Tabaro, G., Vallabhaneni, S., Thomas, A., Vasireddi, N., Dhawan, N. S., Ma'ayan, A., Sharma, N., Galsky, M. D., Ohlmeyer, M., Sangodkar, J. & Narla, G., 2019, In: JCI insight. 4, 4, e125693.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Protein Phosphatase 2 100%
  • Adenocarcinoma of Lung 82%
  • Protein-Tyrosine Kinases 70%
  • Phosphatidylinositol 3-Kinases 43%
  • Afatinib 16%
  30 Scopus citations

• Drug Gene Budger (DGB): An application for ranking drugs to modulate a specific gene based on transcriptomic signatures

  Wang, Z., He, E., Sani, K., Jagodnik, K. M., Silverstein, M. C. & Ma'Ayan, A., 1 Apr 2019, In: Bioinformatics. 35, 7, p. 1247-1248 2 p.

  Research output: Contribution to journal › Article › peer-review

  • Drugs 100%
  • Ranking 99%
  • Gene 95%
  • Genes 93%
  • Signature 92%
  14 Scopus citations

• Geneshot: search engine for ranking genes from arbitrary text queries

  Lachmann, A., Schilder, B. M., Wojciechowicz, M. L., Torre, D., Kuleshov, M. V., Keenan, A. B. & Ma'ayan, A., 1 Jul 2019, In: Nucleic Acids Research. 47, W1, p. W571-W577

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Search Engine 100%
  • Genes 31%
  • RNA-Seq 7%
  • Gene Frequency 5%
  • Research Personnel 4%
  31 Scopus citations

• Habenular TCF7L2 links nicotine addiction to diabetes

  Duncan, A., Heyer, M. P., Ishikawa, M., Caligiuri, S. P. B., Liu, X. A., Chen, Z., Vittoria Micioni Di Bonaventura, M., Elayouby, K. S., Ables, J. L., Howe, W. M., Bali, P., Fillinger, C., Williams, M., O’Connor, R. M., Wang, Z., Lu, Q., Kamenecka, T. M., Ma’ayan, A., O’Neill, H. C., Ibanez-Tallon, I., & 2 othersGeurts, A. M. & Kenny, P. J., 17 Oct 2019, In: Nature. 574, 7778, p. 372-377 6 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Nicotine 100%
  • Habenula 93%
  • Blood Glucose 27%
  • Nicotinic Receptors 18%
  • Glucagon 17%
  59 Scopus citations

• ModEnrichr: A suite of gene set enrichment analysis tools for model organisms

  Kuleshov, M. V., Diaz, J. E. L., Flamholz, Z. N., Keenan, A. B., Lachmann, A., Wojciechowicz, M. L., Cagan, R. L. & Ma'ayan, A., 1 Jul 2019, In: Nucleic Acids Research. 47, W1, p. W183-W190

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Genes 100%
  • Metadata 60%
  • Protein Databases 53%
  • Pseudogenes 52%
  • Databases 49%
  34 Scopus citations

• Predicting opioid dependence from electronic health records with machine learning

  Ellis, R. J., Wang, Z., Genes, N. & Ma'Ayan, A., 29 Jan 2019, In: BioData Mining. 12, 1, 3.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Opioids 100%
  • Classifier 76%
  • Opioid-Related Disorders 67%
  • Machine Learning 62%
  • Electronics 57%
  44 Scopus citations

• Single-cell immune landscape of human atherosclerotic plaques

  Fernandez, D. M., Rahman, A. H., Fernandez, N. F., Chudnovskiy, A., Amir, E. A. D., Amadori, L., Khan, N. S., Wong, C. K., Shamailova, R., Hill, C. A., Wang, Z., Remark, R., Li, J. R., Pina, C., Faries, C., Awad, A. J., Moss, N., Bjorkegren, J. L. M., Kim-Schulze, S., Gnjatic, S., & 5 othersMa’ayan, A., Mocco, J., Faries, P., Merad, M. & Giannarelli, C., 1 Oct 2019, In: Nature Medicine. 25, 10, p. 1576-1588 13 p.

  Research output: Contribution to journal › Article › peer-review

  • Atherosclerotic Plaques 100%
  • Marker 83%
  • T-Lymphocytes 59%
  • T-Lymphocyte Subsets 51%
  • Macrophages 50%
  342 Scopus citations

• The Signaling Pathways Project, an integrated ‘omics knowledgebase for mammalian cellular signaling pathways

  Ochsner, S. A., Abraham, D., Martin, K., Ding, W., McOwiti, A., Kankanamge, W., Wang, Z., Andreano, K., Hamilton, R. A., Chen, Y., Hamilton, A., Gantner, M. L., Dehart, M., Qu, S., Hilsenbeck, S. G., Becnel, L. B., Bridges, D., Ma’ayan, A., Huss, J. M., Stossi, F., & 4 othersFoulds, C. E., Kralli, A., McDonnell, D. P. & McKenna, N. J., 1 Dec 2019, In: Scientific data. 6, 1, 252.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Cell signaling 100%
  • Signaling Pathways 97%
  • Knowledge Base 82%
  • Pathway 61%
  • Node 45%
  49 Scopus citations