Avi Ma'ayan - RankMe

68 papers C 1Misc 1Journal 61Unranked 5

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Playbook workflow builder: Interactive construction of bioinformatics workflows. PLoS Comput. Biol. Daniel J. B. Clarke, John Erol Evangelista, Zhuorui Xie, Giacomo B. Marino, Anna I. Byrd, Mano Ram Maurya, Sumana Srinivasan, Keyang Yu, Varduhi Petrosyan, Matthew E. Roth, Miroslav Milinkov, Charles Hadley King, Jeet Kiran Vora, Jonathon Keeney, Christopher Nemarich, William Khan, Alexander Lachmann, Nasheath Ahmed, Alexandra Agris, Juncheng Pan, Srinivasan Ramachandran, Eoin Fahy, Emmanuel Esquivel, Aleksandar Mihajlovic, Bosko Jevtic, Vuk Milinovic, Sean Kim, Patrick McNeely, Tianyi Wang, Eric Wenger, Miguel A. Brown, Alexander Sickler, Yuankun Zhu, Sherry L. Jenkins, Philip D. Blood, Deanne M. Taylor, Adam C. Resnick, Raja Mazumder, Aleksandar Milosavljevic, Shankar Subramaniam, Avi Ma'ayan
2024	J	`jnl`	RummaGEO: Automatic mining of human and mouse gene sets from GEO. Patterns Giacomo B. Marino, Daniel J. B. Clarke, Alexander Lachmann, Eden Z. Deng, Avi Ma'ayan
2023	J	`jnl`	Enrichr-KG: bridging enrichment analysis across multiple libraries. Nucleic Acids Res. John Erol Evangelista, Zhuorui Xie, Giacomo B. Marino, Nhi Nguyen, Daniel J. B. Clarke, Avi Ma'ayan
2023	J	`jnl`	GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery. Nucleic Acids Res. Giacomo B. Marino, Michael Ngai, Daniel J. B. Clarke, Reid H. Fleishman, Eden Z. Deng, Zhuorui Xie, Nasheath Ahmed, Avi Ma'ayan
2023	J	`jnl`	lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs. Database J. Biol. Databases Curation Giacomo B. Marino, Megan L. Wojciechowicz, Daniel J. B. Clarke, Maxim V. Kuleshov, Zhuorui Xie, Minji Jeon, Alexander Lachmann, Avi Ma'ayan
2022	J	`jnl`	DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. BMC Bioinform. Eryk Kropiwnicki, Alexander Lachmann, Daniel J. B. Clarke, Zhuorui Xie, Kathleen M. Jagodnik, Avi Ma'ayan
2022	J	`jnl`	SigCom LINCS: data and metadata search engine for a million gene expression signatures. Nucleic Acids Res. John Erol Evangelista, Daniel J. B. Clarke, Zhuorui Xie, Alexander Lachmann, Minji Jeon, Kerwin Chen, Kathleen M. Jagodnik, Sherry L. Jenkins, Maxim V. Kuleshov, Megan L. Wojciechowicz, Stephan C. Schürer, Mario Medvedovic, Avi Ma'ayan
2022	J	`jnl`	Transforming L1000 profiles to RNA-seq-like profiles with deep learning. BMC Bioinform. Minji Jeon, Zhuorui Xie, John Erol Evangelista, Megan L. Wojciechowicz, Daniel J. B. Clarke, Avi Ma'ayan
2022	J	`jnl`	blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation. Bioinform. Alexander Lachmann, Zhuorui Xie, Avi Ma'ayan
2021	J	`jnl`	Appyters: Turning Jupyter Notebooks into data-driven web apps. Patterns Daniel J. B. Clarke, Minji Jeon, Daniel J. Stein, Nicole Moiseyev, Eryk Kropiwnicki, Charles Dai, Zhuorui Xie, Megan L. Wojciechowicz, Skylar Litz, Jason Hom, John Erol Evangelista, Lucas Goldman, Serena Zhang, Christine Yoon, Tahmid Ahamed, Samantha Bhuiyan, Minxuan Cheng, Julie Karam, Kathleen M. Jagodnik, Ingrid Shu, Alexander Lachmann, Sam Ayling, Sherry L. Jenkins, Avi Ma'ayan
2021	J	`jnl`	Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning. Database J. Biol. Databases Curation Eryk Kropiwnicki, John Erol Evangelista, Daniel J. Stein, Daniel J. B. Clarke, Alexander Lachmann, Maxim V. Kuleshov, Minji Jeon, Kathleen M. Jagodnik, Avi Ma'ayan
2021	J	`jnl`	KEA3: improved kinase enrichment analysis via data integration. Nucleic Acids Res. Maxim V. Kuleshov, Zhuorui Xie, Alexandra B. K. London, Janice Yang, John Erol Evangelista, Alexander Lachmann, Ingrid Shu, Denis Torre, Avi Ma'ayan
2020	J	`jnl`	EnrichrBot: Twitter bot tracking tweets about human genes. Bioinform. Alon Bartal, Alexander Lachmann, Daniel J. B. Clarke, Allison H. Seiden, Kathleen M. Jagodnik, Avi Ma'ayan
2020	J	`jnl`	LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. Nucleic Acids Res. Vasileios Stathias, John Paul Turner, Amar Koleti, Dusica Vidovic, Daniel J. Cooper, Mehdi Fazel-Najafabadi, Marcin Pilarczyk, Raymond Terryn, Caty Chung, Afoma Umeano, Daniel J. B. Clarke, Alexander Lachmann, John Erol Evangelista, Avi Ma'ayan, Mario Medvedovic, Stephan C. Schürer
2020	J	`jnl`	The COVID-19 Drug and Gene Set Library. Patterns Maxim V. Kuleshov, Daniel J. Stein, Daniel J. B. Clarke, Eryk Kropiwnicki, Kathleen M. Jagodnik, Alon Bartal, John Erol Evangelista, Jason Hom, Minxuan Cheng, Allison Bailey, Abigail Zhou, Laura B. Ferguson, Alexander Lachmann, Avi Ma'ayan
2020	J	`jnl`	piNET: a versatile web platform for downstream analysis and visualization of proteomics data. Nucleic Acids Res. Behrouz Shamsaei, Szymon Chojnacki, Marcin Pilarczyk, Mehdi Fazel-Najafabadi, Wen Niu, Chuming Chen, Karen Ross, Andrea Matlock, Jeremy Muhlich, Somchai Chutipongtanate, Jie Zheng, John Turner, Dusica Vidovic, Jake Jaffe, Michael J. MacCoss, Cathy Wu, Ajay Pillai, Avi Ma'ayan, Stephan C. Schürer, Michal Kouril, Mario Medvedovic, Jarek Meller
2019	J	`jnl`	ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Res. Alexandra B. Keenan, Denis Torre, Alexander Lachmann, Ariel K. Leong, Megan L. Wojciechowicz, Vivian Utti, Kathleen M. Jagodnik, Eryk Kropiwnicki, Zichen Wang, Avi Ma'ayan
2019	J	`jnl`	Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures. Bioinform. Zichen Wang, Edward He, Kevin Sani, Kathleen M. Jagodnik, Moshe C. Silverstein, Avi Ma'ayan
2019	J	`jnl`	Geneshot: search engine for ranking genes from arbitrary text queries. Nucleic Acids Res. Alexander Lachmann, Brian M. Schilder, Megan L. Wojciechowicz, Denis Torre, Maxim V. Kuleshov, Alexandra B. Keenan, Avi Ma'ayan
2019	J	`jnl`	Predicting opioid dependence from electronic health records with machine learning. BioData Min. Randall J. Ellis, Zichen Wang, Nicholas Genes, Avi Ma'ayan
2019	J	`jnl`	modEnrichr: a suite of gene set enrichment analysis tools for model organisms. Nucleic Acids Res. Maxim V. Kuleshov, Jennifer E. L. Diaz, Zachary N. Flamholz, Alexandra B. Keenan, Alexander Lachmann, Megan L. Wojciechowicz, Ross L. Cagan, Avi Ma'ayan
2018	Misc	`conf`	Cell-specific prediction and application of drug-induced gene expression . PSB Rachel Hodos, Ping Zhang, Hao-Chih Lee, Qiaonan Duan, Zichen Wang, Neil R. Clark, Avi Ma'ayan, Fei Wang, Brian A. Kidd, Jianying Hu, David A. Sontag, Joel Dudley
2018	J	`jnl`	Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. Nucleic Acids Res. Amar Koleti, Raymond Terryn, Vasileios Stathias, Caty Chung, Daniel J. Cooper, John Paul Turner, Dusica Vidovic, Michele Forlin, Tanya T. Kelley, Alessandro D'Urso, Bryce K. Allen, Denis Torre, Kathleen M. Jagodnik, Lily Wang, Sherry L. Jenkins, Christopher Mader, Wen Niu, Mehdi Fazel, Naim Al Mahi, Marcin Pilarczyk, Nicholas A. Clark, Behrouz Shamsaei, Jarek Meller, Juozas Vasiliauskas, John Reichard, Mario Medvedovic, Avi Ma'ayan, Ajay Pillai, Stephan C. Schürer
2018	J	`jnl`	Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition. PLoS Comput. Biol. Simon Koplev, Katie Lin, Anders B. Dohlman, Avi Ma'ayan
2018	J	`jnl`	L1000FWD: fireworks visualization of drug-induced transcriptomic signatures. Bioinform. Zichen Wang, Alexander Lachmann, Alexandra B. Keenan, Avi Ma'ayan
2018	J	`jnl`	Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. Briefings Bioinform. Khader Shameer, Benjamin S. Glicksberg, Rachel Hodos, Kipp W. Johnson, Marcus A. Badgeley, Ben Readhead, Max S. Tomlinson, Timothy O'Connor, Riccardo Miotto, Brian A. Kidd, Rong Chen, Avi Ma'ayan, Joel T. Dudley
2018	—	`conf`	The Art of Connectivity Mapping. BCB Avi Ma'ayan
2018	J	`jnl`	eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks. Nucleic Acids Res. Daniel J. B. Clarke, Maxim V. Kuleshov, Brian M. Schilder, Denis Torre, Mary E. Duffy, Alexandra B. Keenan, Alexander Lachmann, Axel S. Feldmann, Gregory W. Gundersen, Moshe C. Silverstein, Zichen Wang, Avi Ma'ayan
2017	J	`jnl`	Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop. J. Biomed. Informatics Kathleen M. Jagodnik, Simon Koplev, Sherry L. Jenkins, Lucila Ohno-Machado, Benedict Paten, Stephan C. Schürer, Michel Dumontier, Ruben Verborgh, Alex A. T. Bui, Peipei Ping, Neil J. McKenna, Ravi K. Madduri, Ajay Pillai, Avi Ma'ayan
2017	J	`jnl`	Pharos: Collating protein information to shed light on the druggable genome. Nucleic Acids Res. Dac-Trung Nguyen, Stephen L. Mathias, Cristian Bologa, Søren Brunak, Nicolas F. Fernandez, Anna Gaulton, Anne Hersey, Jayme Holmes, Lars Juhl Jensen, Anneli Karlsson, Guixia Liu, Avi Ma'ayan, Geetha Mandava, Subramani Mani, Saurabh Mehta, John P. Overington, Juhee Patel, Andrew D. Rouillard, Stephan C. Schürer, Timothy Sheils, Anton Simeonov, Larry A. Sklar, Noel Southall, Oleg Ursu, Dusica Vidovic, Anna Waller, Jeremy J. Yang, Ajit Jadhav, Tudor I. Oprea, Rajarshi Guha
2017	J	`jnl`	Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age. J. Biomed. Informatics Zichen Wang, Li Li, Benjamin S. Glicksberg, Ariel Israel, Joel T. Dudley, Avi Ma'ayan
2016	J	`jnl`	An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study. F1000Research Zichen Wang, Avi Ma'ayan
2016	J	`jnl`	Drug-induced adverse events prediction with the LINCS L1000 data. Bioinform. Zichen Wang, Neil R. Clark, Avi Ma'ayan
2016	J	`jnl`	Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. Maxim V. Kuleshov, Matthew R. Jones, Andrew D. Rouillard, Nicolas F. Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L. Jenkins, Kathleen M. Jagodnik, Alexander Lachmann, Michael G. McDermott, Caroline D. Monteiro, Gregory W. Gundersen, Avi Ma'ayan
2016	J	`jnl`	GEN3VA: aggregation and analysis of gene expression signatures from related studies. BMC Bioinform. Gregory W. Gundersen, Kathleen M. Jagodnik, Holly Woodland, Nicolas F. Fernandez, Kevin Sani, Anders B. Dohlman, Peter Man-Un Ung, Caroline D. Monteiro, Avner Schlessinger, Avi Ma'ayan
2016	J	`jnl`	Large Collection of Diverse Gene Set Search Queries Recapitulate Known Protein-Protein Interactions and Gene-Gene Functional Associations. CoRR Avi Ma'ayan, Neil R. Clark
2016	J	`jnl`	The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database J. Biol. Databases Curation Andrew D. Rouillard, Gregory W. Gundersen, Nicolas F. Fernandez, Zichen Wang, Caroline D. Monteiro, Michael G. McDermott, Avi Ma'ayan
2015	J	`jnl`	Dynamics of the discovery process of protein-protein interactions from low content studies. BMC Syst. Biol. Zichen Wang, Neil R. Clark, Avi Ma'ayan
2015	J	`jnl`	GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions. Bioinform. Gregory W. Gundersen, Matthew R. Jones, Andrew D. Rouillard, Yan Kou, Caroline D. Monteiro, Axel S. Feldmann, Kevin S. Hu, Avi Ma'ayan
2015	—	`conf`	Principle Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool. BIBM Neil R. Clark, Maciej Szymkiewicz, Zichen Wang, Caroline D. Monteiro, Matthew R. Jones, Avi Ma'ayan
2015	J	`jnl`	Reprint of "Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction". Comput. Biol. Chem. Andrew D. Rouillard, Zichen Wang, Avi Ma'ayan
2014	J	`jnl`	Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells. PLoS Comput. Biol. Huilei Xu, Yen-Sin Ang, Ana Sevilla, Ihor Lemischka, Avi Ma'ayan
2014	J	`jnl`	Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets. Bioinform. Qiaonan Duan, Zichen Wang, Nicolas F. Fernandez, Andrew D. Rouillard, Christopher M. Tan, Cyril H. Benes, Avi Ma'ayan
2014	J	`jnl`	LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. Nucleic Acids Res. Qiaonan Duan, Corey Flynn, Mario Niepel, Marc Hafner, Jeremy Muhlich, Nicolas F. Fernandez, Andrew D. Rouillard, Christopher M. Tan, Edward Y. Chen, Todd R. Golub, Peter K. Sorger, Aravind Subramanian, Avi Ma'ayan
2014	J	`jnl`	The characteristic direction: a geometrical approach to identify differentially expressed genes. BMC Bioinform. Neil R. Clark, Kevin S. Hu, Axel S. Feldmann, Yan Kou, Edward Y. Chen, Qiaonan Duan, Avi Ma'ayan
2013	—	`conf`	ChEA2: Gene-Set Libraries from ChIP-X Experiments to Decode the Transcription Regulome. CD-ARES Yan Kou, Edward Y. Chen, Neil R. Clark, Qiaonan Duan, Christopher M. Tan, Avi Ma'ayan
2013	J	`jnl`	ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells. Database J. Biol. Databases Curation Huilei Xu, Caroline Baroukh, Ruth Dannenfelser, Edward Y. Chen, Christopher M. Tan, Yan Kou, Yujin E. Kim, Ihor Lemischka, Avi Ma'ayan
2013	J	`jnl`	Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinform. Edward Y. Chen, Christopher M. Tan, Yan Kou, Qiaonan Duan, Zichen Wang, Gabriela Vaz Meirelles, Neil R. Clark, Avi Ma'ayan
2013	J	`jnl`	Network2Canvas: network visualization on a canvas with enrichment analysis. Bioinform. Christopher M. Tan, Edward Y. Chen, Ruth Dannenfelser, Neil R. Clark, Avi Ma'ayan
2012	—	`conf`	Connecting clusters of patient to drug responses of cell lines to suggest personalized therapeutics for breast cancer. BIBM Workshops Simon Gordonov, Avi Ma'ayan
2012	J	`jnl`	Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. Bioinform. Edward Y. Chen, Huilei Xu, Simon Gordonov, Maribel P. Lim, Matthew H. Perkins, Avi Ma'ayan
2012	J	`jnl`	Genes2FANs: connecting genes through functional association networks. BMC Bioinform. Ruth Dannenfelser, Neil R. Clark, Avi Ma'ayan
2012	J	`jnl`	Sets2Networks: network inference from repeated observations of sets. BMC Syst. Biol. Neil R. Clark, Ruth Dannenfelser, Christopher M. Tan, Michael E. Komosinski, Avi Ma'ayan
2011	J	`jnl`	FNV: light-weight flash-based network and pathway viewer. Bioinform. Ruth Dannenfelser, Alexander Lachmann, Mariola Szenk, Avi Ma'ayan
2011	J	`jnl`	Genes2WordCloud: a quick way to identify biological themes from gene lists and free text. Source Code Biol. Medicine Caroline Baroukh, Sherry L. Jenkins, Ruth Dannenfelser, Avi Ma'ayan
2011	J	`jnl`	Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes. PLoS Comput. Biol. Amin R. Mazloom, Ruth Dannenfelser, Neil R. Clark, Arsen V. Grigoryan, Kathryn M. Linder, Timothy Cardozo, Julia C. Bond, Aislyn D. W. Boran, Ravi Iyengar, Anna Malovannaya, Rainer B. Lanz, Avi Ma'ayan
2011	J	`jnl`	Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format. Source Code Biol. Medicine Ryan L. Webb, Avi Ma'ayan
2011	—	`conf`	Visualization of Patient Samples by Dimensionality Reduction of Genome-Wide Measurements. USAB Huilei Xu, Avi Ma'ayan
2010	J	`jnl`	ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinform. Alexander Lachmann, Huilei Xu, Jayanth Krishnan, Seth I. Berger, Amin R. Mazloom, Avi Ma'ayan
2010	J	`jnl`	GATE: software for the analysis and visualization of high-dimensional time series expression data. Bioinform. Ben D. MacArthur, Alexander Lachmann, Ihor Lemischka, Avi Ma'ayan
2010	C	`conf`	Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome Network. BIBE Marylens Hernandez, Alexander Lachmann, Shan Zhao, Kunhong Xiao, Avi Ma'ayan
2010	J	`jnl`	Lists2Networks: Integrated analysis of gene/protein lists. BMC Bioinform. Alexander Lachmann, Avi Ma'ayan
2010	J	`jnl`	SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells. BMC Syst. Biol. Huilei Xu, Ihor Lemischka, Avi Ma'ayan
2009	J	`jnl`	KEA: kinase enrichment analysis. Bioinform. Alexander Lachmann, Avi Ma'ayan
2009	J	`jnl`	SNAVI: Desktop application for analysis and visualization of large-scale signaling networks. BMC Syst. Biol. Avi Ma'ayan, Sherry L. Jenkins, Ryan L. Webb, Seth I. Berger, Sudarshan P. Purushothaman, Noura S. Abul-Husn, Jeremy M. Posner, Tony Flores, Ravi Iyengar
2008	J	`jnl`	PubMedAlertMe - Standalone Windows-based PubMed SDI software application. Comput. Biol. Medicine Avi Ma'ayan
2007	J	`jnl`	AVIS: AJAX viewer of interactive signaling networks. Bioinform. Seth I. Berger, Ravi Iyengar, Avi Ma'ayan
2007	J	`jnl`	Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. BMC Bioinform. Seth I. Berger, Jeremy M. Posner, Avi Ma'ayan