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Avi Ma'ayan
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2020 – today
- 2023
- [j57]Giacomo B. Marino
, Megan L. Wojciechowicz, Daniel J. B. Clarke
, Maxim V. Kuleshov
, Zhuorui Xie, Minji Jeon, Alexander Lachmann
, Avi Ma'ayan
:
lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs. Database J. Biol. Databases Curation 2023 (2023) - [j56]John Erol Evangelista
, Zhuorui Xie, Giacomo B. Marino
, Nhi Nguyen, Daniel J. B. Clarke
, Avi Ma'ayan
:
Enrichr-KG: bridging enrichment analysis across multiple libraries. Nucleic Acids Res. 51(W1): 168-179 (2023) - [j55]Giacomo B. Marino
, Michael Ngai, Daniel J. B. Clarke
, Reid H. Fleishman, Eden Z. Deng, Zhuorui Xie, Nasheath Ahmed, Avi Ma'ayan
:
GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery. Nucleic Acids Res. 51(W1): 213-224 (2023) - 2022
- [j54]Alexander Lachmann
, Zhuorui Xie
, Avi Ma'ayan
:
blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation. Bioinform. 38(8): 2356-2357 (2022) - [j53]Eryk Kropiwnicki, Alexander Lachmann, Daniel J. B. Clarke
, Zhuorui Xie, Kathleen M. Jagodnik, Avi Ma'ayan
:
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. BMC Bioinform. 23(1): 76 (2022) - [j52]Minji Jeon, Zhuorui Xie, John Erol Evangelista, Megan L. Wojciechowicz, Daniel J. B. Clarke
, Avi Ma'ayan:
Transforming L1000 profiles to RNA-seq-like profiles with deep learning. BMC Bioinform. 23(1): 374 (2022) - [j51]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
:
SigCom LINCS: data and metadata search engine for a million gene expression signatures. Nucleic Acids Res. 50(W1): 697-709 (2022) - 2021
- [j50]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:
Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning. Database J. Biol. Databases Curation 2021 (2021) - [j49]Maxim V. Kuleshov, Zhuorui Xie, Alexandra B. K. London, Janice Yang
, John Erol Evangelista
, Alexander Lachmann
, Ingrid Shu, Denis Torre, Avi Ma'ayan
:
KEA3: improved kinase enrichment analysis via data integration. Nucleic Acids Res. 49(Webserver-Issue): 304-316 (2021) - [j48]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
:
Appyters: Turning Jupyter Notebooks into data-driven web apps. Patterns 2(3): 100213 (2021) - 2020
- [j47]Alon Bartal, Alexander Lachmann, Daniel J. B. Clarke
, Allison H. Seiden, Kathleen M. Jagodnik, Avi Ma'ayan
:
EnrichrBot: Twitter bot tracking tweets about human genes. Bioinform. 36(12): 3932-3934 (2020) - [j46]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
:
LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. Nucleic Acids Res. 48(Database-Issue): D431-D439 (2020) - [j45]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
:
piNET: a versatile web platform for downstream analysis and visualization of proteomics data. Nucleic Acids Res. 48(Webserver-Issue): W85-W93 (2020) - [j44]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:
The COVID-19 Drug and Gene Set Library. Patterns 1(6): 100090 (2020)
2010 – 2019
- 2019
- [j43]Randall J. Ellis
, Zichen Wang
, Nicholas Genes, Avi Ma'ayan
:
Predicting opioid dependence from electronic health records with machine learning. BioData Min. 12(1): 3:1-3:19 (2019) - [j42]Zichen Wang
, Edward He, Kevin Sani, Kathleen M. Jagodnik, Moshe C. Silverstein, Avi Ma'ayan
:
Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures. Bioinform. 35(7): 1247-1248 (2019) - [j41]Maxim V. Kuleshov
, Jennifer E. L. Diaz, Zachary N. Flamholz
, Alexandra B. Keenan, Alexander Lachmann, Megan L. Wojciechowicz, Ross L. Cagan
, Avi Ma'ayan
:
modEnrichr: a suite of gene set enrichment analysis tools for model organisms. Nucleic Acids Res. 47(Webserver-Issue): W183-W190 (2019) - [j40]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
:
ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Res. 47(Webserver-Issue): W212-W224 (2019) - [j39]Alexander Lachmann, Brian M. Schilder, Megan L. Wojciechowicz, Denis Torre
, Maxim V. Kuleshov
, Alexandra B. Keenan, Avi Ma'ayan
:
Geneshot: search engine for ranking genes from arbitrary text queries. Nucleic Acids Res. 47(Webserver-Issue): W571-W577 (2019) - 2018
- [j38]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:
Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. Briefings Bioinform. 19(4): 656-678 (2018) - [j37]Zichen Wang
, Alexander Lachmann, Alexandra B. Keenan, Avi Ma'ayan
:
L1000FWD: fireworks visualization of drug-induced transcriptomic signatures. Bioinform. 34(12): 2150-2152 (2018) - [j36]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
:
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. 46(Database-Issue): D558-D566 (2018) - [j35]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
:
eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks. Nucleic Acids Res. 46(Webserver-Issue): W171-W179 (2018) - [j34]Simon Koplev
, Katie Lin, Anders B. Dohlman, Avi Ma'ayan
:
Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition. PLoS Comput. Biol. 14(1) (2018) - [c7]Avi Ma'ayan:
The Art of Connectivity Mapping. BCB 2018: 563 - [c6]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:
Cell-specific prediction and application of drug-induced gene expression . PSB 2018: 32-43 - 2017
- [j33]Kathleen M. Jagodnik, Simon Koplev
, Sherry L. Jenkins
, Lucila Ohno-Machado, Benedict Paten, Stephan C. Schürer, Michel Dumontier
, Ruben Verborgh
, Alex Bui, Peipei Ping, Neil J. McKenna, Ravi K. Madduri
, Ajay Pillai
, Avi Ma'ayan
:
Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop. J. Biomed. Informatics 71: 49-57 (2017) - [j32]Zichen Wang
, Li Li
, Benjamin S. Glicksberg
, Ariel Israel
, Joel T. Dudley, Avi Ma'ayan
:
Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age. J. Biomed. Informatics 76: 59-68 (2017) - [j31]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:
Pharos: Collating protein information to shed light on the druggable genome. Nucleic Acids Res. 45(Database-Issue): D995-D1002 (2017) - 2016
- [j30]Andrew D. Rouillard
, Gregory W. Gundersen, Nicolas F. Fernandez, Zichen Wang
, Caroline D. Monteiro, Michael G. McDermott, Avi Ma'ayan
:
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database J. Biol. Databases Curation 2016 (2016) - [j29]Zichen Wang, Neil R. Clark, Avi Ma'ayan
:
Drug-induced adverse events prediction with the LINCS L1000 data. Bioinform. 32(15): 2338-2345 (2016) - [j28]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
:
GEN3VA: aggregation and analysis of gene expression signatures from related studies. BMC Bioinform. 17: 461:1-461:12 (2016) - [j27]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
:
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 44(Webserver-Issue): W90-W97 (2016) - [i2]Avi Ma'ayan, Neil R. Clark:
Large Collection of Diverse Gene Set Search Queries Recapitulate Known Protein-Protein Interactions and Gene-Gene Functional Associations. CoRR abs/1601.01653 (2016) - [i1]Zichen Wang
, Avi Ma'ayan
:
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study. F1000Research 5: 1574 (2016) - 2015
- [j26]Gregory W. Gundersen, Matthew R. Jones, Andrew D. Rouillard
, Yan Kou, Caroline D. Monteiro, Axel S. Feldmann, Kevin S. Hu
, Avi Ma'ayan
:
GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions. Bioinform. 31(18): 3060-3062 (2015) - [j25]Zichen Wang
, Neil R. Clark
, Avi Ma'ayan
:
Dynamics of the discovery process of protein-protein interactions from low content studies. BMC Syst. Biol. 9: 26 (2015) - [j24]Andrew D. Rouillard
, Zichen Wang
, Avi Ma'ayan
:
Reprint of "Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction". Comput. Biol. Chem. 59: 123-138 (2015) - [c5]Neil R. Clark
, Maciej Szymkiewicz
, Zichen Wang, Caroline D. Monteiro, Matthew R. Jones, Avi Ma'ayan
:
Principle Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool. BIBM 2015: 256-262 - 2014
- [j23]Qiaonan Duan, Zichen Wang
, Nicolas F. Fernandez, Andrew D. Rouillard
, Christopher M. Tan, Cyril H. Benes, Avi Ma'ayan
:
Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets. Bioinform. 30(22): 3289-3290 (2014) - [j22]Neil R. Clark
, Kevin S. Hu
, Axel S. Feldmann, Yan Kou, Edward Y. Chen, Qiaonan Duan, Avi Ma'ayan
:
The characteristic direction: a geometrical approach to identify differentially expressed genes. BMC Bioinform. 15: 79 (2014) - [j21]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
:
LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. Nucleic Acids Res. 42(Webserver-Issue): 449-460 (2014) - [j20]Huilei Xu, Yen-Sin Ang, Ana Sevilla
, Ihor Lemischka, Avi Ma'ayan
:
Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells. PLoS Comput. Biol. 10(8) (2014) - 2013
- [j19]Huilei Xu, Caroline Baroukh
, Ruth Dannenfelser
, Edward Y. Chen, Christopher M. Tan, Yan Kou, Yujin E. Kim, Ihor Lemischka, Avi Ma'ayan
:
ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells. Database J. Biol. Databases Curation 2013 (2013) - [j18]Christopher M. Tan, Edward Y. Chen, Ruth Dannenfelser
, Neil R. Clark
, Avi Ma'ayan
:
Network2Canvas: network visualization on a canvas with enrichment analysis. Bioinform. 29(15): 1872-1878 (2013) - [j17]Edward Y. Chen, Christopher M. Tan, Yan Kou, Qiaonan Duan, Zichen Wang
, Gabriela Vaz Meirelles
, Neil R. Clark
, Avi Ma'ayan
:
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinform. 14: 128 (2013) - [c4]Yan Kou, Edward Y. Chen, Neil R. Clark, Qiaonan Duan, Christopher M. Tan, Avi Ma'ayan
:
ChEA2: Gene-Set Libraries from ChIP-X Experiments to Decode the Transcription Regulome. CD-ARES 2013: 416-430 - 2012
- [j16]Edward Y. Chen, Huilei Xu, Simon Gordonov, Maribel P. Lim, Matthew H. Perkins
, Avi Ma'ayan
:
Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. Bioinform. 28(1): 105-111 (2012) - [j15]Ruth Dannenfelser
, Neil R. Clark
, Avi Ma'ayan
:
Genes2FANs: connecting genes through functional association networks. BMC Bioinform. 13: 156 (2012) - [j14]Neil R. Clark
, Ruth Dannenfelser
, Christopher M. Tan, Michael E. Komosinski, Avi Ma'ayan
:
Sets2Networks: network inference from repeated observations of sets. BMC Syst. Biol. 6: 89 (2012) - [c3]Simon Gordonov, Avi Ma'ayan
:
Connecting clusters of patient to drug responses of cell lines to suggest personalized therapeutics for breast cancer. BIBM Workshops 2012: 529-534 - 2011
- [j13]Ruth Dannenfelser
, Alexander Lachmann, Mariola Szenk
, Avi Ma'ayan
:
FNV: light-weight flash-based network and pathway viewer. Bioinform. 27(8): 1181-1182 (2011) - [j12]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
:
Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes. PLoS Comput. Biol. 7(12) (2011) - [j11]Ryan L. Webb, Avi Ma'ayan
:
Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format. Source Code Biol. Medicine 6: 5 (2011) - [j10]Caroline Baroukh
, Sherry L. Jenkins
, Ruth Dannenfelser
, Avi Ma'ayan
:
Genes2WordCloud: a quick way to identify biological themes from gene lists and free text. Source Code Biol. Medicine 6: 15 (2011) - [c2]Huilei Xu, Avi Ma'ayan
:
Visualization of Patient Samples by Dimensionality Reduction of Genome-Wide Measurements. USAB 2011: 15-22 - 2010
- [j9]Ben D. MacArthur
, Alexander Lachmann, Ihor Lemischka, Avi Ma'ayan
:
GATE: software for the analysis and visualization of high-dimensional time series expression data. Bioinform. 26(1): 143-144 (2010) - [j8]Alexander Lachmann, Huilei Xu, Jayanth Krishnan, Seth I. Berger
, Amin R. Mazloom, Avi Ma'ayan
:
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinform. 26(19): 2438-2444 (2010) - [j7]Alexander Lachmann, Avi Ma'ayan
:
Lists2Networks: Integrated analysis of gene/protein lists. BMC Bioinform. 11: 87 (2010) - [j6]Huilei Xu, Ihor Lemischka, Avi Ma'ayan
:
SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells. BMC Syst. Biol. 4: 173 (2010) - [c1]Marylens Hernandez, Alexander Lachmann, Shan Zhao, Kunhong Xiao, Avi Ma'ayan
:
Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome Network. BIBE 2010: 180-184
2000 – 2009
- 2009
- [j5]Alexander Lachmann, Avi Ma'ayan
:
KEA: kinase enrichment analysis. Bioinform. 25(5): 684-686 (2009) - [j4]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:
SNAVI: Desktop application for analysis and visualization of large-scale signaling networks. BMC Syst. Biol. 3: 10 (2009) - 2008
- [j3]Avi Ma'ayan
:
PubMedAlertMe - Standalone Windows-based PubMed SDI software application. Comput. Biol. Medicine 38(5): 620-622 (2008) - 2007
- [j2]Seth I. Berger
, Ravi Iyengar, Avi Ma'ayan
:
AVIS: AJAX viewer of interactive signaling networks. Bioinform. 23(20): 2803-2805 (2007) - [j1]Seth I. Berger
, Jeremy M. Posner, Avi Ma'ayan
:
Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. BMC Bioinform. 8 (2007)
Coauthor Index
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