Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses

by Torre, Denis, Krawczuk, Patrycja, Jagodnik, Kathleen M., Lachmann, Alexander, Wang, Zichen, Wang, Lily, Kuleshov, Maxim V., Ma’ayan, Avi
Published in Sci Data (2018)

Geneshot: search engine for ranking genes from arbitrary text queries

by Lachmann, Alexander, Schilder, Brian M, Wojciechowicz, Megan L, Torre, Denis, Kuleshov, Maxim V, Keenan, Alexandra B, Ma’ayan, Avi
Published in Nucleic Acids Res (2019)

KEA3: improved kinase enrichment analysis via data integration

by Kuleshov, Maxim V, Xie, Zhuorui, London, Alexandra B K, Yang, Janice, Evangelista, John Erol, Lachmann, Alexander, Shu, Ingrid, Torre, Denis, Ma’ayan, Avi
Published in Nucleic Acids Res (2021)

modEnrichr: a suite of gene set enrichment analysis tools for model organisms

by Kuleshov, Maxim V, Diaz, Jennifer E L, Flamholz, Zachary N, Keenan, Alexandra B, Lachmann, Alexander, Wojciechowicz, Megan L, Cagan, Ross L, Ma’ayan, Avi
Published in Nucleic Acids Res (2019)

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

by Kropiwnicki, Eryk, Evangelista, John E, Stein, Daniel J, Clarke, Daniel J B, Lachmann, Alexander, Kuleshov, Maxim V, Jeon, Minji, Jagodnik, Kathleen M, Ma’ayan, Avi
Published in Database (Oxford) (2021)

The COVID-19 Gene and Drug Set Library

by Kuleshov, Maxim V., Clarke, Daniel J.B., Kropiwnicki, Eryk, Jagodnik, Kathleen M., Bartal, Alon, Evangelista, John E., Zhou, Abigail, Ferguson, Laura B., Lachmann, Alexander, Ma’ayan, Avi
Published in Res Sq (2020)

Gene Set Knowledge Discovery with Enrichr

by Xie, Zhuorui, Bailey, Allison, Kuleshov, Maxim V., Clarke, Daniel J.B., Evangelista, John E., Jenkins, Sherry L., Lachmann, Alexander, Wojciechowicz, Megan L., Kropiwnicki, Eryk, Jagodnik, Kathleen M., Jeon, Minji, Ma’ayan, Avi
Published in Curr Protoc (2021)

eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks

by Clarke, Daniel J B, Kuleshov, Maxim V, Schilder, Brian M, Torre, Denis, Duffy, Mary E, Keenan, Alexandra B, Lachmann, Alexander, Feldmann, Axel S, Gundersen, Gregory W, Silverstein, Moshe C, Wang, Zichen, Ma’ayan, Avi
Published in Nucleic Acids Res (2018)

The COVID-19 Drug and Gene Set Library

by Kuleshov, Maxim V., Stein, Daniel J., Clarke, Daniel J.B., Kropiwnicki, Eryk, Jagodnik, Kathleen M., Bartal, Alon, Evangelista, John E., Hom, Jason, Cheng, Minxuan, Bailey, Allison, Zhou, Abigail, Ferguson, Laura B., Lachmann, Alexander, Ma'ayan, Avi
Published in Patterns (N Y) (2020)

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

by Kuleshov, Maxim V., Jones, Matthew R., Rouillard, Andrew D., Fernandez, Nicolas F., Duan, Qiaonan, Wang, Zichen, Koplev, Simon, Jenkins, Sherry L., Jagodnik, Kathleen M., Lachmann, Alexander, McDermott, Michael G., Monteiro, Caroline D., Gundersen, Gregory W., Ma'ayan, Avi
Published in Nucleic Acids Res (2016)

The Library of Integrated Network-based Cellular Signatures (LINCS) NIH Program: System-level Cataloging of Human Cells Response to Perturbations

by Keenan, Alexandra B., Jenkins, Sherry L., Jagodnik, Kathleen M., Koplev, Simon, He, Edward, Torre, Denis, Wang, Zichen, Dohlman, Anders B., Silverstein, Moshe C., Lachmann, Alexander, Kuleshov, Maxim V., Ma’ayan, Avi, Stathias, Vasileios, Terryn, Raymond, Cooper, Daniel, Forlin, Michele, Koleti, Amar, Vidovic, Dusica, Chung, Caty, Schürer, Stephan C., Vasiliauskas, Jouzas, Pilarczyk, Marcin, Shamsaei, Behrouz, Fazel, Mehdi, Ren, Yan, Niu, Wen, Clark, Nicholas A., White, Shana, Mahi, Naim, Zhang, Lixia, Kouril, Michal, Reichard, John F., Sivaganesan, Siva, Medvedovic, Mario, Meller, Jaroslaw, Koch, Rick J., Birtwistle, Marc R., Iyengar, Ravi, Sobie, Eric A., Azeloglu, Evren, Kaye, Julia, Osterloh, Jeannette, Haston, Kelly, Kalra, Jaslin, Finkbiener, Steve M., Li, Jonathan, Milani, Pamela, Adam, Miriam, Escalante, Renan, Sachs, Karen, Lenail, Alex, Ramamoorthy, Divya, Fraenkel, Ernest, Daigle, Gavin, Hussain, Uzma, Coye, Alyssa, Rothstein, Jeffrey, Sareen, Dhruv, Ornelas, Loren, Banuelos, Maria, Mandefro, Berhan, Ho, Ritchie, Svendsen, Clive N., Lim, Ryan, Stocksdale, Jennifer, Casale, Malcolm, Thompson, Terri, Wu, Jenny, Thompson, Leslie M., Dardov, Victoria, Venkatraman, Vidya, Matlock, Andrea, Van Eyk, Jenny, Jaffe, Jacob D., Papanastasiou, Malvina, Subramanian, Aravind, Golub, Todd R., Erickson, Sean D., Fallahi-Sichani, Mohammad, Hafner, Marc, Gray, Nathanael S., Lin, Jia-Ren, Mills, Caitlin E., Muhlich, Jeremy L., Niepel, Mario, Shamu, Caroline E., Williams, Elizabeth H., Wrobel, David, Sorger, Peter K., Heiser, Laura M., Gray, Joe W., Korkola, James E., Mills, Gordon B., LaBarge, Mark, Feiler, Heidi S., Dane, Mark A., Bucher, Elmar, Nederlof, Michel, Sudar, Damir, Gross, Sean, Kilburn, David F., Smith, Rebecca, Devlin, Kaylyn, Margolis, Ron, Derr, Leslie, Lee, Albert, Pilai, Ajay
Published in Cell Syst (2017)