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eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks.
Published in:
Nucleic Acids Research, 2018, v. 46, n. W1, p. W171, doi. 10.1093/nar/gky458
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.;
- Zichen Wang;
- Ma’ayan, Avi
Publication type:
Article
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.
Published in:
Nucleic Acids Research, 2016, v. 44, n. W1, p. W90, doi. 10.1093/nar/gkw377
By:
- Kuleshov, Maxim V.;
- Jones, Matthew R.;
- Rouillard, Andrew D.;
- Fernandez, Nicolas F.;
- Qiaonan Duan;
- Zichen Wang;
- Koplev, Simon;
- Jenkins, Sherry L.;
- Jagodnik, Kathleen M.;
- Lachmann, Alexander;
- McDermott, Michael G.;
- Monteiro, Caroline D.;
- Gundersen, Gregory W.;
- Ma'ayan, Avi
Publication type:
Article
Integration of protein phosphorylation, acetylation, and methylation data sets to outline lung cancer signaling networks.
Published in:
Science Signaling, 2018, v. 11, n. 531, p. 1, doi. 10.1126/scisignal.aaq1087
By:
- Grimes, Mark;
- Hall, Benjamin;
- Foltz, Lauren;
- Levy, Tyler;
- Rikova, Klarisa;
- Gaiser, Jeremiah;
- Cook, William;
- Smirnova, Ekaterina;
- Wheeler, Travis;
- Clark, Neil R.;
- Lachmann, Alexander;
- Zhang, Bin;
- Hornbeck, Peter;
- Ma'ayan, Avi;
- Comb, Michael
Publication type:
Article
Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses.
Published in:
Nature Biotechnology, 2021, v. 39, n. 2, p. 215, doi. 10.1038/s41587-020-0652-7
By:
- Broyde, Joshua;
- Simpson, David R.;
- Murray, Diana;
- Paull, Evan O.;
- Chu, Brennan W.;
- Tagore, Somnath;
- Jones, Sunny J.;
- Griffin, Aaron T.;
- Giorgi, Federico M.;
- Lachmann, Alexander;
- Jackson, Peter;
- Sweet-Cordero, E. Alejandro;
- Honig, Barry;
- Califano, Andrea
Publication type:
Article
blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation.
Published in:
Bioinformatics, 2022, v. 38, n. 8, p. 2356, doi. 10.1093/bioinformatics/btac076
By:
- Lachmann, Alexander;
- Xie, Zhuorui;
- Ma'ayan, Avi
Publication type:
Article
Receptor Heteromerization Expands the Repertoire of Cannabinoid Signaling in Rodent Neurons.
Published in:
PLoS ONE, 2012, v. 7, n. 1, p. 1, doi. 10.1371/journal.pone.0029239
By:
- Rozenfeld, Raphael;
- Bushlin, Ittai;
- Gomes, Ivone;
- Tzavaras, Nikos;
- Gupta, Achla;
- Neves, Susana;
- Battini, Lorenzo;
- Gusella, G. Luca;
- Lachmann, Alexander;
- Ma'ayan, Avi;
- Blitzer, Robert D.;
- Devi, Lakshmi A.
Publication type:
Article
lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs.
Published in:
Database: The Journal of Biological Databases & Curation, 2023, v. 2023, p. 1, doi. 10.1093/database/baad009
By:
- Marino, Giacomo B;
- Wojciechowicz, Megan L;
- Clarke, Daniel J B;
- Kuleshov, Maxim V;
- Xie, Zhuorui;
- Jeon, Minji;
- Lachmann, Alexander;
- Ma'ayan, Avi
Publication type:
Article
Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning.
Published in:
Database: The Journal of Biological Databases & Curation, 2021, v. 2021, p. 1, doi. 10.1093/database/baab017
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
Publication type:
Article
Lists2Networks: Integrated analysis ofgene/protein lists.
Published in:
BMC Bioinformatics, 2010, v. 11, p. 87, doi. 10.1186/1471-2105-11-87
By:
- Lachmann, Alexander;
- Ma'ayan, Avi
Publication type:
Article
Systems-level dynamic analyses of fate change in murine embryonic stem cells.
Published in:
Nature, 2009, v. 462, n. 7271, p. 358, doi. 10.1038/nature08575
By:
- Lu, Rong;
- Markowetz, Florian;
- Unwin, Richard D.;
- Leek, Jeffrey T.;
- Airoldi, Edoardo M.;
- MacArthur, Ben D.;
- Lachmann, Alexander;
- Rozov, Roye;
- Ma'ayan, Avi;
- Boyer, Laurie A.;
- Troyanskaya, Olga G.;
- Whetton, Anthony D.;
- Lemischka, Ihor R.
Publication type:
Article
SigCom LINCS: data and metadata search engine for a million gene expression signatures.
Published in:
Nucleic Acids Research, 2022, v. 50, n. W1, p. W697, doi. 10.1093/nar/gkac328
By:
- Evangelista, John Erol;
- Clarke, Daniel J B;
- Xie, Zhuorui;
- Lachmann, Alexander;
- Jeon, Minji;
- Chen, Kerwin;
- Jagodnik, Kathleen M;
- Jenkins, Sherry L;
- Kuleshov, Maxim V;
- Wojciechowicz, Megan L;
- Schürer, Stephan C;
- Medvedovic, Mario;
- Ma'ayan, Avi
Publication type:
Article
KEA3: improved kinase enrichment analysis via data integration.
Published in:
Nucleic Acids Research, 2021, v. 49, n. W1, p. W304, doi. 10.1093/nar/gkab359
By:
- Kuleshov, Maxim V;
- Xie, Zhuorui;
- London, Alexandra B K;
- Yang, Janice;
- Evangelista, John Erol;
- Lachmann, Alexander;
- Shu, Ingrid;
- Torre, Denis;
- Ma'ayan, Avi
Publication type:
Article
LINCS Data Portal 2.0: next generation access point for perturbation-response signatures.
Published in:
Nucleic Acids Research, 2020, v. 48, n. D1, p. D431, doi. 10.1093/nar/gkz1023
By:
- Stathias, Vasileios;
- Turner, John;
- Koleti, Amar;
- Vidovic, Dusica;
- Cooper, Daniel;
- Fazel-Najafabadi, Mehdi;
- Pilarczyk, Marcin;
- Terryn, Raymond;
- Chung, Caty;
- Umeano, Afoma;
- Clarke, Daniel J B;
- Lachmann, Alexander;
- Evangelista, John Erol;
- Ma'ayan, Avi;
- Medvedovic, Mario;
- Schürer, Stephan C
Publication type:
Article
ChEA3: transcription factor enrichment analysis by orthogonal omics integration.
Published in:
Nucleic Acids Research, 2019, v. 47, n. W1, p. W212, doi. 10.1093/nar/gkz446
By:
- Keenan, Alexandra B;
- Torre, Denis;
- Lachmann, Alexander;
- Leong, Ariel K;
- Wojciechowicz, Megan L;
- Utti, Vivian;
- Jagodnik, Kathleen M;
- Kropiwnicki, Eryk;
- Wang, Zichen;
- Ma'ayan, Avi
Publication type:
Article
Geneshot: search engine for ranking genes from arbitrary text queries.
Published in:
Nucleic Acids Research, 2019, v. 47, n. W1, p. W571, doi. 10.1093/nar/gkz393
By:
- Lachmann, Alexander;
- Schilder, Brian M;
- Wojciechowicz, Megan L;
- Torre, Denis;
- Kuleshov, Maxim V;
- Keenan, Alexandra B;
- Ma'ayan, Avi
Publication type:
Article
modEnrichr: a suite of gene set enrichment analysis tools for model organisms.
Published in:
Nucleic Acids Research, 2019, v. 47, n. W1, p. W183, doi. 10.1093/nar/gkz347
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
Publication type:
Article
Massive mining of publicly available RNA-seq data from human and mouse.
Published in:
Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-03751-6
By:
- Lachmann, Alexander;
- Torre, Denis;
- Keenan, Alexandra B.;
- Jagodnik, Kathleen M.;
- Lee, Hoyjin J.;
- Lily Wang;
- Silverstein, Moshe C.;
- Ma’ayan, Avi
Publication type:
Article
D2H2: diabetes data and hypothesis hub.
Published in:
Bioinformatics Advances, 2023, v. 3, n. 1, p. 1, doi. 10.1093/bioadv/vbad178
By:
- Marino, Giacomo B;
- Ahmed, Nasheath;
- Xie, Zhuorui;
- Jagodnik, Kathleen M;
- Han, Jason;
- Clarke, Daniel J B;
- Lachmann, Alexander;
- Keller, Mark P;
- Attie, Alan D;
- Ma'ayan, Avi
Publication type:
Article
Getting Started with LINCS Datasets and Tools.
Published in:
Current Protocols, 2022, v. 2, n. 7, p. 1, doi. 10.1002/cpz1.487
By:
- Xie, Zhuorui;
- Kropiwnicki, Eryk;
- Wojciechowicz, Megan L.;
- Jagodnik, Kathleen M.;
- Shu, Ingrid;
- Bailey, Allison;
- Clarke, Daniel J. B.;
- Jeon, Minji;
- Evangelista, John Erol;
- V. Kuleshov, Maxim;
- Lachmann, Alexander;
- Parigi, Abhijna A.;
- Sanchez, Jose M.;
- Jenkins, Sherry L.;
- Ma'ayan, Avi
Publication type:
Article
Getting Started with the IDG KMC Datasets and Tools.
Published in:
Current Protocols, 2022, v. 2, n. 1, p. 1, doi. 10.1002/cpz1.355
By:
- Kropiwnicki, Eryk;
- Binder, Jessica L.;
- Yang, Jeremy J.;
- Holmes, Jayme;
- Lachmann, Alexander;
- Clarke, Daniel J. B.;
- Sheils, Timothy;
- Kelleher, Keith J.;
- Metzger, Vincent T.;
- Bologa, Cristian G.;
- Oprea, Tudor I.;
- Ma'ayan, Avi
Publication type:
Article
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules.
Published in:
BMC Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s12859-022-04590-5
By:
- Kropiwnicki, Eryk;
- Lachmann, Alexander;
- Clarke, Daniel J. B.;
- Xie, Zhuorui;
- Jagodnik, Kathleen M.;
- Ma'ayan, Avi
Publication type:
Article
EnrichrBot: Twitter bot tracking tweets about human genes.
Published in:
Bioinformatics, 2020, v. 36, n. 12, p. 3932, doi. 10.1093/bioinformatics/btaa240
By:
- Bartal, Alon;
- Lachmann, Alexander;
- Clarke, Daniel J B;
- Seiden, Allison H;
- Jagodnik, Kathleen M;
- Ma'ayan, Avi
Publication type:
Article
L1000FWD: fireworks visualization of drug-induced transcriptomic signatures.
Published in:
Bioinformatics, 2018, v. 34, n. 12, p. 2150, doi. 10.1093/bioinformatics/bty060
By:
- Wang, Zichen;
- Lachmann, Alexander;
- Keenan, Alexandra B;
- Ma'ayan, Avi
Publication type:
Article
ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information.
Published in:
Bioinformatics, 2016, v. 32, n. 14, p. 2233, doi. 10.1093/bioinformatics/btw216
By:
- Lachmann, Alexander;
- Giorgi, Federico M.;
- Lopez, Gonzalo;
- Califano, Andrea
Publication type:
Article
Detection and removal of spatial bias in multiwell assays.
Published in:
Bioinformatics, 2016, v. 32, n. 13, p. 1959, doi. 10.1093/bioinformatics/btw092
By:
- Lachmann, Alexander;
- Giorgi, Federico M.;
- Alvarez, Mariano J.;
- Califano, Andrea
Publication type:
Article
FNV: light-weight flash-based network and pathway viewer.
Published in:
Bioinformatics, 2011, v. 27, n. 8, p. 1181, doi. 10.1093/bioinformatics/btr098
By:
- Dannenfelser, Ruth;
- Lachmann, Alexander;
- Szenk, Mariola;
- Ma'ayan, Avi
Publication type:
Article
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments.
Published in:
Bioinformatics, 2010, v. 26, n. 19, p. 2438, doi. 10.1093/bioinformatics/btq466
By:
- Lachmann, Alexander;
- Huilei Xu;
- Krishnan, Jayanth;
- Berger, Seth I.;
- Mazloom, Amin R.;
- Ma'ayan, Avi
Publication type:
Article
GATE: software for the analysis and visualization of high-dimensional time series expression data.
Published in:
Bioinformatics, 2010, v. 26, n. 1, p. 143, doi. 10.1093/bioinformatics/btp628
By:
- MacArthur, Ben D.;
- Lachmann, Alexander;
- Lemischka, Ihor R.;
- Ma'ayan, Avi
Publication type:
Article
KEA: kinase enrichment analysis.
Published in:
Bioinformatics, 2009, v. 25, n. 5, p. 684, doi. 10.1093/bioinformatics/btp026
By:
- Alexander Lachmann;
- Avi Maayan
Publication type:
Article
Systematic, network-based characterization of therapeutic target inhibitors.
Published in:
PLoS Computational Biology, 2017, v. 13, n. 10, p. 1, doi. 10.1371/journal.pcbi.1005599
By:
- Shen, Yao;
- Alvarez, Mariano J.;
- Bisikirska, Brygida;
- Lachmann, Alexander;
- Realubit, Ronald;
- Pampou, Sergey;
- Coku, Jorida;
- Karan, Charles;
- Califano, Andrea
Publication type:
Article

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