Works matching AU Lachmann, Alexander

Results: 31

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

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

Playbook workflow builder: Interactive construction of bioinformatics workflows.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012901

By:

Clarke, Daniel J.B.;
Evangelista, John Erol;
Xie, Zhuorui;
Marino, Giacomo B.;
Byrd, Anna I.;
Maurya, Mano R.;
Srinivasan, Sumana;
Yu, Keyang;
Petrosyan, Varduhi;
Roth, Matthew E.;
Milinkov, Miroslav;
King, Charles Hadley;
Vora, Jeet Kiran;
Keeney, Jonathon;
Nemarich, Christopher;
Khan, William;
Lachmann, Alexander;
Ahmed, Nasheath;
Agris, Alexandra;
Pan, Juncheng

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

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

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

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

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

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

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

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

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

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

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

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

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