Alexander Lachmann

Alexander Lachmann

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Alexander Lachmann

Alexander Lachmann

Publications by authors named "Alexander Lachmann"

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

Nucleic Acids Res 2019 Jul;47(W1):W183-W190

Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA.

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http://dx.doi.org/10.1093/nar/gkz347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602483PMC
July 2019

Geneshot: search engine for ranking genes from arbitrary text queries.

Nucleic Acids Res 2019 Jul;47(W1):W571-W577

Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029 USA.

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http://dx.doi.org/10.1093/nar/gkz393DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602493PMC
July 2019

ChEA3: transcription factor enrichment analysis by orthogonal omics integration.

Nucleic Acids Res 2019 Jul;47(W1):W212-W224

Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA.

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http://dx.doi.org/10.1093/nar/gkz446DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602523PMC
July 2019

Mining data and metadata from the gene expression omnibus.

Biophys Rev 2019 Feb 29;11(1):103-110. Epub 2018 Dec 29.

BD2K-LINCS Data Coordination and Integration Center; Knowledge Management Center for the Illuminating the Druggable Genome; Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, Box 1603, One Gustave L. Levy Place, New York, NY, 10029, USA.

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http://dx.doi.org/10.1007/s12551-018-0490-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381352PMC
February 2019

Cooperative Transcription Factor Induction Mediates Hemogenic Reprogramming.

Cell Rep 2018 12;25(10):2821-2835.e7

Centre for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês do Pombal 3004-517, Coimbra, Portugal; Molecular Medicine and Gene Therapy, Lund Stem Cell Centre, Lund University, BMC A12, 221 84, Lund, Sweden; Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247183179
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http://dx.doi.org/10.1016/j.celrep.2018.11.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6571141PMC
December 2018

BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud.

Cell Syst 2018 11 14;7(5):556-561.e3. Epub 2018 Nov 14.

Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center (DCIC), Mount Sinai Center for Bioinformatics, Knowledge Management Center (KMC) for Illuminating the Druggable Genome (IDG), Team Nitrogen of the NIH Data Commons Pilot Project Consortium (DCPPC), Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S24054712183043
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http://dx.doi.org/10.1016/j.cels.2018.10.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265050PMC
November 2018

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

Nucleic Acids Res 2018 07;46(W1):W171-W179

DBD2K-LINCS Data Coordination and Integration Center; Knowledge Management Center for the Illuminating the Druggable Genome; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA.

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http://dx.doi.org/10.1093/nar/gky458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030863PMC
July 2018

L1000FWD: fireworks visualization of drug-induced transcriptomic signatures.

Bioinformatics 2018 06;34(12):2150-2152

Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454499PMC
June 2018

Massive mining of publicly available RNA-seq data from human and mouse.

Nat Commun 2018 04 10;9(1):1366. Epub 2018 Apr 10.

Department of Pharmacological Sciences; Mount Sinai Center for Bioinformatics; Big Data to Knowledge, Library of Integrated Network-based Cellular Signatures, Data Coordination and Integration Center (BD2K-LINCS DCIC); Knowledge Management Center for Illuminating the Druggable Genome (KMC-IDG), Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY, 10029, USA.

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http://dx.doi.org/10.1038/s41467-018-03751-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5893633PMC
April 2018

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

Sci Data 2018 02 27;5:180023. Epub 2018 Feb 27.

Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, BD2K-LINCS Data Coordination and Integration Center (DCIC), Team Nitrogen of the NIH Data Commons Pilot Project Consortium (DCPPC), Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA.

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http://dx.doi.org/10.1038/sdata.2018.23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5827688PMC
February 2018

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.

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

Cell Syst 2018 01 29;6(1):13-24. Epub 2017 Nov 29.

NIH, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1016/j.cels.2017.11.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5799026PMC
January 2018

Systematic, network-based characterization of therapeutic target inhibitors.

PLoS Comput Biol 2017 Oct 12;13(10):e1005599. Epub 2017 Oct 12.

Department of Systems Biology, Columbia University, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005599DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5638208PMC
October 2017

Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration.

Nat Neurosci 2016 10 15;19(10):1321-30. Epub 2016 Aug 15.

Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5088783PMC
http://dx.doi.org/10.1038/nn.4360DOI Listing
October 2016

Functional characterization of somatic mutations in cancer using network-based inference of protein activity.

Nat Genet 2016 08 20;48(8):838-47. Epub 2016 Jun 20.

Department of Systems Biology, Columbia University, New York, New York, USA.

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http://dx.doi.org/10.1038/ng.3593DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5040167PMC
August 2016

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

Nucleic Acids Res 2016 07 3;44(W1):W90-7. Epub 2016 May 3.

Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA

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http://dx.doi.org/10.1093/nar/gkw377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987924PMC
July 2016

ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information.

Bioinformatics 2016 07 23;32(14):2233-5. Epub 2016 Apr 23.

Department of Systems Biology, Columbia University, New York, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937200PMC
July 2016

Detection and removal of spatial bias in multiwell assays.

Bioinformatics 2016 07 28;32(13):1959-65. Epub 2016 Feb 28.

Department of Biomedical Informatics (DBMI) Department of Systems Biology Center for Computational Biology and Bioinformatics (C2B2), Columbia University, New York, NY, USA Department of Biochemistry and Molecular Biophysics Institute for Cancer Genetics Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw092DOI Listing
July 2016

FNV: light-weight flash-based network and pathway viewer.

Bioinformatics 2011 Apr 23;27(8):1181-2. Epub 2011 Feb 23.

Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btr098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072557PMC
April 2011

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments.

Bioinformatics 2010 Oct 13;26(19):2438-44. Epub 2010 Aug 13.

Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Mount Sinai School of Medicine, One Gustave Levy Place, New York, NY 10029, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq466DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2944209PMC
October 2010

Lists2Networks: integrated analysis of gene/protein lists.

BMC Bioinformatics 2010 Feb 12;11:87. Epub 2010 Feb 12.

Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA.

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http://dx.doi.org/10.1186/1471-2105-11-87DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2843617PMC
February 2010

GATE: software for the analysis and visualization of high-dimensional time series expression data.

Bioinformatics 2010 Jan 5;26(1):143-4. Epub 2009 Nov 5.

Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, New York, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp628DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796822PMC
January 2010

Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome Network.

Proc IEEE Int Symp Bioinformatics Bioeng 2010 ;2010:180-184

Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA.

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http://dx.doi.org/10.1109/BIBE.2010.75DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087296PMC
January 2010

KEA: kinase enrichment analysis.

Bioinformatics 2009 Mar 28;25(5):684-6. Epub 2009 Jan 28.

Department of Pharmacology and Systems Therapeutics, Systems Biology Center in New York, Icahn Medical Institute, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2647829PMC
March 2009