Alexander Lachmann

28 papers C 1Journal 27
YearRankTypeTitle / Venue / Authors
2025 J jnl
Playbook workflow builder: Interactive construction of bioinformatics workflows.
PLoS Comput. Biol.
Daniel J. B. Clarke, John Erol Evangelista, Zhuorui Xie, Giacomo B. Marino, Anna I. Byrd, Mano Ram Maurya, Sumana Srinivasan, Keyang Yu, Varduhi Petrosyan, Matthew E. Roth, Miroslav Milinkov, Charles Hadley King, Jeet Kiran Vora, Jonathon Keeney, Christopher Nemarich, William Khan, Alexander Lachmann, Nasheath Ahmed, Alexandra Agris, Juncheng Pan, Srinivasan Ramachandran, Eoin Fahy, Emmanuel Esquivel, Aleksandar Mihajlovic, Bosko Jevtic, Vuk Milinovic, Sean Kim, Patrick McNeely, Tianyi Wang, Eric Wenger, Miguel A. Brown, Alexander Sickler, Yuankun Zhu, Sherry L. Jenkins, Philip D. Blood, Deanne M. Taylor, Adam C. Resnick, Raja Mazumder, Aleksandar Milosavljevic, Shankar Subramaniam, Avi Ma'ayan
2024 J jnl
RummaGEO: Automatic mining of human and mouse gene sets from GEO.
Patterns
Giacomo B. Marino, Daniel J. B. Clarke, Alexander Lachmann, Eden Z. Deng, Avi Ma'ayan
2023 J jnl
lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs.
Database J. Biol. Databases Curation
Giacomo B. Marino, Megan L. Wojciechowicz, Daniel J. B. Clarke, Maxim V. Kuleshov, Zhuorui Xie, Minji Jeon, Alexander Lachmann, Avi Ma'ayan
2022 J jnl
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules.
BMC Bioinform.
Eryk Kropiwnicki, Alexander Lachmann, Daniel J. B. Clarke, Zhuorui Xie, Kathleen M. Jagodnik, Avi Ma'ayan
2022 J jnl
SigCom LINCS: data and metadata search engine for a million gene expression signatures.
Nucleic Acids Res.
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
2022 J jnl
blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation.
Bioinform.
Alexander Lachmann, Zhuorui Xie, Avi Ma'ayan
2021 J jnl
Appyters: Turning Jupyter Notebooks into data-driven web apps.
Patterns
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
2021 J jnl
Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning.
Database J. Biol. Databases Curation
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
2021 J jnl
KEA3: improved kinase enrichment analysis via data integration.
Nucleic Acids Res.
Maxim V. Kuleshov, Zhuorui Xie, Alexandra B. K. London, Janice Yang, John Erol Evangelista, Alexander Lachmann, Ingrid Shu, Denis Torre, Avi Ma'ayan
2020 J jnl
EnrichrBot: Twitter bot tracking tweets about human genes.
Bioinform.
Alon Bartal, Alexander Lachmann, Daniel J. B. Clarke, Allison H. Seiden, Kathleen M. Jagodnik, Avi Ma'ayan
2020 J jnl
LINCS Data Portal 2.0: next generation access point for perturbation-response signatures.
Nucleic Acids Res.
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
2020 J jnl
The COVID-19 Drug and Gene Set Library.
Patterns
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
2019 J jnl
ChEA3: transcription factor enrichment analysis by orthogonal omics integration.
Nucleic Acids Res.
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
2019 J jnl
Geneshot: search engine for ranking genes from arbitrary text queries.
Nucleic Acids Res.
Alexander Lachmann, Brian M. Schilder, Megan L. Wojciechowicz, Denis Torre, Maxim V. Kuleshov, Alexandra B. Keenan, Avi Ma'ayan
2019 J jnl
modEnrichr: a suite of gene set enrichment analysis tools for model organisms.
Nucleic Acids Res.
Maxim V. Kuleshov, Jennifer E. L. Diaz, Zachary N. Flamholz, Alexandra B. Keenan, Alexander Lachmann, Megan L. Wojciechowicz, Ross L. Cagan, Avi Ma'ayan
2018 J jnl
L1000FWD: fireworks visualization of drug-induced transcriptomic signatures.
Bioinform.
Zichen Wang, Alexander Lachmann, Alexandra B. Keenan, Avi Ma'ayan
2018 J jnl
eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks.
Nucleic Acids Res.
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
2017 J jnl
Systematic, network-based characterization of therapeutic target inhibitors.
PLoS Comput. Biol.
Yao Shen, Mariano J. Alvarez, Brygida C. Bisikirska, Alexander Lachmann, Ronald Realubit, Sergey Pampou, Jorida Coku, Charles Karan, Andrea Califano
2016 J jnl
ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information.
Bioinform.
Alexander Lachmann, Federico M. Giorgi, Gonzalo López, Andrea Califano
2016 J jnl
Detection and removal of spatial bias in multiwell assays.
Bioinform.
Alexander Lachmann, Federico M. Giorgi, Mariano J. Alvarez, Andrea Califano
2016 J jnl
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.
Nucleic Acids Res.
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
2011 J jnl
FNV: light-weight flash-based network and pathway viewer.
Bioinform.
Ruth Dannenfelser, Alexander Lachmann, Mariola Szenk, Avi Ma'ayan
2010 J jnl
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments.
Bioinform.
Alexander Lachmann, Huilei Xu, Jayanth Krishnan, Seth I. Berger, Amin R. Mazloom, Avi Ma'ayan
2010 J jnl
GATE: software for the analysis and visualization of high-dimensional time series expression data.
Bioinform.
Ben D. MacArthur, Alexander Lachmann, Ihor Lemischka, Avi Ma'ayan
2010 C conf
Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome Network.
BIBE
Marylens Hernandez, Alexander Lachmann, Shan Zhao, Kunhong Xiao, Avi Ma'ayan
2010 J jnl
Lists2Networks: Integrated analysis of gene/protein lists.
BMC Bioinform.
Alexander Lachmann, Avi Ma'ayan
2009 J jnl
KEA: kinase enrichment analysis.
Bioinform.
Alexander Lachmann, Avi Ma'ayan
2008 J jnl
Finding relevant patterns in bursty sequences.
Proc. VLDB Endow.
Alexander Lachmann, Mirek Riedewald