Finding relevant patterns in bursty sequences. - Alexander Lachmann; Mirek Riedewald (Proc. VLDB Endow., 2008)

KEA: kinase enrichment analysis. - Alexander Lachmann; Avi Ma'ayan (Bioinform., 2009)

Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome Network. - Marylens Hernandez; Alexander Lachmann; Shan Zhao; Kunhong Xiao; Avi Ma'ayan (BIBE, 2010)

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. - Alexander Lachmann; Huilei Xu; Jayanth Krishnan; Seth I. Berger; Amin R. Mazloom; Avi Ma'ayan (Bioinform., 2010)

GATE: software for the analysis and visualization of high-dimensional time series expression data. - Ben D. MacArthur; Alexander Lachmann; Ihor Lemischka; Avi Ma'ayan (Bioinform., 2010)

Lists2Networks: Integrated analysis of gene/protein lists. - Alexander Lachmann; Avi Ma'ayan (BMC Bioinform., 2010)

FNV: light-weight flash-based network and pathway viewer. - Ruth Dannenfelser; Alexander Lachmann; Mariola Szenk; Avi Ma'ayan (Bioinform., 2011)

Detection and removal of spatial bias in multiwell assays. - Alexander Lachmann; Federico M. Giorgi; Mariano J. Alvarez; Andrea Califano (Bioinform., 2016)

ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information. - Alexander Lachmann; Federico M. Giorgi; Gonzalo López; Andrea Califano (Bioinform., 2016)

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. - Maxim V. Kuleshov; Matthew R. Jones; Andrew D. Rouillard; Nicolas F. Fernandez; Qiaonan Duan; Zichen Wang 002; Simon Koplev; Sherry L. Jenkins; Kathleen M. Jagodnik; Alexander Lachmann; Michael G. McDermott; Caroline D. Monteiro; et al. (Nucleic Acids Res., 2016)

Systematic, network-based characterization of therapeutic target inhibitors. - Yao Shen; Mariano J. Alvarez; Brygida C. Bisikirska; Alexander Lachmann; Ronald Realubit; Sergey Pampou; Jorida Coku; Charles Karan; Andrea Califano (PLoS Comput. Biol., 2017)

L1000FWD: fireworks visualization of drug-induced transcriptomic signatures. - Zichen Wang 002; Alexander Lachmann; Alexandra B. Keenan; Avi Ma'ayan (Bioinform., 2018)

eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks. - 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 002; Avi Ma'ayan (Nucleic Acids Res., 2018)

ChEA3: transcription factor enrichment analysis by orthogonal omics integration. - Alexandra B. Keenan; Denis Torre; Alexander Lachmann; Ariel K. Leong; Megan L. Wojciechowicz; Vivian Utti; Kathleen M. Jagodnik; Eryk Kropiwnicki; Zichen Wang 002; Avi Ma'ayan (Nucleic Acids Res., 2019)

modEnrichr: a suite of gene set enrichment analysis tools for model organisms. - Maxim V. Kuleshov; Jennifer E. L. Diaz; Zachary N. Flamholz; Alexandra B. Keenan; Alexander Lachmann; Megan L. Wojciechowicz; Ross L. Cagan; Avi Ma'ayan (Nucleic Acids Res., 2019)

Geneshot: search engine for ranking genes from arbitrary text queries. - Alexander Lachmann; Brian M. Schilder; Megan L. Wojciechowicz; Denis Torre; Maxim V. Kuleshov; Alexandra B. Keenan; Avi Ma'ayan (Nucleic Acids Res., 2019)

EnrichrBot: Twitter bot tracking tweets about human genes. - Alon Bartal; Alexander Lachmann; Daniel J. B. Clarke; Allison H. Seiden; Kathleen M. Jagodnik; Avi Ma'ayan (Bioinform., 2020)

LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. - 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; et al. (Nucleic Acids Res., 2020)

The COVID-19 Drug and Gene Set Library. - 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; et al. (Patterns, 2020)

Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning. - 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 (Database J. Biol. Databases Curation, 2021)

KEA3: improved kinase enrichment analysis via data integration. - Maxim V. Kuleshov; Zhuorui Xie; Alexandra B. K. London; Janice Yang; John Erol Evangelista; Alexander Lachmann; Ingrid Shu; Denis Torre; Avi Ma'ayan (Nucleic Acids Res., 2021)

Appyters: Turning Jupyter Notebooks into data-driven web apps. - 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; et al. (Patterns, 2021)

blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation. - Alexander Lachmann; Zhuorui Xie; Avi Ma'ayan (Bioinform., 2022)

DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. - Eryk Kropiwnicki; Alexander Lachmann; Daniel J. B. Clarke; Zhuorui Xie; Kathleen M. Jagodnik; Avi Ma'ayan (BMC Bioinform., 2022)

SigCom LINCS: data and metadata search engine for a million gene expression signatures. - 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; et al. (Nucleic Acids Res., 2022)

lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs. - Giacomo B. Marino; Megan L. Wojciechowicz; Daniel J. B. Clarke; Maxim V. Kuleshov; Zhuorui Xie; Minji Jeon; Alexander Lachmann; Avi Ma'ayan (Database J. Biol. Databases Curation, 2023)

RummaGEO: Automatic mining of human and mouse gene sets from GEO. - Giacomo B. Marino; Daniel J. B. Clarke; Alexander Lachmann; Eden Z. Deng; Avi Ma'ayan (Patterns, 2024)

Playbook workflow builder: Interactive construction of bioinformatics workflows. - 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; et al. (PLoS Comput. Biol., 2025)