Author

Chris Zaleski

Cold Spring Harbor Laboratory

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 2 Genomics· 2

Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 4 Approach:statistical model· 3 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Organism:human· 2 Organism:mouse· 2 Research Focus:benchmarking· 1 Research Focus:cancer & tumor microenvironment· 1

Frequent Co-Authors

Alessandra BreschiiD· 3 shared Alexander DobiniD· 3 shared Carrie Davis· 3 shared Jörg Drenkow· 3 shared T GingerasiD· 3 shared Roderic GuigóiD· 2 shared Sarah DjebaliiD· 2 shared Alex Dobin· 1 shared

Activity by Year

2012-2020 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

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3 shared papersGenomics

Alessandra BreschiORCID

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Author profile →

4 papers

Recent·Most cited

A limited set of transcriptional programs define major cell types

Alessandra Breschi, Manuel Muñoz-Aguirre, Valentin Wucher, Carrie Davis, Diego Garrido-Martín, Sarah Djebali, Jesse A Gillis, Dmitri Davidovich Pervouchine, Anna V Vlasova, Alexander Dobin, Chris Zaleski, Jörg Drenkow, Cassidy Danyko, Alexandra Scavelli, Ferrán Reverter, , Roderic Guigó

The paper identifies five major cell types based on transcriptional programs in human tissues and shows their composition correlates with tissue morphology and disease.

Genome Research · Jul 1, 2020Peer-reviewedGenomics

Dynamics of microRNA expression during mouse prenatal development

Sorena Rahmanian, Rabi Murad, Alessandra Breschi, Weihua Zeng, Mark Mackiewicz, Brian A. Williams, Carrie Davis, Brian S. Roberts, Sarah Kristen Meadows, Dianna E. Moore, Diane E. Trout, Chris Zaleski, Alexander Dobin, Lei-Hoon Sei, Jörg Drenkow, , Ali Mortazavi

The paper analyzes miRNA expression dynamics across mouse embryonic development, identifying tissue-specific clusters and their regulatory roles.

Genome Research · Nov 1, 2019Peer-reviewedGenomics

Enhanced Transcriptome Maps from Multiple Mouse Tissues Reveal Evolutionary Constraint in Gene Expression for Thousands of Genes

Dmitri Pervouchine, Sarah Djebali, Alessandra Breschi, Carrie A Davis, Pablo Prieto Barja, Alex Dobin, Andrea Tanzer, Julien Lagarde, Chris Zaleski, Lei-Hoon See, Meagan Fastuca, Jorg Drenkow, Huaien Wang, Giovanni Bussotti, Baikang Pei, , Thomas R Gingeras

The paper analyzes RNA-seq data from multiple mouse tissues to identify genes with conserved expression patterns across species and cell types, revealing evolutionary constraints in gene expression.

bioRxiv · Oct 30, 2014Bioinformatics

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin, Carrie Davis, Felix J. Schlesinger, Jörg Drenkow, Chris Zaleski, Sonali Jha, Philippe J. Batut, Mark Chaisson, T Gingeras

Maximum mappable seed search in uncompressed suffix arrays, then seed clustering and stitching, aligns 550 million paired-end reads per hour on 12 cores with better sensitivity and precision.

Bioinformatics · Oct 25, 2012Peer-reviewedBioinformatics