Author

Rick Farouni

Broad InstituteORCID 0000-0002-3454-2946Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:statistical model· 6 Approach:experimental assay· 4 Research Focus:benchmarking· 3 Research Focus:differential expression· 3 Assay:DNA methylation· 3 Research Focus:gene regulatory network inference· 3 Research Focus:software / tool· 3 Organism:human· 2

Frequent Co-Authors

Luca PinelloiD· 4 shared Daniel E. BaueriD· 3 shared Kendell ClementiD· 3 shared Hamed Shateri NajafabadiiD· 2 shared J. Keith JoungiD· 2 shared Jiannis RagoussisiD· 2 shared Jonathan Y. HsuiD· 2 shared Matthew C. CanveriD· 2 shared

Activity by Year

2016-2023 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 22 mutual co-author links

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4 shared papersBioinformatics

Luca PinelloORCID

Mutual co-authors in cluster

Author profile →

9 papers

Recent·Most cited

Transcriptional Reprogramming of Skeletal Muscle Stem Cells by the Niche Environment

Felicia Lazure, Rick Farouni, Korin Sahinyan, Darren M. Blackburn, Aldo Hernández-Corchado, Gabrielle Perron, Tianyuan Lu, Adrien Osakwe, Jiannis Ragoussis, Colin G. Crist, Theodore J. Perkins, Arezu Jahani‐Asl, Hamed Shateri Najafabadi, Vahab D. Soleimani

This study shows that the niche environment significantly influences skeletal muscle stem cell transcriptional activity, with some age-related changes being reversible through exposure to a young niche.

Nature Communications · Feb 1, 2023Peer-reviewedGenetics

Statistical modeling, estimation, and remediation of sample index hopping in multiplexed droplet-based single-cell RNA-seq data

Rick Farouni, Haig Hugo Vrej Djambazian, Lorenzo Edwin Ferri, Jiannis Ragoussis, Hamed Shateri Najafabadi

The paper introduces a probabilistic model to estimate and correct sample index hopping in single-cell RNA-seq data, reducing phantom molecules by up to 85%.

Nature Communications · Jun 1, 2020Peer-reviewedBioinformatics

Legacy Data Confounds Genomics Studies

Luke Anderson-Trocmé, Rick Farouni, Mathieu Bourgey, Yoichiro Kamatani, Koichiro Higasa, Jeong‐Sun Seo, Changhoon Kim, Fumihiko Matsuda, Simon Gravel

The paper identifies a batch effect in 1000 Genomes Project data causing spurious mutation calls and affecting GWAS results, suggesting legacy data may need to be retired or upgraded.

Molecular Biology and Evolution · Aug 28, 2019Peer-reviewedBioinformatics

Analysis and comparison of genome editing using CRISPResso2

Kendell Clement, Holly A. Rees, Matthew C. Canver, Jason M. Gehrke, Rick Farouni, Jonathan Y. Hsu, Mitchel A. Cole, David R. Liu, J. Keith Joung, Daniel E. Bauer, Luca Pinello

CRISPResso2 is a software tool for analyzing genome editing data, providing allele-specific quantification and scalable alignment to assess editing efficiency and safety.

Nature Biotechnology · Feb 26, 2019Peer-reviewedBioinformatics

CRISPR-SURF: Discovering regulatory elements by deconvolution of CRISPR tiling screen data

Jonathan Y. Hsu, Charles P. Fulco, Mitchel A. Cole, Matthew C. Canver, Danilo Pellin, Falak Sher, Rick Farouni, Kendell Clement, Jimmy A. Guo, Luca Biasco, Stuart H. Orkin, J Engreitz, Eric S. Lander, J. Keith Joung, Daniel E. Bauer, Luca Pinello

CRISPR-SURF deconvolves CRISPR tiling screen data to identify functional regulatory elements across CRISPR-Cas, CRISPRi, and CRISPRa experiments.

Nature Methods · Nov 20, 2018Peer-reviewedBioinformatics

Bioconda: A sustainable and comprehensive software distribution for the life sciences

Björn Grüning, Ryan Dale, Andreas Sjödin, Brad Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Adam Caprez, Bérénice Batut, Mathias Haudgaard, Thomas Cokelaer, Kyle A. Beauchamp, Brent S. Pedersen, Youri Hoogstrate, Anthony Bretaudeau, , Matthew L. Workentine

Bioconda provides a sustainable, comprehensive distribution of bioinformatics software using Conda for reproducible analysis across platforms.

Nature Methods · Jun 25, 2018Peer-reviewedBioinformatics

AmpUMI: Design and analysis of unique molecular identifiers for deep amplicon sequencing

Kendell Clement, Rick Farouni, Daniel E. Bauer, Luca Pinello

The paper introduces AmpUMI, a tool for designing and analyzing UMI-based amplicon sequencing experiments, providing a model to determine optimal UMI length and quality control features.

Bioinformatics · Apr 16, 2018Peer-reviewedBioinformatics

Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements

Luca Pinello, Rick Farouni, Guo‐Cheng Yuan

Haystack identifies epigenetic variability hotspots and cell-type specific regulatory elements across multiple cell types using a computational pipeline.

Bioinformatics · Jan 16, 2018Peer-reviewedBioinformatics

ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data

Elizabeth Baskin, Rick Farouni, Ewy A. Mathé

ALTRE is an R package and web app for analyzing chromatin accessibility data to identify altered regulatory elements across cell types.

Bioinformatics · Oct 26, 2016Peer-reviewedBioinformatics