Selected publications

Selected publications by theme

A selection of our papers, grouped by theme, with a short note on how each set fits into the lab story. For the complete list, see Manuel Garber's Google Scholar profile ↗.

Skin autoimmunity and inflammation

Human skin disease is our main system for understanding autoimmunity thanks for sample availability.

Explaining UV sensitivity through a three cell type circuitA spatially coordinated keratinocyte-fibroblast circuit recruits MMP9+ myeloid cells to drive type I interferon-driven inflammation in photosensitive autoimmunity.Wang Y, Afshari K, Haddadi NS, Lopes CS, Eng CL, Whiteman LM, Martinez N, Kyawe PP, Anufrieva KS, Wei K, Frieda K, Rosenbach M, Vleugels RA, Gallucci S, Harris JE, Rashighi M, Garber M.

Nat Immunol, 2026 · doi:10.1038/s41590-026-02502-w

Eczema and allergic skin reactions present similarly, but are they molecularly distinct?Single-Cell RNA Sequencing Reveals Molecular Signatures that Distinguish Allergic from Irritant Contact Dermatitis.Frisoli ML, Ko WC, Martinez N, Afshari K, Wang Y, Garber M, Harris JE.

J Invest Dermatol, 2025 · doi:10.1016/j.jid.2024.09.008

Initial forays into single-cell genomics

Early single-cell projects, including work built around in-house inDrop and related profiling approaches, shaped how we think about heterogeneous cellular responses.

ESAT: we developed a 3' end bulk RNA-seq protocol and analysis method, then adapted it to 3' end single-cell RNA-seq. Our current single-cell pipeline still builds on this approachEnd Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data.Derr A, Yang C, Zilionis R, Sergushichev A, Blodgett DM, Redick S, Bortell R, Luban J, Harlan DM, Kadener S, Greiner DL, Klein A, Artyomov MN, Garber M.

Genome Res, 2016 · doi:10.1101/gr.207902.116

Our first application of in-drop to blister byopsies revealed a pre-clinical state in non-lesional skin and a key role for the IL15 receptorscRNA-seq of human vitiligo reveals complex networks of subclinical immune activation and a role for CCR5 in Treg function.Gellatly KJ, Strassner JP, Essien K, Refat MA, Murphy RL, Coffin-Schmitt A, Pandya AG, Tovar-Garza A, Frisoli ML, Fan X, Ding X, Kim EE, Abbas Z, McDonel P, Garber M, Harris JE.

Sci Transl Med, 2021 · doi:10.1126/scitranslmed.abd8995

Pinpointed cell type specific transcriptional state in a mouse fragile X modelSingle cell transcriptomics reveals dysregulated cellular and molecular networks in a fragile X syndrome model.Donnard E, Shu H, Garber M.

PLoS Genet, 2022 · doi:10.1371/journal.pgen.1010221

Gene regulation in immune cells

Foundational lab work on how immune cell gene programs are built and dynamically controlled — the toolkit and comparative framework underneath our current disease work.

A high-throughput ChIP-seq approach revealing principles of dynamic gene regulation as dendritic cells respond to pathogen stimulationA high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals.Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, Robinson J, Minie B, Chevrier N, Itzhaki Z, Blecher-Gonen R, Bornstein C, Amann-Zalcenstein D, Weiner A, Friedrich D, Meldrim J, Ram O, Cheng C, Gnirke A, Fisher S, Friedman N, Wong B, Bernstein BE, Nusbaum C, Hacohen N, Regev A, Amit I.

Mol Cell, 2012 · doi:10.1016/j.molcel.2012.07.030

Comparing regulatory elements across immune cell types reveals a conserved regulatory lexiconComparative Analysis of Immune Cells Reveals a Conserved Regulatory Lexicon.Donnard E, Vangala P, Afik S, McCauley S, Nowosielska A, Kucukural A, Tabak B, Zhu X, Diehl W, McDonel P, Yosef N, Luban J, Garber M.

Cell Syst, 2018 · doi:10.1016/j.cels.2018.01.002

Multiway proximal interactions mapped by SPRITE coupled with immunoprecipitation (SIP) revealed transcriptional hubs in the early response of dendritic cells to LPSHigh-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection.Vangala P, Murphy R, Quinodoz SA, Gellatly K, McDonel P, Guttman M, Garber M.

Mol Cell, 2020 · doi:10.1016/j.molcel.2020.09.005

Method and application development

Computational and experimental methods that make it possible to measure regulatory programs, perturbations, and cell states at scale.

Worm Perturb-Seq methods, analytical framework, and library constructionWorm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq.Zhang H, Li X, Song D, Yukselen O, Nanda S, Kucukural A, Li JJ, Garber M, Walhout AJM.

Nat Commun, 2025 · doi:10.1038/s41467-025-60154-0

Our automated, versioned controlled pipeline designer and runner -- developed by Alper Kucukural in the bioinformatics coreDolphinNext: a distributed data processing platform for high throughput genomics.Yukselen O, Turkyilmaz O, Ozturk AR, Garber M, Kucukural A.

BMC Genomics, 2020 · doi:10.1186/s12864-020-6714-x

Scripture: one of the first transcript assemblers from RNA-seq dataAb initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs.Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A.

Nat Biotechnol, 2010 · doi:10.1038/nbt.1633

SiPhy: Single site estimation of evolutionary constraint using biased substitution patternsIdentifying novel constrained elements by exploiting biased substitution patterns.Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X.

Bioinformatics, 2009 · doi:10.1093/bioinformatics/btp190