Publications

Highlighted

* (co-) first author, ^ (co-) senior author

Reading the epigenome

Multiscale footprints reveal the organization of cis-regulatory elements.

Yan Hu*, Max A Horlbeck*, Ruochi Zhang*, Sai Ma, Rojesh Shrestha, …, Andrew S Earl, Noam Shoresh, Charles B Epstein, Amy J Wagers, Jason D Buenrostro^

Nature · 22 Jan 2025 · pmid:39843737

A new computational method for dissecting transcription factor binding and nucleosome binding from bulk and single-cell ATAC-seq data.

Twitter

GitHub

Mapping genetic interactions to identify new gene functions

Mapping the Genetic Landscape of Human Cells.

Max A Horlbeck*, Albert Xu, Min Wang, Neal K Bennett, Chong Y Park, …, Tim R Peterson, Ken Nakamura, Michael A Fischbach, Jonathan S Weissman^, Luke A Gilbert^

Cell · 19 Jul 2018 · pmid:30033366

Dual CRISPRi targeting to map genetic interactions among genes required for cell fitness.

GitHub

Exploring genetic interaction manifolds constructed from rich single-cell phenotypes.

Thomas M Norman*, Max A Horlbeck*, Joseph M Replogle, Alex Y Ge, Albert Xu, Marco Jost, Luke A Gilbert, Jonathan S Weissman^

Science (New York, N.Y.) · 08 Aug 2019 · pmid:31395745

Mapping genetic interactions using CRISPRa and using single-cell RNA sequencing as a rich phenotypic readout.

GitHub

Systematically identifying lncRNA function with CRISPRi

CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells.

S John Liu*, Max A Horlbeck*, Seung Woo Cho, Harjus S Birk, Martina Malatesta, …, Luke A Gilbert, Bruce R Conklin, Howard Y Chang, Jonathan S Weissman^, Daniel A Lim^

Science (New York, N.Y.) · 15 Dec 2016 · pmid:27980086

Functional screening discovers cellular phenotypes for hundreds of new lncRNA-expressing loci.

Libraries (addgene)

Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells.

David Wu*, Aunoy Poddar, Elpiniki Ninou, Elizabeth Hwang, Mitchel A Cole, …, Nicolas W L Eng, Jonghoon Chang, Yin Shen, Jonathan S Weissman, Daniel A Lim^

Cell genomics · 14 Sep 2022 · pmid:36381608

An iPSC platform for high-throughput screening of neural differentiation phenotypes.

ShinyApp

Genome-scale CRISPR interference and activation screening platforms

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.

Luke A Gilbert*, Max A Horlbeck*, Britt Adamson, Jacqueline E Villalta, Yuwen Chen, …, Hidde L Ploegh, Michael C Bassik, Lei S Qi, Martin Kampmann, Jonathan S Weissman^

Cell · 09 Oct 2014 · pmid:25307932

Generation of the first genome-scale CRISPRi and CRISPRa libraries.

GitHub

Nucleosomes impede Cas9 access to DNA in vivo and in vitro.

Max A Horlbeck*, Lea B Witkowsky*, Benjamin Guglielmi, Joseph M Replogle, Luke A Gilbert, Jacqueline E Villalta, Sharon E Torigoe, Robert Tjian^, Jonathan S Weissman^

eLife · 17 Mar 2016 · pmid:26987018

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation.

Max A Horlbeck*, Luke A Gilbert, Jacqueline E Villalta, Britt Adamson, Ryan A Pak, …, Alexander P Fields, Chong Yon Park, Jacob E Corn, Martin Kampmann, Jonathan S Weissman^

eLife · 23 Sep 2016 · pmid:27661255

Next-generation libraries for CRISPRi and CRISPRa in humans and mice.

GitHub

hCRISPRi-v2 library (addgene)

hCRISPRa-v2 library (addgene)

All

2025

Multiscale footprints reveal the organization of cis-regulatory elements.

Yan Hu*, Max A Horlbeck*, Ruochi Zhang*, Sai Ma, Rojesh Shrestha, …, Andrew S Earl, Noam Shoresh, Charles B Epstein, Amy J Wagers, Jason D Buenrostro^

Nature · 22 Jan 2025 · pmid:39843737

Novel Phenotypes and Genotype-Phenotype Correlations in a Large Clinical Cohort of Patients With Kleefstra Syndrome.

Zoë J Frazier, Seyda Kilic, Hailey Osika, Alisa Mo, Meg Quinn, …, Anne O’Donnell-Luria, Joe Kossowsky, Jonathan O Lipton, Tjitske Kleefstra, Siddharth Srivastava

Clinical genetics · 02 Jan 2025 · pmid:39746677

2024

CRISPRi screens identify the lncRNA,

Haley Halasz, Eric Malekos, Sergio Covarrubias, Samira Yitiz, Christy Montano, …, S John Liu, Max A Horlbeck, Leila Namvar, Jonathan S Weissman, Susan Carpenter

Proceedings of the National Academy of Sciences of the United States of America · 23 May 2024 · pmid:38781216

2023

FET fusion oncoproteins disrupt physiologic DNA repair networks and induce ATR synthetic lethality in cance

Asmin Tulpule, Shruti Menon, Marcus Breese, Yone Lin, Hannah Allegakoen, …, Ann Heslin, Max Horlbeck, Jonathan Weissman, Alejandro Sweet-Cordero, Trever Bivona

[no publisher info] · 01 Jan 2023 · ppr:PPR667653

2022

GATOR2-dependent mTORC1 activity is a therapeutic vulnerability in FOXO1 fusion-positive rhabdomyosarcoma.

Jacqueline Morales, David V Allegakoen, José A Garcia, Kristen Kwong, Pushpendra K Sahu, …, Max A Horlbeck, Jonathan S Weissman, W Clay Gustafson, Trever G Bivona, Amit J Sabnis

JCI insight · 08 Dec 2022 · pmid:36282590

Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells.

David Wu*, Aunoy Poddar, Elpiniki Ninou, Elizabeth Hwang, Mitchel A Cole, …, Nicolas W L Eng, Jonghoon Chang, Yin Shen, Jonathan S Weissman, Daniel A Lim^

Cell genomics · 14 Sep 2022 · pmid:36381608

2021

Genome-wide CRISPRi screening identifies OCIAD1 as a prohibitin client and regulatory determinant of mitochondrial Complex III assembly in human cells.

Maxence Le Vasseur, Jonathan Friedman, Marco Jost, Jiawei Xu, Justin Yamada, …, Max A Horlbeck, Michelle R Salemi, Brett S Phinney, Jonathan S Weissman, Jodi Nunnari

eLife · 26 May 2021 · pmid:34034859

High-content imaging-based pooled CRISPR screens in mammalian cells.

Xiaowei Yan, Nico Stuurman, Susana A Ribeiro, Marvin E Tanenbaum, Max A Horlbeck, Christina R Liem, Marco Jost, Jonathan S Weissman, Ronald D Vale

The Journal of cell biology · 01 Feb 2021 · pmid:33465779

Genome-Scale Perturbation of Long Noncoding RNA Expression Using CRISPR Interference.

S John Liu, Max A Horlbeck, Jonathan S Weissman, Daniel A Lim

Methods in molecular biology (Clifton, N.J.) · 01 Jan 2021 · pmid:33326085

2020

Pharmaceutical-Grade Rigosertib Is a Microtubule-Destabilizing Agent.

Marco Jost, Yuwen Chen, Luke A Gilbert, Max A Horlbeck, Lenno Krenning, …, Martin Kampmann, Anna Akhmanova, Michel O Steinmetz, Marvin E Tanenbaum, Jonathan S Weissman

Molecular cell · 02 Jul 2020 · pmid:32619469

CRISPRi-based radiation modifier screen identifies long non-coding RNA therapeutic targets in glioma.

S John Liu, Martina Malatesta, Brian V Lien, Parna Saha, Shivani S Thombare, …, Michelle Monje, Nalin Gupta, David R Raleigh, Erik M Ullian, Daniel A Lim

Genome biology · 31 Mar 2020 · pmid:32234056

Fitness effects of CRISPR/Cas9-targeting of long noncoding RNA genes.

Max A Horlbeck, S John Liu, Howard Y Chang, Daniel A Lim, Jonathan S Weissman

Nature biotechnology · 24 Feb 2020 · pmid:32094656

Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs.

Marco Jost, Daniel A Santos, Reuben A Saunders, Max A Horlbeck, John S Hawkins, …, Thomas M Norman, Jeffrey A Hussmann, Christina R Liem, Carol A Gross, Jonathan S Weissman

Nature biotechnology · 13 Jan 2020 · pmid:31932729

2019

New factors for protein transport identified by a genome-wide CRISPRi screen in mammalian cells.

Laia Bassaganyas, Stephanie J Popa, Max Horlbeck, Claudia Puri, Sarah E Stewart, …, David C Rubinsztein, Randy Schekman, Vivek Malhotra, Kevin Moreau, Julien Villeneuve

The Journal of cell biology · 05 Sep 2019 · pmid:31488582

Exploring genetic interaction manifolds constructed from rich single-cell phenotypes.

Thomas M Norman*, Max A Horlbeck*, Joseph M Replogle, Alex Y Ge, Albert Xu, Marco Jost, Luke A Gilbert, Jonathan S Weissman^

Science (New York, N.Y.) · 08 Aug 2019 · pmid:31395745

Cellular response to small molecules that selectively stall protein synthesis by the ribosome.

Nadège Liaud, Max A Horlbeck, Luke A Gilbert, Ketrin Gjoni, Jonathan S Weissman, Jamie H D Cate

PLoS genetics · 15 Mar 2019 · pmid:30875366

2018

A high-throughput screen of real-time ATP levels in individual cells reveals mechanisms of energy failure.

Bryce A Mendelsohn, Neal K Bennett, Maxwell A Darch, Katharine Yu, Mai K Nguyen, …, Luke A Gilbert, William Hyun, Martin Kampmann, Jean L Nakamura, Ken Nakamura

PLoS biology · 27 Aug 2018 · pmid:30148842

Mapping the Genetic Landscape of Human Cells.

Max A Horlbeck*, Albert Xu, Min Wang, Neal K Bennett, Chong Y Park, …, Tim R Peterson, Ken Nakamura, Michael A Fischbach, Jonathan S Weissman^, Luke A Gilbert^

Cell · 19 Jul 2018 · pmid:30033366

Combinatorial genetics in liver repopulation and carcinogenesis with a in vivo CRISPR activation platform.

Kirk J Wangensteen, Yue J Wang, Zhixun Dou, Amber W Wang, Elham Mosleh-Shirazi, Max A Horlbeck, Luke A Gilbert, Jonathan S Weissman, Shelley L Berger, Klaus H Kaestner

Hepatology (Baltimore, Md.) · 14 May 2018 · pmid:29091290

Identification of a transporter complex responsible for the cytosolic entry of nitrogen-containing bisphosphonates.

Zhou Yu, Lauren E Surface, Chong Yon Park, Max A Horlbeck, Gregory A Wyant, Monther Abu-Remaileh, Timothy R Peterson, David M Sabatini, Jonathan S Weissman, Erin K O’Shea

eLife · 10 May 2018 · pmid:29745899

Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element.

Seung Woo Cho, Jin Xu, Ruping Sun, Maxwell R Mumbach, Ava C Carter, …, Max A Horlbeck, Daniel A Lim, Jonathan S Weissman, Christina Curtis, Howard Y Chang

Cell · 03 May 2018 · pmid:29731168

Targeting RAS-driven human cancer cells with antibodies to upregulated and essential cell-surface proteins.

Alexander J Martinko, Charles Truillet, Olivier Julien, Juan E Diaz, Max A Horlbeck, …, Josip Blonder, Jonathan S Weissman, Sourav Bandyopadhyay, Michael J Evans, James A Wells

eLife · 23 Jan 2018 · pmid:29359686

2017

Combined CRISPRi/a-Based Chemical Genetic Screens Reveal that Rigosertib Is a Microtubule-Destabilizing Agent.

Marco Jost, Yuwen Chen, Luke A Gilbert, Max A Horlbeck, Lenno Krenning, …, Martin Kampmann, Anna Akhmanova, Michel O Steinmetz, Marvin E Tanenbaum, Jonathan S Weissman

Molecular cell · 05 Oct 2017 · pmid:28985505

2016

CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells.

S John Liu*, Max A Horlbeck*, Seung Woo Cho, Harjus S Birk, Martina Malatesta, …, Luke A Gilbert, Bruce R Conklin, Howard Y Chang, Jonathan S Weissman^, Daniel A Lim^

Science (New York, N.Y.) · 15 Dec 2016 · pmid:27980086

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.

Britt Adamson, Thomas M Norman, Marco Jost, Min Y Cho, James K Nuñez, …, Carol A Gross, Atray Dixit, Oren Parnas, Aviv Regev, Jonathan S Weissman

Cell · 15 Dec 2016 · pmid:27984733

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation.

Max A Horlbeck*, Luke A Gilbert, Jacqueline E Villalta, Britt Adamson, Ryan A Pak, …, Alexander P Fields, Chong Yon Park, Jacob E Corn, Martin Kampmann, Jonathan S Weissman^

eLife · 23 Sep 2016 · pmid:27661255

Versatile in vivo regulation of tumor phenotypes by dCas9-mediated transcriptional perturbation.

Christian J Braun, Peter M Bruno, Max A Horlbeck, Luke A Gilbert, Jonathan S Weissman, Michael T Hemann

Proceedings of the National Academy of Sciences of the United States of America · 20 Jun 2016 · pmid:27325776

Single-cell analysis of long non-coding RNAs in the developing human neocortex.

Siyuan John Liu, Tomasz J Nowakowski, Alex A Pollen, Jan H Lui, Max A Horlbeck, …, Daniel He, Jonathan S Weissman, Arnold R Kriegstein, Aaron A Diaz, Daniel A Lim

Genome biology · 14 Apr 2016 · pmid:27081004

Parallel shRNA and CRISPR-Cas9 screens enable antiviral drug target identification.

Richard M Deans, David W Morgens, Ayşe Ökesli, Sirika Pillay, Max A Horlbeck, …, Mark Smith, Jeffrey S Glenn, Jan E Carette, Chaitan Khosla, Michael C Bassik

Nature chemical biology · 28 Mar 2016 · pmid:27018887

Nucleosomes impede Cas9 access to DNA in vivo and in vitro.

Max A Horlbeck*, Lea B Witkowsky*, Benjamin Guglielmi, Joseph M Replogle, Luke A Gilbert, Jacqueline E Villalta, Sharon E Torigoe, Robert Tjian^, Jonathan S Weissman^

eLife · 17 Mar 2016 · pmid:26987018

CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs.

Mohammad A Mandegar, Nathaniel Huebsch, Ekaterina B Frolov, Edward Shin, Annie Truong, …, Søren P Sheikh, Jonathan S Weissman, Lei S Qi, Po-Lin So, Bruce R Conklin

Cell stem cell · 10 Mar 2016 · pmid:26971820

2015

Next-generation libraries for robust RNA interference-based genome-wide screens.

Martin Kampmann, Max A Horlbeck, Yuwen Chen, Jordan C Tsai, Michael C Bassik, …, Jacqueline E Villalta, S Chul Kwon, Hyeshik Chang, V Narry Kim, Jonathan S Weissman

Proceedings of the National Academy of Sciences of the United States of America · 15 Jun 2015 · pmid:26080438

2014

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.

Luke A Gilbert*, Max A Horlbeck*, Britt Adamson, Jacqueline E Villalta, Yuwen Chen, …, Hidde L Ploegh, Michael C Bassik, Lei S Qi, Martin Kampmann, Jonathan S Weissman^

Cell · 09 Oct 2014 · pmid:25307932

2013

A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility.

Michael C Bassik, Martin Kampmann, Robert Jan Lebbink, Shuyi Wang, Marco Y Hein, …, Matthias Mann, Anthony A Hyman, Emily M Leproust, Michael T McManus, Jonathan S Weissman

Cell · 08 Feb 2013 · pmid:23394947

2012

ER cargo properties specify a requirement for COPII coat rigidity mediated by Sec13p.

Alenka Copic, Catherine F Latham, Max A Horlbeck, Jennifer G D’Arcangelo, Elizabeth A Miller

Science (New York, N.Y.) · 02 Feb 2012 · pmid:22300850