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

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

Europe PMC

[no publisher info] · [no date info] · ppr:PPR667653