Jonathan Weissman, PhD

Professor
Cellular Molecular Pharmacology
+1 415 502-7642
Publications: 

Ribosome Profiling: Global Views of Translation.

Cold Spring Harbor perspectives in biology

Ingolia NT, Hussmann JA, Weissman JS

Mapping the Genetic Landscape of Human Cells.

Cell

Horlbeck MA, Xu A, Wang M, Bennett NK, Park CY, Bogdanoff D, Adamson B, Chow ED, Kampmann M, Peterson TR, Nakamura K, Fischbach MA, Weissman JS, Gilbert LA

Reprogramming human T cell function and specificity with non-viral genome targeting.

Nature

Roth TL, Puig-Saus C, Yu R, Shifrut E, Carnevale J, Li PJ, Hiatt J, Saco J, Krystofinski P, Li H, Tobin V, Nguyen DN, Lee MR, Putnam AL, Ferris AL, Chen JW, Schickel JN, Pellerin L, Carmody D, Alkorta-Aranburu G, Del Gaudio D, Matsumoto H, Morell M, Mao Y, Cho M, Quadros RM, Gurumurthy CB, Smith B, Haugwitz M, Hughes SH, Weissman JS, Schumann K, Esensten JH, May AP, Ashworth A, Kupfer GM, Greeley SAW, Bacchetta R, Meffre E, Roncarolo MG, Romberg N, Herold KC, Ribas A, Leonetti MD, Marson A

Engineering ER-stress dependent non-conventional mRNA splicing.

eLife

Li W, Okreglak V, Peschek J, Kimmig P, Zubradt M, Weissman JS, Walter P

Exploration of Benzothiazole-Rhodacyanines as Allosteric Inhibitors of Protein-Protein Interactions with Heat Shock Protein 70 (Hsp70).

Journal of medicinal chemistry

Shao H, Li X, Moses MA, Gilbert LA, Kalyanaraman C, Young ZT, Chernova M, Journey SN, Weissman JS, Hann B, Jacobson MP, Neckers LM, Gestwicki JE

The helicase Ded1p controls use of near-cognate translation initiation codons in 5' UTRs.

Nature

Guenther UP, Weinberg DE, Zubradt MM, Tedeschi FA, Stawicki BN, Zagore LL, Brar GA, Licatalosi DD, Bartel DP, Weissman JS, Jankowsky E

The ER membrane protein complex interacts cotranslationally to enable biogenesis of multipass membrane proteins.

eLife

Shurtleff MJ, Itzhak DN, Hussmann JA, Schirle Oakdale NT, Costa EA, Jonikas M, Weibezahn J, Popova KD, Jan CH, Sinitcyn P, Vembar SS, Hernandez H, Cox J, Burlingame AL, Brodsky J, Frost A, Borner GH, Weissman JS

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

eLife

Yu Z, Surface LE, Park CY, Horlbeck MA, Wyant GA, Abu-Remaileh M, Peterson TR, Sabatini DM, Weissman JS, O'Shea EK

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

Cell

Cho SW, Xu J, Sun R, Mumbach MR, Carter AC, Chen YG, Yost KE, Kim J, He J, Nevins SA, Chin SF, Caldas C, Liu SJ, Horlbeck MA, Lim DA, Weissman JS, Curtis C, Chang HY

A Stress Response that Monitors and Regulates mRNA Structure Is Central to Cold Shock Adaptation.

Molecular cell

Zhang Y, Burkhardt DH, Rouskin S, Li GW, Weissman JS, Gross CA

CRISPR Approaches to Small Molecule Target Identification.

ACS chemical biology

Jost M, Weissman JS

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

eLife

Martinko AJ, Truillet C, Julien O, Diaz JE, Horlbeck MA, Whiteley G, Blonder J, Weissman JS, Bandyopadhyay S, Evans MJ, Wells JA

Defining the physiological role of SRP in protein-targeting efficiency and specificity.

Science (New York, N.Y.)

Costa EA, Subramanian K, Nunnari J, Weissman JS

Lipid Homeostasis Is Maintained by Dual Targeting of the Mitochondrial PE Biosynthesis Enzyme to the ER.

Developmental cell

Friedman JR, Kannan M, Toulmay A, Jan CH, Weissman JS, Prinz WA, Nunnari J

The Human Cell Atlas.

eLife

Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N

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

Hepatology (Baltimore, Md.)

Wangensteen KJ, Wang YJ, Dou Z, Wang AW, Mosleh-Shirazi E, Horlbeck MA, Gilbert LA, Weissman JS, Berger SL, Kaestner KH

Inducible and multiplex gene regulation using CRISPR-Cpf1-based transcription factors.

Nature methods

Tak YE, Kleinstiver BP, Nuñez JK, Hsu JY, Horng JE, Gong J, Weissman JS, Joung JK

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

Molecular cell

Jost M, Chen Y, Gilbert LA, Horlbeck MA, Krenning L, Menchon G, Rai A, Cho MY, Stern JJ, Prota AE, Kampmann M, Akhmanova A, Steinmetz MO, Tanenbaum ME, Weissman JS

CAT-tailing as a fail-safe mechanism for efficient degradation of stalled nascent polypeptides.

Science (New York, N.Y.)

Kostova KK, Hickey KL, Osuna BA, Hussmann JA, Frost A, Weinberg DE, Weissman JS

Suppression of B-cell development genes is key to glucocorticoid efficacy in treatment of acute lymphoblastic leukemia.

Blood

Kruth KA, Fang M, Shelton DN, Abu-Halawa O, Mahling R, Yang H, Weissman JS, Loh ML, Müschen M, Tasian SK, Bassik MC, Kampmann M, Pufall MA

Operon mRNAs are organized into ORF-centric structures that predict translation efficiency.

eLife

Burkhardt DH, Rouskin S, Zhang Y, Li GW, Weissman JS, Gross CA

Translation from unconventional 5' start sites drives tumour initiation.

Nature

Sendoel A, Dunn JG, Rodriguez EH, Naik S, Gomez NC, Hurwitz B, Levorse J, Dill BD, Schramek D, Molina H, Weissman JS, Fuchs E

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

Cell

Adamson B, Norman TM, Jost M, Cho MY, Nuñez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, Pak RA, Gray AN, Gross CA, Dixit A, Parnas O, Regev A, Weissman JS

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

Science (New York, N.Y.)

Liu SJ, Horlbeck MA, Cho SW, Birk HS, Malatesta M, He D, Attenello FJ, Villalta JE, Cho MY, Chen Y, Mandegar MA, Olvera MP, Gilbert LA, Conklin BR, Chang HY, Weissman JS, Lim DA

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.

Cell

Dixit A, Parnas O, Li B, Chen J, Fulco CP, Jerby-Arnon L, Marjanovic ND, Dionne D, Burks T, Raychowdhury R, Adamson B, Norman TM, Lander ES, Weissman JS, Friedman N, Regev A

The mTOR Complex Controls HIV Latency.

Cell host & microbe

Besnard E, Hakre S, Kampmann M, Lim HW, Hosmane NN, Martin A, Bassik MC, Verschueren E, Battivelli E, Chan J, Svensson JP, Gramatica A, Conrad RJ, Ott M, Greene WC, Krogan NJ, Siliciano RF, Weissman JS, Verdin E

The SND proteins constitute an alternative targeting route to the endoplasmic reticulum.

Nature

Aviram N, Ast T, Costa EA, Arakel EC, Chuartzman SG, Jan CH, Haßdenteufel S, Dudek J, Jung M, Schorr S, Zimmermann R, Schwappach B, Weissman JS, Schuldiner M

Model-guided optogenetic study of PKA signaling in budding yeast.

Molecular biology of the cell

Stewart-Ornstein J, Chen S, Bhatnagar R, Weissman JS, El-Samad H

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo.

Nature methods

Zubradt M, Gupta P, Persad S, Lambowitz AM, Weissman JS, Rouskin S

Dynamic translation regulation in Caulobacter cell cycle control.

Proceedings of the National Academy of Sciences of the United States of America

Schrader JM, Li GW, Childers WS, Perez AM, Weissman JS, Shapiro L, McAdams HH

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

eLife

Horlbeck MA, Gilbert LA, Villalta JE, Adamson B, Pak RA, Chen Y, Fields AP, Park CY, Corn JE, Kampmann M, Weissman JS

Combined chemical-genetic approach identifies cytosolic HSP70 dependence in rhabdomyosarcoma.

Proceedings of the National Academy of Sciences of the United States of America

Sabnis AJ, Guerriero CJ, Olivas V, Sayana A, Shue J, Flanagan J, Asthana S, Paton AW, Paton JC, Gestwicki JE, Walter P, Weissman JS, Wipf P, Brodsky JL, Bivona TG

Ligand-binding domains of nuclear receptors facilitate tight control of split CRISPR activity.

Nature communications

Nguyen DP, Miyaoka Y, Gilbert LA, Mayerl SJ, Lee BH, Weissman JS, Conklin BR, Wells JA

Htm1p-Pdi1p is a folding-sensitive mannosidase that marks N-glycoproteins for ER-associated protein degradation.

Proceedings of the National Academy of Sciences of the United States of America

Liu YC, Fujimori DG, Weissman JS

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

Proceedings of the National Academy of Sciences of the United States of America

Braun CJ, Bruno PM, Horlbeck MA, Gilbert LA, Weissman JS, Hemann MT

A scalable strategy for high-throughput GFP tagging of endogenous human proteins.

Proceedings of the National Academy of Sciences of the United States of America

Leonetti MD, Sekine S, Kamiyama D, Weissman JS, Huang B

A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria.

Cell

Peters JM, Colavin A, Shi H, Czarny TL, Larson MH, Wong S, Hawkins JS, Lu CHS, Koo BM, Marta E, Shiver AL, Whitehead EH, Weissman JS, Brown ED, Qi LS, Huang KC, Gross CA

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

Genome biology

Liu SJ, Nowakowski TJ, Pollen AA, Lui JH, Horlbeck MA, Attenello FJ, He D, Weissman JS, Kriegstein AR, Diaz AA, Lim DA

Versatile protein tagging in cells with split fluorescent protein.

Nature communications

Kamiyama D, Sekine S, Barsi-Rhyne B, Hu J, Chen B, Gilbert LA, Ishikawa H, Leonetti MD, Marshall WF, Weissman JS, Huang B

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

eLife

Horlbeck MA, Witkowsky LB, Guglielmi B, Replogle JM, Gilbert LA, Villalta JE, Torigoe SE, Tjian R, Weissman JS

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

Cell stem cell

Mandegar MA, Huebsch N, Frolov EB, Shin E, Truong A, Olvera MP, Chan AH, Miyaoka Y, Holmes K, Spencer CI, Judge LM, Gordon DE, Eskildsen TV, Villalta JE, Horlbeck MA, Gilbert LA, Krogan NJ, Sheikh SP, Weissman JS, Qi LS, So PL, Conklin BR

A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation.

Molecular cell

Fields AP, Rodriguez EH, Jovanovic M, Stern-Ginossar N, Haas BJ, Mertins P, Raychowdhury R, Hacohen N, Carr SA, Ingolia NT, Regev A, Weissman JS

Targeting the AAA ATPase p97 as an Approach to Treat Cancer through Disruption of Protein Homeostasis.

Cancer cell

Anderson DJ, Le Moigne R, Djakovic S, Kumar B, Rice J, Wong S, Wang J, Yao B, Valle E, Kiss von Soly S, Madriaga A, Soriano F, Menon MK, Wu ZY, Kampmann M, Chen Y, Weissman JS, Aftab BT, Yakes FM, Shawver L, Zhou HJ, Wustrow D, Rolfe M

Ribosome profiling reveals the what, when, where and how of protein synthesis.

Nature reviews. Molecular cell biology

Brar GA, Weissman JS

Paradoxical resistance of multiple myeloma to proteasome inhibitors by decreased levels of 19S proteasomal subunits.

eLife

Acosta-Alvear D, Cho MY, Wild T, Buchholz TJ, Lerner AG, Simakova O, Hahn J, Korde N, Landgren O, Maric I, Choudhary C, Walter P, Weissman JS, Kampmann M

Regulation of mRNA translation during mitosis.

eLife

Tanenbaum ME, Stern-Ginossar N, Weissman JS, Vale RD

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

Proceedings of the National Academy of Sciences of the United States of America

Kampmann M, Horlbeck MA, Chen Y, Tsai JC, Bassik MC, Gilbert LA, Villalta JE, Kwon SC, Chang H, Kim VN, Weissman JS

Pharmacological dimerization and activation of the exchange factor eIF2B antagonizes the integrated stress response.

eLife

Sidrauski C, Tsai JC, Kampmann M, Hearn BR, Vedantham P, Jaishankar P, Sokabe M, Mendez AS, Newton BW, Tang EL, Verschueren E, Johnson JR, Krogan NJ, Fraser CS, Weissman JS, Renslo AR, Walter P

Biotechnology. A prudent path forward for genomic engineering and germline gene modification.

Science (New York, N.Y.)

Baltimore D, Berg P, Botchan M, Carroll D, Charo RA, Church G, Corn JE, Daley GQ, Doudna JA, Fenner M, Greely HT, Jinek M, Martin GS, Penhoet E, Puck J, Sternberg SH, Weissman JS, Yamamoto KR

Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens.

Science (New York, N.Y.)

Jovanovic M, Rooney MS, Mertins P, Przybylski D, Chevrier N, Satija R, Rodriguez EH, Fields AP, Schwartz S, Raychowdhury R, Mumbach MR, Eisenhaure T, Rabani M, Gennert D, Lu D, Delorey T, Weissman JS, Carr SA, Hacohen N, Regev A

Validation of the Hsp70-Bag3 protein-protein interaction as a potential therapeutic target in cancer.

Molecular cancer therapeutics

Li X, Colvin T, Rauch JN, Acosta-Alvear D, Kampmann M, Dunyak B, Hann B, Aftab BT, Murnane M, Cho M, Walter P, Weissman JS, Sherman MY, Gestwicki JE

Protein synthesis. Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains.

Science (New York, N.Y.)

Shen PS, Park J, Qin Y, Li X, Parsawar K, Larson MH, Cox J, Cheng Y, Lambowitz AM, Weissman JS, Brandman O, Frost A

Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation.

Molecular systems biology

Pop C, Rouskin S, Ingolia NT, Han L, Phizicky EM, Weissman JS, Koller D

Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds.

Cell

Zalatan JG, Lee ME, Almeida R, Gilbert LA, Whitehead EH, La Russa M, Tsai JC, Weissman JS, Dueber JE, Qi LS, Lim WA

The general mode of translation inhibition by macrolide antibiotics.

Proceedings of the National Academy of Sciences of the United States of America

Kannan K, Kanabar P, Schryer D, Florin T, Oh E, Bahroos N, Tenson T, Weissman JS, Mankin AS

Genetic influences on translation in yeast.

PLoS genetics

Albert FW, Muzzey D, Weissman JS, Kruglyak L

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

Cell

Gilbert LA, Horlbeck MA, Adamson B, Villalta JE, Chen Y, Whitehead EH, Guimaraes C, Panning B, Ploegh HL, Bassik MC, Qi LS, Kampmann M, Weissman JS

Unraveling the mechanism of cell death induced by chemical fibrils.

Nature chemical biology

Julien O, Kampmann M, Bassik MC, Zorn JA, Venditto VJ, Shimbo K, Agard NJ, Shimada K, Rheingold AL, Stockwell BR, Weissman JS, Wells JA

Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes.

Cell reports

Ingolia NT, Brar GA, Stern-Ginossar N, Harris MS, Talhouarne GJ, Jackson SE, Wills MR, Weissman JS

Misfolded proteins induce aggregation of the lectin Yos9.

The Journal of biological chemistry

Smith MH, Rodriguez EH, Weissman JS

The coding and noncoding architecture of the Caulobacter crescentus genome.

PLoS genetics

Schrader JM, Zhou B, Li GW, Lasker K, Childers WS, Williams B, Long T, Crosson S, McAdams HH, Weissman JS, Shapiro L

A high-coverage shRNA screen identifies TMEM129 as an E3 ligase involved in ER-associated protein degradation.

Nature communications

van de Weijer ML, Bassik MC, Luteijn RD, Voorburg CM, Lohuis MA, Kremmer E, Hoeben RC, LeProust EM, Chen S, Hoelen H, Ressing ME, Patena W, Weissman JS, McManus MT, Wiertz EJ, Lebbink RJ

A pause sequence enriched at translation start sites drives transcription dynamics in vivo.

Science (New York, N.Y.)

Larson MH, Mooney RA, Peters JM, Windgassen T, Nayak D, Gross CA, Block SM, Greenleaf WJ, Landick R, Weissman JS

Uniform nomenclature for the mitochondrial contact site and cristae organizing system.

The Journal of cell biology

Pfanner N, van der Laan M, Amati P, Capaldi RA, Caudy AA, Chacinska A, Darshi M, Deckers M, Hoppins S, Icho T, Jakobs S, Ji J, Kozjak-Pavlovic V, Meisinger C, Odgren PR, Park SK, Rehling P, Reichert AS, Sheikh MS, Taylor SS, Tsuchida N, van der Bliek AM, van der Klei IJ, Weissman JS, Westermann B, Zha J, Neupert W, Nunnari J

Differential scales of protein quality control.

Cell

Wolff S, Weissman JS, Dillin A

KSHV 2.0: a comprehensive annotation of the Kaposi's sarcoma-associated herpesvirus genome using next-generation sequencing reveals novel genomic and functional features.

PLoS pathogens

Arias C, Weisburd B, Stern-Ginossar N, Mercier A, Madrid AS, Bellare P, Holdorf M, Weissman JS, Ganem D

Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system.

Cell

Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo.

Nature

Rouskin S, Zubradt M, Washietl S, Kellis M, Weissman JS

Msn2 coordinates a stoichiometric gene expression program.

Current biology : CB

Stewart-Ornstein J, Nelson C, DeRisi J, Weissman JS, El-Samad H

Next-generation NAMPT inhibitors identified by sequential high-throughput phenotypic chemical and functional genomic screens.

Chemistry & biology

Matheny CJ, Wei MC, Bassik MC, Donnelly AJ, Kampmann M, Iwasaki M, Piloto O, Solow-Cordero DE, Bouley DM, Rau R, Brown P, McManus MT, Weissman JS, Cleary ML

Global cellular response to chemotherapy-induced apoptosis.

eLife

Wiita AP, Ziv E, Wiita PJ, Urisman A, Julien O, Burlingame AL, Weissman JS, Wells JA

CRISPR interference (CRISPRi) for sequence-specific control of gene expression.

Nature protocols

Larson MH, Gilbert LA, Wang X, Lim WA, Weissman JS, Qi LS

A developmentally regulated translational control pathway establishes the meiotic chromosome segregation pattern.

Genes & development

Berchowitz LE, Gajadhar AS, van Werven FJ, De Rosa AA, Samoylova ML, Brar GA, Xu Y, Xiao C, Futcher B, Weissman JS, White FM, Amon A

CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes.

Cell

Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna JA, Lim WA, Weissman JS, Qi LS

Genome-wide annotation and quantitation of translation by ribosome profiling.

Current protocols in molecular biology

Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS

Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins.

Cell

Guttman M, Russell P, Ingolia NT, Weissman JS, Lander ES

Integrated platform for genome-wide screening and construction of high-density genetic interaction maps in mammalian cells.

Proceedings of the National Academy of Sciences of the United States of America

Kampmann M, Bassik MC, Weissman JS

rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments.

Bioinformatics (Oxford, England)

O'Connor PB, Li GW, Weissman JS, Atkins JF, Baranov PV

Aneuploid yeast strains exhibit defects in cell growth and passage through START.

Molecular biology of the cell

Thorburn RR, Gonzalez C, Brar GA, Christen S, Carlile TM, Ingolia NT, Sauer U, Weissman JS, Amon A

Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.

Cell

Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA

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

Cell

Bassik MC, Kampmann M, Lebbink RJ, Wang S, Hein MY, Poser I, Weibezahn J, Horlbeck MA, Chen S, Mann M, Hyman AA, Leproust EM, McManus MT, Weissman JS

Decoding human cytomegalovirus.

Science (New York, N.Y.)

Stern-Ginossar N, Weisburd B, Michalski A, Le VT, Hein MY, Huang SX, Ma M, Shen B, Qian SB, Hengel H, Mann M, Ingolia NT, Weissman JS

A ribosome-bound quality control complex triggers degradation of nascent peptides and signals translation stress.

Cell

Brandman O, Stewart-Ornstein J, Wong D, Larson A, Williams CC, Li GW, Zhou S, King D, Shen PS, Weibezahn J, Dunn JG, Rouskin S, Inada T, Frost A, Weissman JS

Proto-genes and de novo gene birth.

Nature

Carvunis AR, Rolland T, Wapinski I, Calderwood MA, Yildirim MA, Simonis N, Charloteaux B, Hidalgo CA, Barbette J, Santhanam B, Brar GA, Weissman JS, Regev A, Thierry-Mieg N, Cusick ME, Vidal M

Functional repurposing revealed by comparing S. pombe and S. cerevisiae genetic interactions.

Cell

Frost A, Elgort MG, Brandman O, Ives C, Collins SR, Miller-Vedam L, Weibezahn J, Hein MY, Poser I, Mann M, Hyman AA, Weissman JS

Special issue: the molecular and cellular mechanisms of amyloidosis.

Journal of molecular biology

Radford SE, Weissman JS

Native elongating transcript sequencing (NET-seq).

Current protocols in molecular biology

Churchman LS, Weissman JS

Cellular noise regulons underlie fluctuations in Saccharomyces cerevisiae.

Molecular cell

Stewart-Ornstein J, Weissman JS, El-Samad H

The translational landscape of mTOR signalling steers cancer initiation and metastasis.

Nature

Hsieh AC, Liu Y, Edlind MP, Ingolia NT, Janes MR, Sher A, Shi EY, Stumpf CR, Christensen C, Bonham MJ, Wang S, Ren P, Martin M, Jessen K, Feldman ME, Weissman JS, Shokat KM, Rommel C, Ruggero D

High-resolution view of the yeast meiotic program revealed by ribosome profiling.

Science (New York, N.Y.)

Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS

Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo.

Cell

Oh E, Becker AH, Sandikci A, Huber D, Chaba R, Gloge F, Nichols RJ, Typas A, Gross CA, Kramer G, Weissman JS, Bukau B

Genetics: Noise rules.

Nature

El-Samad H, Weissman JS

Road to ruin: targeting proteins for degradation in the endoplasmic reticulum.

Science (New York, N.Y.)

Smith MH, Ploegh HL, Weissman JS

Protein kinase Ypk1 phosphorylates regulatory proteins Orm1 and Orm2 to control sphingolipid homeostasis in Saccharomyces cerevisiae.

Proceedings of the National Academy of Sciences of the United States of America

Roelants FM, Breslow DK, Muir A, Weissman JS, Thorner J

A mitochondrial-focused genetic interaction map reveals a scaffold-like complex required for inner membrane organization in mitochondria.

The Journal of cell biology

Hoppins S, Collins SR, Cassidy-Stone A, Hummel E, Devay RM, Lackner LL, Westermann B, Schuldiner M, Weissman JS, Nunnari J

Ganglion-specific splicing of TRPV1 underlies infrared sensation in vampire bats.

Nature

Gracheva EO, Cordero-Morales JF, González-Carcacía JA, Ingolia NT, Manno C, Aranguren CI, Weissman JS, Julius D

H3K4 trimethylation by Set1 promotes efficient termination by the Nrd1-Nab3-Sen1 pathway.

Molecular and cellular biology

Terzi N, Churchman LS, Vasiljeva L, Weissman J, Buratowski S

Strain conformation, primary structure and the propagation of the yeast prion [PSI+].

Nature structural & molecular biology

Verges KJ, Smith MH, Toyama BH, Weissman JS

Radically different amyloid conformations dictate the seeding specificity of a chimeric Sup35 prion.

Journal of molecular biology

Foo CK, Ohhashi Y, Kelly MJ, Tanaka M, Weissman JS

Amyloid structure: conformational diversity and consequences.

Annual review of biochemistry

Toyama BH, Weissman JS

The epistemology of cell biology.

Molecular biology of the cell

Weissman JS

Mammalian microRNAs predominantly act to decrease target mRNA levels.

Nature

Guo H, Ingolia NT, Weissman JS, Bartel DP

Automated identification of pathways from quantitative genetic interaction data.

Molecular systems biology

Battle A, Jonikas MC, Walter P, Weissman JS, Koller D

A general lack of compensation for gene dosage in yeast.

Molecular systems biology

Springer M, Weissman JS, Kirschner MW

J domain co-chaperone specificity defines the role of BiP during protein translocation.

The Journal of biological chemistry

Vembar SS, Jonikas MC, Hendershot LM, Weissman JS, Brodsky JL

Molecular basis of infrared detection by snakes.

Nature

Gracheva EO, Ingolia NT, Kelly YM, Cordero-Morales JF, Hollopeter G, Chesler AT, Sánchez EE, Perez JC, Weissman JS, Julius D

Orm family proteins mediate sphingolipid homeostasis.

Nature

Breslow DK, Collins SR, Bodenmiller B, Aebersold R, Simons K, Shevchenko A, Ejsing CS, Weissman JS

Differences in prion strain conformations result from non-native interactions in a nucleus.

Nature chemical biology

Ohhashi Y, Ito K, Toyama BH, Weissman JS, Tanaka M

From information to knowledge: new technologies for defining gene function.

Nature methods

Collins SR, Weissman JS, Krogan NJ

Regulated Ire1-dependent decay of messenger RNAs in mammalian cells.

The Journal of cell biology

Hollien J, Lin JH, Li H, Stevens N, Walter P, Weissman JS

An ER-mitochondria tethering complex revealed by a synthetic biology screen.

Science (New York, N.Y.)

Kornmann B, Currie E, Collins SR, Schuldiner M, Nunnari J, Weissman JS, Walter P

Rapid creation and quantitative monitoring of high coverage shRNA libraries.

Nature methods

Bassik MC, Lebbink RJ, Churchman LS, Ingolia NT, Patena W, LeProust EM, Schuldiner M, Weissman JS, McManus MT

Analysis of Dom34 and its function in no-go decay.

Molecular biology of the cell

Passos DO, Doma MK, Shoemaker CJ, Muhlrad D, Green R, Weissman J, Hollien J, Parker R

Comprehensive characterization of genes required for protein folding in the endoplasmic reticulum.

Science (New York, N.Y.)

Jonikas MC, Collins SR, Denic V, Oh E, Quan EM, Schmid V, Weibezahn J, Schwappach B, Walter P, Weissman JS, Schuldiner M

Functional organization of the S. cerevisiae phosphorylation network.

Cell

Fiedler D, Braberg H, Mehta M, Chechik G, Cagney G, Mukherjee P, Silva AC, Shales M, Collins SR, van Wageningen S, Kemmeren P, Holstege FC, Weissman JS, Keogh MC, Koller D, Shokat KM, Krogan NJ

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.

Science (New York, N.Y.)

Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS

Defining the glycan destruction signal for endoplasmic reticulum-associated degradation.

Molecular cell

Quan EM, Kamiya Y, Kamiya D, Denic V, Weibezahn J, Kato K, Weissman JS

A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing.

Molecular cell

Wilmes GM, Bergkessel M, Bandyopadhyay S, Shales M, Braberg H, Cagney G, Collins SR, Whitworth GB, Kress TL, Weissman JS, Ideker T, Guthrie C, Krogan NJ

Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network.

Nature biotechnology

Chechik G, Oh E, Rando O, Weissman J, Regev A, Koller D

Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast.

Science (New York, N.Y.)

Roguev A, Bandyopadhyay S, Zofall M, Zhang K, Fischer T, Collins SR, Qu H, Shales M, Park HO, Hayles J, Hoe KL, Kim DU, Ideker T, Grewal SI, Weissman JS, Krogan NJ

High-throughput, quantitative analyses of genetic interactions in E. coli.

Nature methods

Typas A, Nichols RJ, Siegele DA, Shales M, Collins SR, Lim B, Braberg H, Yamamoto N, Takeuchi R, Wanner BL, Mori H, Weissman JS, Krogan NJ, Gross CA

Systems biology: Reverse engineering the cell.

Nature

Ingolia NT, Weissman JS

The GET complex mediates insertion of tail-anchored proteins into the ER membrane.

Cell

Schuldiner M, Metz J, Schmid V, Denic V, Rakwalska M, Schmitt HD, Schwappach B, Weissman JS

A comprehensive strategy enabling high-resolution functional analysis of the yeast genome.

Nature methods

Breslow DK, Cameron DM, Collins SR, Schuldiner M, Stewart-Ornstein J, Newman HW, Braun S, Madhani HD, Krogan NJ, Weissman JS

Small-molecule aggregates inhibit amyloid polymerization.

Nature chemical biology

Feng BY, Toyama BH, Wille H, Colby DW, Collins SR, May BC, Prusiner SB, Weissman J, Shoichet BK

Identification of yeast proteins necessary for cell-surface function of a potassium channel.

Proceedings of the National Academy of Sciences of the United States of America

Haass FA, Jonikas M, Walter P, Weissman JS, Jan YN, Jan LY, Schuldiner M

The structural basis of yeast prion strain variants.

Nature

Toyama BH, Kelly MJ, Gross JD, Weissman JS

Mec1/Tel1 phosphorylation of the INO80 chromatin remodeling complex influences DNA damage checkpoint responses.

Cell

Morrison AJ, Kim JA, Person MD, Highland J, Xiao J, Wehr TS, Hensley S, Bao Y, Shen J, Collins SR, Weissman JS, Delrow J, Krogan NJ, Haber JE, Shen X

Backup without redundancy: genetic interactions reveal the cost of duplicate gene loss.

Molecular systems biology

Ihmels J, Collins SR, Schuldiner M, Krogan NJ, Weissman JS

CCR4/NOT complex associates with the proteasome and regulates histone methylation.

Proceedings of the National Academy of Sciences of the United States of America

Laribee RN, Shibata Y, Mersman DP, Collins SR, Kemmeren P, Roguev A, Weissman JS, Briggs SD, Krogan NJ, Strahl BD

Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map.

Nature

Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, Chu CS, Schuldiner M, Gebbia M, Recht J, Shales M, Ding H, Xu H, Han J, Ingvarsdottir K, Cheng B, Andrews B, Boone C, Berger SL, Hieter P, Zhang Z, Brown GW, Ingles CJ, Emili A, Allis CD, Toczyski DP, Weissman JS, Greenblatt JF, Krogan NJ

Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae.

Molecular & cellular proteomics : MCP

Collins SR, Kemmeren P, Zhao XC, Greenblatt JF, Spencer F, Holstege FC, Weissman JS, Krogan NJ

Systems biology: many things from one.

Nature

Newman JR, Weissman JS

The physical basis of how prion conformations determine strain phenotypes.

Nature

Tanaka M, Collins SR, Toyama BH, Weissman JS

Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise.

Nature

Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS

Molecular chaperones and protein quality control.

Cell

Bukau B, Weissman J, Horwich A

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.

Nature

Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF

A strategy for extracting and analyzing large-scale quantitative epistatic interaction data.

Genome biology

Collins SR, Schuldiner M, Krogan NJ, Weissman JS

Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex.

Cell

Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, Collins SR, Schuldiner M, Chin K, Punna T, Thompson NJ, Boone C, Emili A, Weissman JS, Hughes TR, Strahl BD, Grunstein M, Greenblatt JF, Buratowski S, Krogan NJ

Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile.

Cell

Schuldiner M, Collins SR, Thompson NJ, Denic V, Bhamidipati A, Punna T, Ihmels J, Andrews B, Boone C, Greenblatt JF, Weissman JS, Krogan NJ

Construction, verification and experimental use of two epitope-tagged collections of budding yeast strains.

Comparative and functional genomics

Howson R, Huh WK, Ghaemmaghami S, Falvo JV, Bower K, Belle A, Dephoure N, Wykoff DD, Weissman JS, O'Shea EK

2004 Irving Sigal Young Investigator Award.

Protein science : a publication of the Protein Society

Weissman JS, O'Shea EK

Mechanism of prion propagation: amyloid growth occurs by monomer addition.

PLoS biology

Collins SR, Douglass A, Vale RD, Weissman JS

Dissection and design of yeast prions.

PLoS biology

Osherovich LZ, Cox BS, Tuite MF, Weissman JS

Oxidative protein folding in eukaryotes: mechanisms and consequences.

The Journal of cell biology

Tu BP, Weissman JS

Emerging principles of conformation-based prion inheritance.

Annual review of biochemistry

Chien P, Weissman JS, DePace AH

Global analysis of protein expression in yeast.

Nature

Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS

Global analysis of protein localization in budding yeast.

Nature

Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK

Directed evolution of substrate-optimized GroEL/S chaperonins.

Cell

Wang JD, Herman C, Tipton KA, Gross CA, Weissman JS

Origins and kinetic consequences of diversity in Sup35 yeast prion fibers.

Nature structural biology

DePace AH, Weissman JS

The utility of prions.

Developmental cell

Osherovich LZ, Weissman JS