Recent Publications

Lam M, Marsters SA, Ashkenazi A, Walter P

Misfolded proteins bind and activate death receptor 5 to trigger apoptosis during unresolved endoplasmic reticulum stress.
Elife. 2020 Jan 6;9:e52291.
Glasgow A, Glasgow J, Limonta D, Solomon P, Lui I, Zhang Y, Nix MA, Rettko NJ, Zha S, Yamin R, Kao K, Rosenberg OS, Ravetch JV, Wiita AP, Leung KK, Lim SA, Zhou XX, Hobman TC, Kortemme T, Wells JA

Engineered ACE2 receptor traps potently neutralize SARS-CoV-2.
Proc Natl Acad Sci U S A. 2020 Nov 10;117(45):28046-28055.
Rabouw HH, Visser LJ, Passchier TC, Langereis MA, Liu F, Giansanti P, van Vliet ALW, Dekker JG, van der Grein SG, Saucedo JG, Anand AA, Trellet ME, Bonvin AMJJ, Walter P, Heck AJR, de Groot RJ, van Kuppeveld FJM

Inhibition of the integrated stress response by viral proteins that block p-eIF2-eIF2B association.
Nat Microbiol. 2020 Nov;5(11):1361-1373.
Wang R Y-R, Noddings CM, Kirschke E, Myasnikov AG, Johnson JL, Agard DA

GR chaperone cycle mechanism revealed by cryo-EM: inactivation of GR by GR:Hsp90:Hsp70:Hop client-loading complex.
bioRxiv 2020.11.05.370247.
Schoof M, Faust B, Saunders RA, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbølle CB, Puchades C, Azumaya CM, Kratochvil HT, Zimanyi M, Deshpande I, Liang J, Dickinson S, Nguyen HC, Chio CM, Merz GE, Thompson MC, Diwanji D, Schaefer K, Anand AA, Dobzinski N, Zha BS, Simoneau CR, Leon K, White KM, Chio US, Gupta M, Jin M, Li F, Liu Y, Zhang K, Bulkley D, Sun M, Smith AM, Rizo AN, Moss F, Brilot AF, Pourmal S, Trenker R, Pospiech T, Gupta S, Barsi-Rhyne B, Belyy V, Barile-Hill AW, Nock S, Liu Y, Krogan NJ, Ralston CY, Swaney DL, García-Sastre A, Ott M, Vignuzzi M, QCRG Structural Biology Consortium, Walter P, Manglik A

An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike.
Science. 2020 Nov 5:eabe3255.
Murrow LM, Weber RJ, Caruso J, McGinnis CS, Gascard P, Borowsky AD, Desai TA, Thomson M, Tlsty TM, Gartner ZJ

Changes in epithelial proportions and transcriptional state underlie major premenopausal breast cancer risks.
bioRxiv 430611; 2020 Oct 21.
Chen SY, Osimiri LC, Chevalier M, Bugaj LJ, Nguyen TH, Greenstein RA, Ng AH, Stewart-Ornstein J, Neves LT, El-Samad H

Optogenetic Control Reveals Differential Promoter Interpretation of Transcription Factor Nuclear Translocation Dynamics.
Cell Syst. 2020 Sep 4;S2405-4712(20)30293-3.
Bracken CJ, Lim SA, Solomon P, Rettko NJ, Nguyen DP, Zha BS, Schaefer K, Byrnes JR, Zhou J, Lui I, Liu J, Pance K; QCRG Structural Biology Consortium, Zhou XX, Leung KK, Wells JA

Bi-paratopic and multivalent VH domains block ACE2 binding and neutralize SARS-CoV-2.
Nat Chem Biol. 2020 Oct 20.
Alme EB, Toczyski DP

Redundant targeting of Isr1 by two CDKs in mitotic cells.
Curr Genet. 2020 Oct 15.
Summers DK, Perry DS, Rao B, Madhani HD

Coordinate genomic association of transcription factors controlled by an imported quorum sensing peptide in Cryptococcus neoformans.
PLoS Genet. 2020 Sep 21;16(9):e1008744.
Byrnes JR, Zhou XX, Lui I, Elledge SK, Glasgow JE, Lim SA, Loudermilk RP, Chiu CY, Wang TT, Wilson MR, Leung KK, Wells JA

Competitive SARS-CoV-2 Serology Reveals Most Antibodies Targeting the Spike Receptor-Binding Domain Compete for ACE2 Binding.
mSphere. 2020 Sep 16;5(5):e00802-20.
Noddings CM, Wang R Y-R, Agard DA

GR chaperone cycle mechanism revealed by cryo-EM: reactivation of GR by the GR:Hsp90:p23 client-maturation complex.
bioRxiv 2020.09.12.294975.
Laidlaw BJ, Duan L, Xu Y, Vazquez SE, Cyster JG

The transcription factor Hhex cooperates with the corepressor Tle3 to promote memory B cell development.
Nat Immunol. 2020 Sep;21(9):1082-1093.
Morante N, Sigg SA, Strauskulage L, Raleigh DR, Reiter JF

DYRK2 is a ciliary kinase involved in vertebrate Hedgehog signal transduction.
bioRxiv 2020.08.31.275511.
Elledge SK, Zhou XX, Byrnes JR, Martinko AJ, Lui I, Pance K, Lim SA, Glasgow JE, Glasgow AA, Turcios K, Iyer N, Torres L, Peluso MJ, Henrich TJ, Wang TT, Tato CM, Leung KK, Greenhouse B, Wells JA

Engineering luminescent biosensors for point-of-care SARS-CoV-2 antibody detection.
medRxiv. 2020 Aug 21:2020.08.17.20176925.
Hu KH, Eichorst JP, McGinnis CS, Patterson DM, Chow ED, Kersten K, Jameson SC, Gartner ZJ, Rao AA, Krummel MF

ZipSeq: barcoding for real-time mapping of single cell transcriptomes.
Nat Methods. 2020 Aug;17(8):833-843. Epub 2020 Jul 6. PMID: 32632238.
Cheng KW, Mullins RD

Initiation and disassembly of filopodia tip complexes containing VASP and lamellipodin.
Mol Biol Cell. 2020 Aug 15;31(18):2021-2034.
Van R, Cuevas-Navarro A, Castel P, McCormick F

The molecular functions of RIT1 and its contribution to human disease.
Biochem J. 2020 Aug 14;477(15):2755-2770.
Okhovat M, Nevonen KA, Davis BA, Michener P, Ward S, Milhaven M, Harshman L, Sohota A, Fernandes JD, Salama SR, O'Neill RJ, Ahituv N, Veeramah KR, Carbone L

Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome.
Proc Natl Acad Sci U S A. 2020 Aug 11;117(32):19328-19338.
Schoof M, Faust B, Saunders RA, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbølle CB, Zimanyi M, Deshpande I, Liang J, Anand AA, Dobzinski N, Zha BS, Barsi-Rhyne B, Belyy V, Barile-Hill AW, Gupta S, Simoneau CR, Leon K, White KM, Nock S, Liu Y, Krogan NJ, Ralston CY, Swaney DL, García-Sastre A, Ott M, Vignuzzi M, Walter P, Manglik A

An ultra-high affinity synthetic nanobody blocks SARS-CoV-2 infection by locking Spike into an inactive conformation.
bioRxiv. 2020 Aug 10;2020.08.08.238469.
O'Donovan B, Mandel-Brehm C, Vazquez SE, Liu J, Parent AV, Anderson MS, Kassimatis T, Zekeridou A, Hauser SL, Pittock SJ, Chow E, Wilson MR, DeRisi JL

High-resolution epitope mapping of anti-Hu and anti-Yo autoimmunity by programmable phage display.
Brain Commun. 2020 Aug 3;2(2):fcaa059.
Long AF, Suresh P, Dumont S

Individual kinetochore-fibers locally dissipate force to maintain robust mammalian spindle structure.
J Cell Biol. 2020 Aug 3;219(8):e201911090.
Hickey KL, Dickson K, Cogan JZ, Replogle JM, Schoof M, D'Orazio KN, Sinha NK, Hussmann JA, Jost M, Frost A, Green R, Weissman JS, Kostova KK

GIGYF2 and 4EHP Inhibit Translation Initiation of Defective Messenger RNAs to Assist Ribosome-Associated Quality Control.
Mol Cell. 2020 Sep 17;79(6):950-962.e6. Epub 2020 Jul 28. PMID: 32726578.
Carlson CR, Asfaha JB, Ghent CM, Howard CJ, Hartooni N, Morgan DO

Phosphorylation modulates liquid-liquid phase separation of the SARS-CoV-2 N protein.
bioRxiv [Preprint]. 2020 Jun 29:2020.06.28.176248. PMID: 32637943; PMCID: PMC7337373.
Ibe NU, Mukherjee S

Non-canonical activation of the ER stress sensor ATF6 by Legionella pneumophila effectors.
bioRxiv 2020.06.26.174185.
Alme EB, Stevenson E, Krogan NJ, Swaney DL, Toczyski DP

The kinase Isr1 negatively regulates hexosamine biosynthesis in S. cerevisiae.
PLoS Genet. 2020 Jun 24;16(6):e1008840.
Alme EB, Stevenson E, Krogan NJ, Swaney DL, Toczyski DP

The kinase Isr1 negatively regulates hexosamine biosynthesis in S. cerevisiae.
PLoS Genet. 2020 Jun 24;16(6):e1008840.
Lazar AM, Irannejad R, Baldwin TA, Sundaram AB, Gutkind JS, Inoue A, Dessauer CW, Von Zastrow M

G protein-regulated endocytic trafficking of adenylyl cyclase type 9.
Elife. 2020 Jun 9;9:e58039.
von Appen A, LaJoie D, Johnson IE, Trnka MJ, Pick SM, Burlingame AL, Ullman KS, Frost A

LEM2 phase separation promotes ESCRT-mediated nuclear envelope reformation.
Nature. 2020 Jun;582(7810):115-118.
Byrnes JR, Zhou XX, Lui I, Elledge SK, Glasgow JE, Lim SA, Loudermilk R, Chiu CY, Wilson MR, Leung KK, Wells JA

A SARS-CoV-2 serological assay to determine the presence of blocking antibodies that compete for human ACE2 binding.
medRxiv. 2020 May 29:2020.05.27.20114652.
Lui I, Zhou XX, Lim SA, Elledge SK, Solomon P, Rettko NJ, Zha BS, et al.

Trimeric SARS-CoV-2 Spike interacts with dimeric ACE2 with limited intra-Spike avidity.
bioRxiv 2020.05.21.109157.
Vazquez SE, Ferré EM, Scheel DW, Sunshine S, Miao B, Mandel-Brehm C, Quandt Z, Chan AY, Cheng M, German M, Lionakis M, DeRisi JL, Anderson MS

Identification of novel, clinically correlated autoantigens in the monogenic autoimmune syndrome APS1 by proteome-wide PhIP-Seq.
Elife. 2020 May 15;9:e55053.
Li Y, Shan Y, Desai RV, Cox KH, Weinberger LS, Takahashi JS

Noise-driven cellular heterogeneity in circadian periodicity.
Proc Natl Acad Sci U S A. 2020 May 12;117(19):10350-10356.
Kirschke E, Roe-Zurz Z, Noddings CM, Agard DA

The interplay between Bag-1, Hsp70, and Hsp90 reveals that inhibiting Hsp70 rebinding is essential for Glucocorticoid Receptor activity.
bioRxiv 2020.05.03.075523.
Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, et al.

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.
Nature. 2020 Jul;583(7816):459-468. Epub 2020 Apr 30. PMID: 32353859; PMCID: PMC7431030.
Barad BA, Liu L, Diaz RE, Basilio R, Van Dyken SJ, Locksley RM, Fraser JS

Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates.
Protein Sci. 2020 Apr;29(4):966-977. Epub 2020 Jan 21. PMID: 31930591; PMCID: PMC7096708.
Replogle JM, Norman TM, Xu A, et al.

Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing.
Nat Biotechnol. 2020 Aug;38(8):954-961. Epub 2020 Mar 30. PMID: 32231336; PMCID: PMC7416462.
Schmunk G, Chang KN, Soliman SS, Keefe MG , Bogdanoff D, Tejera D, Ziffra RS, Shin D, Allen DE, Chun BB, McGinnis CS, Winkler EA, Abla AA, Chang EF, Gartner ZJ, Mehta SB, Piao X, Hengen KB, Nowakowski TJ

Human microglia upregulate cytokine signatures and accelerate maturation of neural networks.
bioRxiv 2020.03.24.006874.
Göke A, Schrott S, Mizrak A, Belyy V, Osman C, Walter P

Mrx6 regulates mitochondrial DNA copy number in Saccharomyces cerevisiae by engaging the evolutionarily conserved Lon protease Pim1.
Mol Biol Cell. 2020 Mar 19;31(7):527-545.
Wallace EWJ, Maufrais C, Sales-Lee J, Tuck LR, de Oliveira L, Feuerbach F, Moyrand F, Natarajan P, Madhani HD, Janbon G

Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom.
Nucleic Acids Res. 2020 Mar 18;48(5):2312-2331.
Gamarra N, Narlikar GJ

Histone dynamics within the nucleosome octamer play a critical role in SNF2h-mediated nucleosome sliding.
bioRxiv 2020.03.14.992073; doi: https://doi.org/10.1101/2020.03.14.992073.
Jost M, Santos DA, Saunders RA, Horlbeck MA, Hawkins JS, Scaria SM, Norman TM, Hussmann JA, Liem CR, Gross CA, Weissman JS

Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs.
Nat Biotechnol. 2020 Mar;38(3):355-364.
Stoeber M, Jullié D, Li J, Chakraborty S, Majumdar S, Lambert NA, Manglik A, von Zastrow M

Agonist-selective recruitment of engineered protein probes and of GRK2 by opioid receptors in living cells.
Elife. 2020 Feb 25;9:e54208. PMID: 32096468; PMCID: PMC7041944.
Oh E, Mark KG, Mocciaro A, Watson ER, Prabu JR, Cha DD, Kampmann M, Gamarra N, Zhou CY, Rape M

Gene expression and cell identity controlled by anaphase-promoting complex.
Nature. 2020 Mar;579(7797):136-140. Epub 2020 Feb 19. PMID: 32076268; PMCID: PMC7402266.
McGinnis CS, Siegel DA, Xie G, Stone M, Gartner ZJ, Roan NR, Lee SA

No detectable alloreactive transcriptional responses during donor-multiplexed single-cell RNA sequencing of peripheral blood mononuclear cells.
bioRxiv 2020.02.12.946509.
Belyy V, Tran NH, Walter P

Quantitative microscopy reveals dynamics and fate of clustered IRE1α.
Proc Natl Acad Sci U S A. 2020 Jan 21;117(3):1533-1542.
Britton CS, Sorrells TR, Johnson AD

Protein-coding changes preceded cis-regulatory gains in a newly evolved transcription circuit.
Science. 2020 Jan 3;367(6473):96-100.
Mendoza SD, Nieweglowska ES, Govindarajan S, Leon LM, Berry JD, Tiwari A, Chaikeeratisak V, Pogliano J, Agard DA, Bondy-Denomy J

A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases.
Nature. 2020 Jan;577(7789):244-248.
Greenstein RA, Barrales RR, Sanchez NA, Bisanz JE, Braun, S, Al-Sady B

Set1/COMPASS repels heterochromatin invasion at euchromatic sites by disrupting Suv39/Clr4 activity and nucleosome stability.
Genes Dev. 2020 Jan 1;34(1-2):99-117.
Anand AA, Walter P

Structural insights into ISRIB, a memory-enhancing inhibitor of the integrated stress response.
FEBS J. 2020 Jan;287(2):239-245.
Diaz U, Bergman ZJ, Johnson BM, Edington AR, de Cruz MA, Marshall WF, Riggs B

Microtubules are necessary for proper Reticulon localization during mitosis.
PLoS One. 2019 Dec 26;14(12):e0226327.
Mizrak A, Morgan DO

Polyanions provide selective control of APC/C interactions with the activator subunit.
Nat Commun. 2019 Dec 20;10(1):5807.
Qin L, Mizrak A, Guimarães DSPSF, Tambrin HM, Morgan DO, Hall MC

The pseudosubstrate inhibitor Acm1 inhibits the anaphase-promoting complex/cyclosome by combining high-affinity activator binding with disruption of Doc1/Apc10 function.
J Biol Chem. 2019 Nov 15;294(46):17249-17261.
Fonseca JP, Bonny AR, Kumar GR, Ng AH, Town J, Wu QC, Aslankoohi E, Chen SY, Dods G, Harrigan P, Osimiri LC, Kistler AL, El-Samad H

A Toolkit for Rapid Modular Construction of Biological Circuits in Mammalian Cells.
ACS Synth Biol. 2019 Nov 15;8(11):2593-2606.
Rosen LE, Klebba JE, Asfaha JB, Ghent CM, Campbell MG, Cheng Y, Morgan DO

Cohesin cleavage by separase is enhanced by a substrate motif distinct from the cleavage site.
Nat Commun. 2019 Nov 15;10(1):5189.
Harel ET, Drake PM, Barfield RM, Lui I, Farr-Jones S, Van't Veer L, Gartner ZJ, Green EM, Lourenço AL, Cheng Y, Hann BC, Rabuka D, Craik CS

Antibody-Drug Conjugates Targeting the Urokinase Receptor (uPAR) as a Possible Treatment of Aggressive Breast Cancer.
Antibodies (Basel). 2019 Nov 5;8(4):54. PMID: 31694242; PMCID: PMC6963874.
Witchley JN, Penumetcha PM, Noble SM

Visualization of Candida albicans in the Murine Gastrointestinal Tract Using Fluorescent In Situ Hybridization.
J Vis Exp. 2019 Nov 5;(153).
Kuhn J, Dumont S

Mammalian kinetochores count attached microtubules in a sensitive and switch-like manner.
J Cell Biol. 2019 Nov 4;218(11):3583-3596.
Qu J, Prasad NK, Yu MA, Chen S, Lyden A, Herrera N, Silvis MR, Crawford E, Looney MR, Peters JM, Rosenberg OS

Modulating Pathogenesis with Mobile-CRISPRi.
J Bacteriol. 2019 Oct 21;201(22):e00304-19.
Perlaza K, Toutkoushian H, Boone M, Lam M, Iwai M, Jonikas MC, Walter P, Ramundo S

The Mars1 kinase confers photoprotection through signaling in the chloroplast unfolded protein response.
Elife. 2019 Oct 15;8:e49577.
Jeng EE, Bhadkamkar V, Ibe NU, Gause H, Jiang L, Chan J, Jian R, Jimenez-Morales D, Stevenson E, Krogan NJ, Swaney DL, Snyder MP, Mukherjee S, Bassik MC

Systematic Identification of Host Cell Regulators of Legionella pneumophila Pathogenesis Using a Genome-wide CRISPR Screen.
Cell Host Microbe. 2019 Oct 9;26(4):551-563.e6. Epub 2019 Sep 17. PMID: 31540829; PMCID: PMC6800164.
Long AF, Kuhn J, Dumont S

The mammalian kinetochore-microtubule interface: robust mechanics and computation with many microtubules.
Curr Opin Cell Biol. 2019 Oct;60:60-67.
Gibson BA, Doolittle LK, Schneider MWG, Jensen LE, Gamarra N, Henry L, Gerlich DW, Redding S, Rosen MK

Organization of Chromatin by Intrinsic and Regulated Phase Separation.
Cell. 2019 Oct 3;179(2):470-484.e21. Epub 2019 Sep 19. PMID: 31543265; PMCID: PMC6778041.
Rodriguez L, Voorhies M, Gilmore S, Beyhan S, Myint A, Sil A

Opposing signaling pathways regulate morphology in response to temperature in the fungal pathogen Histoplasma capsulatum.
PLoS Biol. 2019 Sep 30;17(9):e3000168.
Soto-Perez P, Bisanz JE, Berry JD, Lam KN, Bondy-Denomy J, Turnbaugh PJ

CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog.
Cell Host Microbe. 2019 Sep 11;26(3):325-335.e5.
Woldemariam S, Nagpal J, Hill T, Li J, Schneider MW, Shankar R, Futey M, Varshney A, Ali N, Mitchell J, Andersen K, Barsi-Rhyne B, et al.

Using a Robust and Sensitive GFP-Based cGMP Sensor for Real-Time Imaging in Intact Caenorhabditis elegans.
Genetics. 2019 Sep;213(1):59-77.
Ghosh R, Colon-Negron K, Papa FR

Endoplasmic reticulum stress, degeneration of pancreatic islet β-cells, and therapeutic modulation of the unfolded protein response in diabetes.
Mol Metab. 2019 Sep;27S(Suppl):S60-S68.
Benitez M, Tatapudy S, Liu Y, Barber DL, Nystul TG

Drosophila anion exchanger 2 is required for proper ovary development and oogenesis.
Dev Biol. 2019 Aug 15;452(2):127-133.
Norman TM, Horlbeck MA, Replogle JM, Ge AY, Xu A, Jost M, Gilbert LA, Weissman JS

Exploring genetic interaction manifolds constructed from rich single-cell phenotypes.
Science. 2019 Aug 23;365(6455):786-793. Epub 2019 Aug 8. PMID: 31395745; PMCID: PMC6746554.
Lopez ML, Lo M, Kung JE, Dudkiewicz M, Jang GM, Von Dollen J, Johnson JR, Krogan NJ, Pawłowski K, Jura N

PEAK3/C19orf35 pseudokinase, a new NFK3 kinase family member, inhibits CrkII through dimerization.
Proc Natl Acad Sci U S A. 2019 Jul 30;116(31):15495-15504.
Qiu X, Zhang Y, Yang D, Hosseinzadeh S, Wang L, Yuan R, Xu S, Ma Y, Replogle JM, Darmanis S, Xing J, Weissman JS

Mapping Vector Field of Single Cells.
bioRxiv 696724.
Mendoza SD, Bondy-Denomy J

Cas13 Helps Bacteria Play Dead when the Enemy Strikes.
Cell Host Microbe. 2019 Jul 10;26(1):1-2.
Burke JE, Longhurst AD, Natarajan P, Rao B, Liu J, Sales-Lee J, Mortensen Y, Moresco JJ, Diedrich JK, Yates JR 3rd, Madhani HD

A Non-Dicer RNase III and Four Other Novel Factors Required for RNAi-Mediated Transposon Suppression in the Human Pathogenic Yeast Cryptococcus neoformans.
G3 (Bethesda). 2019 Jul 9;9(7):2235-2244.
Mandel-Brehm C, Dubey D, Kryzer TJ, O'Donovan BD, Tran B, Vazquez SE, Sample HA, Zorn KC, Khan LM, Bledsoe IO, McKeon A, Pleasure SJ, Lennon VA, DeRisi JL, Wilson MR, Pittock SJ

Kelch-like Protein 11 Antibodies in Seminoma-Associated Paraneoplastic Encephalitis.
N Engl J Med. 2019 Jul 4;381(1):47-54.
McGinnis CS, Patterson DM, Winkler J, Conrad DN, Hein MY, Srivastava V, Hu JL, Murrow LM, Weissman JS, Werb Z, Chow ED, Gartner ZJ

MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices.
Nat Methods. 2019 Jul;16(7):619-626.
Armache JP, Gamarra N, Johnson SL, Leonard JD, Wu S, Narlikar GJ, Cheng Y

Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome.
Elife. 2019 Jun 18;8:e46057. PMID: 31210637; PMCID: PMC6611695.
Yang B, Chen X, Wang Y, Feng S, Pessino V, Stuurman N, Cho NH, Cheng KW, Lord SJ, Xu L, Xie D, Mullins RD, Leonetti MD, Huang B

Epi-illumination SPIM for volumetric imaging with high spatial-temporal resolution.
Nat Methods. 2019 Jun;16(6):501-504.
Wang Y, Huynh W, Skokan TD, Lu W, Weiss A, Vale RD

CRACR2a is a calcium-activated dynein adaptor protein that regulates endocytic traffic.
J Cell Biol. 2019 May 6;218(5):1619-1633.
Kenner LR, Anand AA, Nguyen HC, Myasnikov AG, Klose CJ, McGeever LA, Tsai JC, Miller-Vedam LE, Walter P, Frost A

eIF2B-catalyzed nucleotide exchange and phosphoregulation by the integrated stress response.
Science. 2019 May 3;364(6439):491-495.
McGinnis CS, Murrow LM, Gartner ZJ

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors.
Cell Syst. 2019 Apr 24;8(4):329-337.e4.
Greenstein RA, Al-Sady B

Epigenetic fates of gene silencing established by heterochromatin spreading in cell identity and genome stabilit.
Curr Genet. 2019 Apr;65(2):423-428.
Castel P, Cheng A, Cuevas-Navarro A, Everman DB, Papageorge AG, Simanshu DK, Tankka A, Galeas J, Urisman A, McCormick F

RIT1 oncoproteins escape LZTR1-mediated proteolysis.
Science. 2019 Mar 15;363(6432):1226-1230.
Witchley JN, Penumetcha P, Abon NV, Woolford CA, Mitchell AP, Noble SM

Candida albicans Morphogenesis Programs Control the Balance between Gut Commensalism and Invasive Infection.
Cell Host Microbe. 2019 Mar 13;25(3):432-443.e6.
Jiang F, Liu JJ, Osuna BA, Xu M, Berry JD, Rauch BJ, Nogales E, Bondy-Denomy J, Doudna JA

Temperature-Responsive Competitive Inhibition of CRISPR-Cas9.
Mol Cell. 2019 Feb 7;73(3):601-610.
Rabouw HH, Langereis MA, Anand AA, Visser LJ, de Groot RJ, Walter P, van Kuppeveld FJM

Small molecule ISRIB suppresses the integrated stress response within a defined window of activation.
Proc Natl Acad Sci U S A. 2019 Feb 5;116(6):2097-2102.
Peters JM, Koo BM, Patino R, Heussler GE, Hearne CC, Qu J, Inclan YF, Hawkins JS, Lu CHS, Silvis MR, Harden MM, Osadnik H, Peters JE, Engel JN, Dutton RJ, Grossman AD, Gross CA, Rosenberg OS

Enabling genetic analysis of diverse bacteria with Mobile-CRISPRi.
Nat Microbiol. 2019 Feb;4(2):244-250.
Ruiz K, Thaker TM, Agnew C, Miller-Vedam L, Trenker R, Herrera C, Ingaramo M, Toso D, Frost A, Jura N

Functional role of PGAM5 multimeric assemblies and their polymerization into filaments.
Nat Commun. 2019 Jan 31;10(1):531.
Longbotham JE, Chio CM, Dharmarajan V, Trnka MJ, Torres IO, Goswami D, Ruiz K, Burlingame AL, Griffin PR, Fujimori DG

Histone H3 binding to the PHD1 domain of histone demethylase KDM5A enables active site remodeling.
Nat Commun. 2019 Jan 9;10(1):94.
Shah KN, Bhatt R, Rotow J, Rohrberg J, Olivas V, Wang VE, Hemmati G, Martins MM, Maynard A, Kuhn J, Galeas J, Donnella HJ, Kaushik S, Ku A, Dumont S, Krings G, Haringsma HJ, Robillard L, Simmons AD, Harding TC, McCormick F, Goga A, Blakely CM, Bivona TG, Bandyopadhyay S

Aurora kinase A drives the evolution of resistance to third-generation EGFR inhibitors in lung cancer.
Nat Med. 2019 Jan;25(1):111-118.
Hultquist JF, Hiatt J, Schumann K, McGregor MJ, Roth TL, Haas P, Doudna JA, Marson A, Krogan NJ.

CRISPR-Cas9 genome engineering of primary CD4 + T cells for the interrogation of HIV-host factor interactions.
Nat Protoc. 2019 Jan;14(1):1-27.
Batra J, Hultquist JF, Liu D, Shtanko O, Von Dollen J, Satkamp L, Jang GM, Luthra P, Schwarz TM, Small GI, Arnett E, Anantpadma M, Reyes A, Leung DW, Kaake R, Haas P, Schmidt CB, Schlesinger LS, LaCount DJ, Davey RA, Amarasinghe GK, Basler CF, Krogan NJ

Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication.
Cell. 2018 Dec 13;175(7):1917-1930.e13.
Sheridan CM, Garcia VE, Ahyong V, DeRisi JL

The Plasmodium falciparum cytoplasmic translation apparatus: a promising therapeutic target not yet exploited by clinically approved anti-malarials.
Malar J. 2018 Dec 12;17(1):465.
Kim-Yip RP, Nystul TG

Wingless promotes EGFR signaling in follicle stem cells to maintain self-renewal.
Development. 2018 Dec 5;145(23):dev168716.
Keenen MM, Larson AG, Narlikar GJ

Visualization and Quantitation of Phase-Separated Droplet Formation by Human HP1α.
Methods Enzymol. 2018;611:51-66.
Laurie MT, White CV, Retallack H, Wu W, Moser MS, Sakanari JA, Ang K, Wilson C, Arkin MR, DeRisi JL

Functional Assessment of 2,177 U.S. and International Drugs Identifies the Quinoline Nitroxoline as a Potent Amoebicidal Agent against the Pathogen Balamuthia mandrillaris.
mBio. 2018 Oct 30;9(5):e02051-18.
Hansen MMK, Desai RV, Simpson ML, Weinberger LS

Cytoplasmic Amplification of Transcriptional Noise Generates Substantial Cell-to-Cell Variability.
Cell Syst. 2018 Oct 24;7(4):384-397.e6.
Hrit J, Goodrich L, Li C, Wang BA, Nie J, Cui X, Martin EA, Simental E, Fernandez J, Liu MY, Nery JR, Castanon R, Kohli RM, Tretyakova N, He C, Ecker JR, Goll M, Panning B

OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development.
Elife. 2018 Oct 16;7:e34870.
Sorrells TR, Johnson AN, Howard CJ, Britton CS, Fowler KR, Feigerle JT, Weil PA, Johnson AD

Intrinsic cooperativity potentiates parallel cis-regulatory evolution.
Elife. 2018 Sep 10;7:e37563.
Willsey AJ, Morris MT, Wang S, Willsey HR, Sun N, Teerikorpi N, Baum TB, Cagney G, Bender KJ, Desai TA, Srivastava D, Davis GW, Doudna J, Chang E, Sohal V, Lowenstein DH, Li H, Agard D, Keiser MJ, Shoichet B, von Zastrow M, Mucke L, Finkbeiner S, Gan L, Sestan N, Ward ME, Huttenhain R, Nowakowski TJ, Bellen HJ, Frank LM, Khokha MK, Lifton RP, Kampmann M, Ideker T, State MW, Krogan NJ

The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders.
Cell. 2018 Jul 26;174(3):505-520.
Greenstein RA, Jones SK, Spivey EC, Rybarski JR, Finkelstein IJ, Al-Sady B

Noncoding RNA-nucleated heterochromatin spreading is intrinsically labile and requires accessory elements for epigenetic stability.
Elife. 2018 Jul 18;7:e32948.
Lin A, Makushok T, Diaz U, Marshall WF

Methods for the Study of Regeneration in Stentor.
J Vis Exp. 2018 Jun 13;(136):57759.
Zurita Rendón O, Fredrickson EK, Howard CJ, Van Vranken J, Fogarty S, Tolley ND, Kalia R, Osuna BA, Shen PS, Hill CP, Frost A, Rutter J

Vms1p is a release factor for the ribosome-associated quality control complex.
Nat Commun. 2018 Jun 6;9(1):2197.
Burke JE, Longhurst AD, Merkurjev D, Sales-Lee J, Rao B, Moresco JJ, Yates JR 3rd, Li JJ, Madhani HD

Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution.
Cell. 2018 May 3;173(4):1014-1030.e17.
Eichel K, Jullié D, Barsi-Rhyne B, Latorraca NR, Masureel M, Sibarita JB, Dror RO, von Zastrow M

Catalytic activation of β-arrestin by GPCRs.
Nature. 2018 May;557(7705):381-386.
Larson AG, Narlikar GJ

The Role of Phase Separation in Heterochromatin Formation, Function, and Regulation.
Biochemistry. 2018 May 1;57(17):2540-2548.
Gamarra N, Johnson SL, Trnka MJ, Burlingame AL, Narlikar GJ

The nucleosomal acidic patch relieves auto-inhibition by the ISWI remodeler SNF2h.
Elife. 2018 Apr 17;7:e35322.
Tsai JC, Miller-Vedam LE, Anand AA, Jaishankar P, Nguyen HC, Renslo AR, Frost A, Walter P

Structure of the nucleotide exchange factor eIF2B reveals mechanism of memory-enhancing molecule.
Science. 2018 Mar 30;359(6383):eaaq0939.
Liang SI, van Lengerich B, Eichel K, Cha M, Patterson DM, Yoon TY, von Zastrow M, Jura N, Gartner ZJ

Phosphorylated EGFR Dimers Are Not Sufficient to Activate Ras.
Cell Rep. 2018 Mar 6;22(10):2593-2600.
Eichel K, von Zastrow M

Subcellular Organization of GPCR Signaling.
Trends Pharmacol Sci. 2018 Feb;39(2):200-208.
Tatapudy S, Aloisio F, Barber D, Nystul T

Cell fate decisions: emerging roles for metabolic signals and cell morphology.
EMBO Rep. 2017 Dec;18(12):2105-2118. doi: 10.15252/embr.201744816.
Carbone CB, Kern N, Fernandes RA, Hui E, Su X, Garcia KC, Vale RD

In vitro reconstitution of T cell receptor-mediated segregation of the CD45 phosphatase.
Proc Natl Acad Sci U S A. 2017 Oct 31;114(44):E9338-E9345.
Huynh W, Vale RD

Disease-associated mutations in human BICD2 hyperactivate motility of dynein-dynactin.
J Cell Biol. 2017 Oct 2;216(10):3051-3060.
Tatapudy S, Benitez M, Nystul T

Methods for Imaging Intracellular pH of the Follicle Stem Cell Lineage in Live Drosophila Ovarian Tissue.
J Vis Exp. 2017 Sep 26;(127):56316.
Seoane A, Morgan DO

Firing of Replication Origins Frees Dbf4-Cdc7 to Target Eco1 for Destruction.
Curr Biol. 2017 Sep 25;27(18):2849-2855.e2.
Kostova KK, Hickey KL, Osuna BA, Hussmann JA, Frost A, Weinberg DE, Weissman JS

CAT-tailing as a fail-safe mechanism for efficient degradation of stalled nascent polypeptides.
Science. 2017 Jul 28;357(6349):414-417.
Osuna BA, Howard CJ, Kc S, Frost A, Weinberg DE

In vitro analysis of RQC activities provides insights into the mechanism and function of CAT tailing.
Elife. 2017 Jul 18;6:e27949.
Larson AG, Elnatan D, Keenen MM, Trnka MJ, Johnston JB, Burlingame AL, Agard DA, Redding S, Narlikar GJ

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin.
Nature. 2017 Jul 13;547(7662):236-240.
Farmer DT, Finley JK, Chen FY, Tarifeño-Saldivia E, McNamara NA, Knox SM, McManus MT

miR-205 is a critical regulator of lacrimal gland development.
Dev Biol. 2017 Jul 1;427(1):12-20.
Farmer DT, Nathan S, Finley JK, Shengyang Yu K, Emmerson E, Byrnes LE, Sneddon JB, McManus MT, Tward AD, Knox SM

Defining epithelial cell dynamics and lineage relationships in the developing lacrimal gland.
Development. 2017 Jul 1;144(13):2517-2528.
Zhou CY, Stoddard CI, Johnston JB, Trnka MJ, Echeverria I, Palovcak E, Sali A, Burlingame AL, Cheng Y, Narlikar GJ

Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones.
Cell Rep. 2017 Jun 6;19(10):2033-2044.
Kuhn J, Dumont S

Spindle assembly checkpoint satisfaction occurs via end-on but not lateral attachments under tension.
J Cell Biol. 2017 Jun 5;216(6):1533-1542.
Baggett NE, Zhang Y, Gross CA

Global analysis of translation termination in E. coli.
PLoS Genet. 2017 Mar 16;13(3):e1006676.
Slabodnick MM, Ruby JG, Reiff SB, Swart EC, Gosai S, Prabakaran S, Witkowska E, Larue GE, Fisher S, Freeman RM Jr, Gunawardena J, Chu W, Stover NA, Gregory BD, Nowacki M, Derisi J, Roy SW, Marshall WF, Sood P

The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell.
Curr Biol. 2017 Feb 20;27(4):569-575.
Farmer DT, McManus MT

MicroRNAs in ectodermal appendages.
Curr Opin Genet Dev. 2017 Jan 16;43:61-66.
Rauch BJ, Silvis MR, Hultquist JF, Waters CS, McGregor MJ, Krogan NJ, Bondy-Denomy J

Inhibition of CRISPR-Cas9 with Bacteriophage Proteins.
Cell. 2017 Jan 12;168(1-2):150-158.e10.
Stewart-Ornstein J, Chen S, Bhatnagar R, Weissman JS, El-Samad H

Model-guided optogenetic study of PKA signaling in budding yeast.
Mol Biol Cell. 2017 Jan 1;28(1):221-227. PMCID: PMC5221627.
Fernandes JD, Faust TB, Strauli NB, Smith C, Crosby DC, Nakamura RL, Hernandez RD, Frankel AD

Functional Segregation of Overlapping Genes in HIV.
Cell. 2016 Dec 15;167(7):1762-1773.e12. PMCID: PMC5287106.
Johnston MJ, Bar-Cohen S, Paroush Z, Nystul TG

Phosphorylated Groucho delays differentiation in the follicle stem cell lineage by providing a molecular memory of EGFR signaling in the niche.
Development. 2016 Dec 15;143(24):4631-4642. PMCID: PMC5201033.
Varandas KC, Irannejad R, von Zastrow M

Retromer Endosome Exit Domains Serve Multiple Trafficking Destinations and Regulate Local G Protein Activation by GPCRs.
Curr Biol. 2016 Dec 5;26(23):3129-3142. PMCID: PMC5140749.
Ulmschneider B, Grillo-Hill BK, Benitez M, Azimova DR, Barber DL, Nystul TG

Increased intracellular pH is necessary for adult epithelial and embryonic stem cell differentiation.
J Cell Biol. 2016 Nov 7;215(3):345-355. PMCID: PMC5100294.
Yuan K, Seller CA, Shermoen AW, O'Farrell PH

Timing the Drosophila Mid-Blastula Transition: A Cell Cycle-Centered View.
Trends Genet. 2016 Aug;32(8):496-507. PMCID: PMC4958567.
Schroeder CM, Vale RD

Assembly and activation of dynein-dynactin by the cargo adaptor protein Hook3.
J Cell Biol. 2016 Aug 1;214(3):309-18. PMCID: PMC4970328.
Lyon AS, Morin G, Moritz M, Yabut KC, Vojnar T, Zelter A, Muller E, Davis TN, Agard DA

Higher-order oligomerization of Spc110p drives γ-tubulin ring complex assembly.
Mol Biol Cell. 2016 Jul 15;27(14):2245-58. PMCID: PMC4945142.
Zhou CY, Johnson SL, Gamarra NI, Narlikar GJ

Mechanisms of ATP-Dependent Chromatin Remodeling Motors.
Annu Rev Biophys. 2016 Jul 5;45:153-81.
Verba KA, Wang RY, Arakawa A, Liu Y, Shirouzu M, Yokoyama S, Agard DA

Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase.
Science. 2016 Jun 24;352(6293):1542-7.
McKenney RJ, Huynh W, Vale RD, Sirajuddin M

Tyrosination of α-tubulin controls the initiation of processive dynein-dynactin motility.
EMBO J. 2016 Jun 1;35(11):1175-85. PMCID: PMC4888239.
Isaac RS, Jiang F, Doudna JA, Lim WA, Narlikar GJ, Almeida R

Nucleosome breathing and remodeling constrain CRISPR-Cas9 function.
Elife. 2016 Apr 28;5. PMCID: PMC4880442.
Eichel K, Jullié D, von Zastrow M

β-Arrestin drives MAP kinase signalling from clathrin-coated structures after GPCR dissociation.
Nat Cell Biol. 2016 Mar;18(3):303-10. PMCID: PMC4767649.
Dinsmore C, Reiter JF

Endothelial primary cilia inhibit atherosclerosis.
EMBO Rep. 2016 Feb;17(2):156-66. PMCID: PMC5290813.
Coyle SM, Lim WA

Mapping the functional versatility and fragility of Ras GTPase signaling circuits through in vitro network reconstitution.
Elife. 2016 Jan 14;5. PMCID: PMC4775219.
Bhaba G, Johnson GT, Schroeder CM, Vale RD

How Dynein Moves Along Microtubules.
Trends Biochem Sci. 2016 Jan;41(1):94-105. PMCID: PMC4706479.
Girard JR, Tenthorey JL, Morgan DO

An E2 Accessory Domain Increases Affinity for the Anaphase-Promoting Complex and Ensures E2 Competition.
J Biol Chem. 2015 Oct 2;290(40):24614-25. PMCID: PMC4591839.
Todhunter ME, Jee NY, Hughes AJ, Coyle MC, Cerchiari A, Farlow J, Garbe JC, LaBarge MA, Desai TA, Gartner ZJ

Programmed synthesis of three-dimensional tissues.
Nat Methods. 2015 Oct;12(10):975-81. PMCID: PMC4589502.
Hansen SD, Mullins RD

Lamellipodin promotes actin assembly by clustering Ena/VASP proteins and tethering them to actin filaments.
Elife. 2015 Aug 21;4. PMCID: PMC4543927.
Mark KG, Meza-Gutierrez F, Johnson JR, Newton BW, Krogan NJ, Toczyski DP

Prb1 Protease Activity Is Required for Its Recognition by the F-Box Protein Saf1.
Biochemistry. 2015 Jul 28;54(29):4423-6.
Leaf A, von Zastrow M

Dopamine receptors reveal an essential role of IFT-B, KIF17, and Rab23 in delivering specific receptors to primary cilia.
Elife. 2015 Jul 16;4. PMCID: PMC4547097.
Loveless TB, Topacio BR, Vashisht AA, Galaang S, Ulrich KM, Young BD, Wohlschlegel JA, Toczyski DP

DNA Damage Regulates Translation through β-TRCP Targeting of CReP.
PLoS Genet. 2015 Jun 19;11(6):e1005292. PMCID: PMC4474599.
Fox EP, Bui CK, Nett JE, Hartooni N, Mui MC, Andes DR, Nobile CJ, Johnson AD

An expanded regulatory network temporally controls Candida albicans biofilm formation.
Mol Microbiol. 2015 Jun;96(6):1226-39. PMCID: PMC4464956.
Sorrells TR, Johnson AD

Making Sense of Transcription Networks.
Cell. 2015 May 7;161:714-723. PMCID: in progress.
Wu J, Pipathsouk A, Keizer-Gunnink A, Fusetti F, Alkema W, Liu S, Altschuler S, Wu L, Kortholt A, Weiner OD

Homer3 regulates the establishment of neutrophil polarity.
Mol Biol Cell. 2015 May 1;26(9):1629-39. PMCID: PMC4436775.
Dovala D, Rosenberg O, Li Z, Bendebury A, Finer-Moore J, Holten J, Cheng Y, Stroud RM, Cox JS

Substrates Control Multimerization and Activation of the Multi-domain ATPase Motor of Type VII Secretion.
Cell. 2015 Apr 23;161(3):501-12. PMCID: PMC4409929.
Edenberg ER, Mark KG, Toczyski DP

Ndd1 turnover by SCF(Grr1) is inhibited by the DNA damage checkpoint in Saccharomyces cerevisiae.
PLoS Genet. 2015 Apr 20;11(4):e1005162. PMCID: PMC4403921.
Roberson EC, Dowdle WE, Ozanturk A, Garcia-Gonzalo FR, Li C, Halbritter J, Elkhartoufi N, Porath JD, Cope H, Ashley-Koch A, Gregory S, Thomas S, Sayer JA, Saunier S, Otto EA, Katsanis N, Davis EE, Attié-Bitach T, Hildebrandt F, Leroux MR, Reiter JF

TMEM231, mutated in orofaciodigital and Meckel syndromes, organizes the ciliary transition zone.
J Cell Biol. 2015 Apr 13;209:129-142. PMCID: PMC4395494.
Ludington WB, Ishikawa H, Serebrenik YV, Ritter A, Hernandez-Lopez RA, Gunzenhauser J, Kannegaard E, Marshall WF

A systematic comparison of mathematical models for inherent measurement of ciliary length: how a cell can measure length and volume.
Biophys J. 2015 Mar 24;108(6):1361-79. PMCID: PMC4375445.
Yee LE, Reiter JF

Ciliary vesicle formation: a prelude to ciliogenesis.
Dev Cell. 2015 Mar 23;32(6):665-6.
Leonard JD, Narlikar GJ

A nucleotide-driven switch regulates flanking DNA length sensing by a dimeric chromatin remodeler.
Mol Cell. 2015 Mar 5;57(5):850-9. PMCID: PMC4355161.
Schulte MB, Draghi JA, Plotkin JB, Andino R

Experimentally guided models reveal replication principles that shape the mutation distribution of RNA viruses.
Elife. 2015 Jan 30;4. PMCID: PMC4311501.
Dumesic PA, Homer CM, Moresco JJ, Pack LR, Shanle EK, Coyle SM, Strahl BD, Fujimori DG, Yates JR 3rd, Madhani HD

Product binding enforces the genomic specificity of a yeast polycomb repressive complex.
Cell. 2015 Jan 15;160:204-18. PMCID: PMC4303595.
Dumesic PA, Homer CM, Moresco JJ, Pack LR, Shanle EK, Coyle SM, Strahl BD, Fujimori DG, Yates JR, Madhani HD

Product binding enforces the genomic specificity of a yeast polycomb repressive complex.
Cell. 2015 Jan 15;160(1-2):204-18. PMCID: PMC4303595.

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