Lead Publications
Additional Publications

Lead Publications

Identifying Ciliary Proteins in Mammalian Retinas using a Gentle Extraction Method
Adeline S. Fredrick, Erin R. Claussen, Samantha N. Fischer, Samson Balasanyants, Akshaya Rajaraman, Andi C. Rosner, and Kevin Drew
microPublication Biology 2024

Scaffold Matcher: A CMA-ES based algorithm for identifying hotspot aligned peptidomimetic scaffolds
Erin R. Claussen, P. Douglas Renfrew, Christian L. Müller, Kevin Drew
Proteins, 2023

hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies
Kevin Drew, John B. Wallingford, Edward M. Marcotte
Molecular Systems Biology, 2021

A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating machinery.
Kevin Drew*, Chanjae Lee*, Rachael M. Cox, Vy Dang, Caitlin C. Devitt, Ophelia Papoulas, Ryan L. Huizar, Edward M. Marcotte and John B. Wallingford (* equal contribution)
Developmental Biology, 2020

Systematic discovery of endogenous human ribonucleoprotein complexes
Anna Mallam*, Wisath Sae-Lee, Jeffrey M. Schaub, Fan Tu, Anna Battenhouse, Yu Jin Jang, Jonghwan Kim, Ilya J. Finkelstein, Edward M. Marcotte, Kevin Drew* (* equal contribution)
Cell Reports, 2019

Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets.
Kevin Drew, Christian L. Müller, Richard Bonneau, Edward M. Marcotte
PLOS Computational Biology, 2017

Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes
Kevin Drew, Chanjae Lee, Ryan L Huizar, Fan Tu, Blake Borgeson, Claire D McWhite, Yun Ma, John B Wallingford, Edward M Marcotte
Molecular Systems Biology, 2017

Rational design of topographical helix mimics as potent inhibitors of protein–protein interactions
Brooke Bullock Lao*, Kevin Drew*, Danielle A Guarracino, Thomas F Brewer, Daniel W Heindel, Richard Bonneau, Paramjit S Arora (* shared first author)
Journal of the American Chemical Society, 2014

Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design
Kevin Drew*, P Douglas Renfrew*, Timothy W Craven, Glenn L Butterfoss, Fang-Chieh Chou, Sergey Lyskov, Brooke N Bullock, Andrew Watkins, Jason W Labonte, Michael Pacella, Krishna Praneeth Kilambi, Andrew Leaver-Fay, Brian Kuhlman, Jeffrey J Gray, Philip Bradley, Kent Kirshenbaum, Paramjit S Arora, Rhiju Das, Richard Bonneau (*shared first author)
PLoS One, 2013

The Proteome Folding Project: proteome-scale prediction of structure and function
Kevin Drew, Patrick Winters, Glenn L Butterfoss, Viktors Berstis, Keith Uplinger, Jonathan Armstrong, Michael Riffle, Erik Schweighofer, Bill Bovermann, David R Goodlett, Trisha N Davis, Dennis Shasha, Lars Malmström, Richard Bonneau
Genome Research, 2011

De novo protein structure prediction: methods and application.
Kevin Drew, Dylan Chivian and Richard Bonneau
Structural Bioinformatics 2nd Edition. 2009 John Wiley & Sons, Inc (Book Chapter)

BioNetBuilder: automatic integration of biological networks
Iliana Avila-Campillo*, Kevin Drew*, John Lin, David J Reiss, Richard Bonneau (* shared first author)
Bioinformatics, 2007

Computationally Analyzing Mass Spectra of Hydrogen Deuterium Exchange Experiments. (pdf)
Drew, K
Masters Dissertation, Tech-Report TR-2005-12, University of Chicago. April 10, 2005.

Additional Publications

Come for the atmosphere, stay for the interactions: Deciphering small molecule partitioning into biomolecular condensates
Bakhtyar Sepehri, Kevin Drew and Jose ́ A. Villegas
Cell Chemical Biology, 2023

The protein organization of a red blood cell
Wisath Sae-Lee, Caitlyn L McCafferty, Eric J Verbeke, Pierre C Havugimana, Ophelia Papoulas, Claire D McWhite, John R Houser, Kim Vanuytsel, George J Murphy, Kevin Drew, Andrew Emili, David W Taylor, Edward M Marcotte
Cell Reports, 2022

Co-fractionation/mass spectrometry to identify protein complexes
Claire D McWhite, Ophelia Papoulas, Kevin Drew, Vy Dang, Janelle C. Leggere, Wisath Sae-Lee, Edward M Marcotte
Star Protocols, 2021

Systematic Identification of Protein Phosphorylation-Mediated Interactions
Brendan M. Floyd, Kevin Drew, Edward M. Marcotte
Journal of Proteome Research, 2021

Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins
Chanjae Lee, Rachael Cox, Ophelia Papoulas, Amjad Horani, Kevin Drew, Caitlin Devitt, Steven L Brody, Edward Marcotte, John B Wallingford
eLife, 2020

A pan-plant protein complex map reveals deep conservation and novel assemblies.
McWhite, C.D., Papoulas, O., Drew, K., Cox, R.M., Oldfield-June, V., Dong, O.X., Kwon, T., Wan C., Salmi, M.L., Roux, S.J., Browning, K.S., Chen, Z.J., Ronald, P.C., Marcotte, E.M.
Cell, 2020

Classification of Single Particles from Human Cell Extract Reveals Distinct Structures
Eric J. Verbeke, Anna L. Mallam, Kevin Drew, Edward M. Marcotte, David W. Taylor
Cell Reports, 2018

An Adaptive Geometric Search Algorithm for Macromolecular Scaffold Selection
Tian Jiang, Douglas Renfrew, Kevin Drew, Noah Youngs, Glenn Butterfoss, Dennis Shasha, Richard Bonneau
Protein Engineering, Design and Selection, 2018

A phase separated organelle at the root of motile ciliopathy
Ryan Huizar, Chanjae Lee, Alexander Boulgakov, Amjad Horani, Fan Tu, Kevin Drew, Edward Marcotte, Steven Brody, John Wallingford
BioRxiv, 2017

The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery.
Michinori Toriyama, Chanjae Lee, S. Paige Taylor, Ivan Duran, Daniel H. Cohn , Ange-Line Bruel, Jacqueline M. Tabler, Kevin Drew, Marcus R. Kelley, Sukyoung Kim, Tae Joo Park, Daniella Braun, Ghislaine Pierquin, Armand Biver, Kerstin Wagner, Anne Malfroot, Inusha Panigrahi, Brunella Franco, Hadeel Adel Al-lami, Yvonne Yeung, Yeon Ja Choi, University of Washington Center for Mendelian Genomics, Yannis Duffourd, L Faivre, JB Rivière, Jiang Chen, Karen J. Liu, Edward M. Marcotte, Friedhelm Hildebrandt, Christel Thauvin-Robinet, Deborah Krakow, Peter K. Jackson, and John B. Wallingford
Nature Genetics, 2016

Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes
Sadhna Phanse, Cuihong Wan, Blake Borgeson, Fan Tu, Kevin Drew, Greg Clark, Xuejian Xiong, Olga Kagan, Julian Kwan, Alexandr Bezginov, Kyle Chessman, Swati Pal, Graham Cromar, Ophelia Papoulas, Zuyao Ni, Daniel R. Boutz, Snejana Stoilova, Pierre C. Havugimana, Xinghua Guo, Ramy H. Malty, Mihail Sarov, Jack Greenblatt, Mohan Babu, W. Brent Derry, Elisabeth R. Tillier, John B. Wallingford, John Parkinson, Edward M. Marcotte, Andrew Emili
Data in Brief, 2015

Panorama of ancient metazoan macromolecular complexes
Cuihong Wan, Blake Borgeson, Sadhna Phanse, Fan Tu, Kevin Drew, Greg Clark, Xuejian Xiong, Olga Kagan, Julian Kwan, Alexandr Bezginov, Kyle Chessman, Swati Pal, Graham Cromar, Ophelia Papoulas, Zuyao Ni, Daniel R Boutz, Snejana Stoilova, Pierre C Havugimana, Xinghua Guo, Ramy H Malty, Mihail Sarov, Jack Greenblatt, Mohan Babu, W Brent Derry, Elisabeth R Tillier, John B Wallingford, John Parkinson, Edward M Marcotte, Andrew Emili
Nature, 2015

Conformational preferences of peptide–peptoid hybrid oligomers
Glenn L Butterfoss, Kevin Drew, P Douglas Renfrew, Kent Kirshenbaum, Richard Bonneau
Peptide Science, 2014

Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20–27
Krishna Praneeth Kilambi, Michael S Pacella, Jianqing Xu, Jason W Labonte, Justin R Porter, Pravin Muthu, Kevin Drew, Daisuke Kuroda, Ora Schueler‐Furman, Richard Bonneau, Jeffrey J Gray
Proteins: Structure, Function, and Bioinformatics, 2013

Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE)
Sergey Lyskov, Fang-Chieh Chou, Shane Ó Conchúir, Bryan S Der, Kevin Drew, Daisuke Kuroda, Jianqing Xu, Brian D Weitzner, P Douglas Renfrew, Parin Sripakdeevong, Benjamin Borgo, James J Havranek, Brian Kuhlman, Tanja Kortemme, Richard Bonneau, Jeffrey J Gray, Rhiju Das
PLoS One, 2013

Parametric Bayesian priors and better choice of negative examples improve protein function prediction
Noah Youngs, Duncan Penfold-Brown, Kevin Drew, Dennis Shasha, Richard Bonneau
Bioinformatics, 2013

The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts
Alexander G Baltz, Mathias Munschauer, Björn Schwanhäusser, Alexandra Vasile, Yasuhiro Murakawa, Markus Schueler, Noah Youngs, Duncan Penfold-Brown, Kevin Drew, Miha Milek, Emanuel Wyler, Richard Bonneau, Matthias Selbach, Christoph Dieterich, Markus Landthaler
Molecular cell, 2012

The plant proteome folding project: structure and positive selection in plant protein families
MM Pentony, P Winters, D Penfold-Brown, K Drew, A Narechania, R DeSalle, R Bonneau, MD Purugganan
Genome biology and evolution, 2012

Rational design of temperature-sensitive alleles using computational structure prediction
Christopher S Poultney, Glenn L Butterfoss, Michelle R Gutwein, Kevin Drew, David Gresham, Kristin C Gunsalus, Dennis E Shasha, Richard Bonneau
PloS one, 2011

The coat morphogenetic protein SpoVID is necessary for spore encasement in Bacillus subtilis
Katherine H Wang, Anabela L Isidro, Lia Domingues, Haig A Eskandarian, Peter T McKenney, Kevin Drew, Paul Grabowski, Ming‐Hsiu Chua, Samantha N Barry, Michelle Guan, Richard Bonneau, Adriano O Henriques, Patrick Eichenberger
Molecular microbiology, 2009

BioNetBuilder2. 0: bringing systems biology to chicken and other model organisms
Jay H Konieczka, Kevin Drew, Alex Pine, Kevin Belasco, Sean Davey, Tatiana A Yatskievych, Richard Bonneau, Parker B Antin
BMC genomics, 2009

A protein domain-based interactome network for C. elegans early embryogenesis
Mike Boxem, Zoltan Maliga, Niels Klitgord, Na Li, Irma Lemmens, Miyeko Mana, Lorenzo de Lichtervelde, Joram D Mul, Diederik van de Peut, Maxime Devos, Nicolas Simonis, Muhammed A Yildirim, Murat Cokol, Huey-Ling Kao, Anne-Sophie De Smet, Haidong Wang, Anne-Lore Schlaitz, Tong Hao, Stuart Milstein, Changyu Fan, Mike Tipsword, Kevin Drew, Matilde Galli, Kahn Rhrissorrakrai, David Drechsel, Daphne Koller, Frederick P Roth, Lilia M Iakoucheva, A Keith Dunker, Richard Bonneau, Kristin C Gunsalus, David E Hill, Fabio Piano, Jan Tavernier, Sander van den Heuvel, Anthony A Hyman, Marc Vidal
Cell, 2008

Investigating quantitation of phosphorylation using MALDI‐TOF mass spectrometry
Laurie Parker, Aaron Engel‐Hall, Kevin Drew, George Steinhardt, Donald L Helseth Jr, David Jabon, Timothy McMurry, David S Angulo, Stephen J Kron
Journal of mass spectrometry, 2008

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