Data driven flexible backbone protein design.

by Mark G F Sun, Philip M Kim
Published 2017-08-01

A computational approach for designing D-proteins with non-canonical amino acid optimised binding affinity.

by Michael Garton, Maryam Sayadi, Philip M Kim
Published 2017-01-01

The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics.

by Haiyuan Yu, Philip M Kim, Emmett Sprecher, Valery Trifonov, Mark Gerstein
Published 2007-04-01

Combining structural modeling with ensemble machine learning to accurately predict protein fold stability and binding affinity effects upon mutation.

by Niklas Berliner, Joan Teyra, Recep Colak, Sebastian Garcia Lopez, Philip M Kim
Published 2014-01-01

Network evolution: rewiring and signatures of conservation in signaling.

by Mark G F Sun, Martin Sikora, Michael Costanzo, Charles Boone, Philip M Kim
Published 2012-01-01

Computational generation of proteins with predetermined three-dimensional shapes using ProteinSolver

by Alexey Strokach, David Becerra, Carles Corbi-Verge, Albert Perez-Riba, Philip M. Kim
Published 2021-06-01

Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding

by Hamed S. Najafabadi, Michael Garton, Matthew T. Weirauch, Sanie Mnaimneh, Ally Yang, Philip M. Kim, Timothy R. Hughes
Published 2017-09-01

The Chemical Fluctuation Theorem governing gene expression

by Seong Jun Park, Sanggeun Song, Gil-Suk Yang, Philip M. Kim, Sangwoon Yoon, Ji-Hyun Kim, Jaeyoung Sung
Published 2018-01-01

Measuring the evolutionary rewiring of biological networks.

by Chong Shou, Nitin Bhardwaj, Hugo Y K Lam, Koon-Kiu Yan, Philip M Kim, Michael Snyder, Mark B Gerstein
Published 2011-01-01

Distinct types of disorder in the human proteome: functional implications for alternative splicing.

by Recep Colak, TaeHyung Kim, Magali Michaut, Mark Sun, Manuel Irimia, Jeremy Bellay, Chad L Myers, Benjamin J Blencowe, Philip M Kim
Published 2013-04-01

High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution.

by Yehudit Hasin, Tsviya Olender, Miriam Khen, Claudia Gonzaga-Jauregui, Philip M Kim, Alexander Eckehart Urban, Michael Snyder, Mark B Gerstein, Doron Lancet, Jan O Korbel
Published 2008-11-01

Semi-supervised Learning Predicts Approximately One Third of the Alternative Splicing Isoforms as Functional Proteins

by Yanqi Hao, Recep Colak, Joan Teyra, Carles Corbi-Verge, Alexander Ignatchenko, Hannes Hahne, Mathias Wilhelm, Bernhard Kuster, Pascal Braun, Daisuke Kaida, Thomas Kislinger, Philip M. Kim
Published 2015-07-01

Large‐scale survey and database of high affinity ligands for peptide recognition modules

by Joan Teyra, Abdellali Kelil, Shobhit Jain, Mohamed Helmy, Raghav Jajodia, Yogesh Hooda, Jun Gu, Akshay A D’Cruz, Sandra E Nicholson, Jinrong Min, Marius Sudol, Philip M Kim, Gary D Bader, Sachdev S Sidhu
Published 2020-12-01

Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins.

by Raffi Tonikian, Xiaofeng Xin, Christopher P Toret, David Gfeller, Christiane Landgraf, Simona Panni, Serena Paoluzi, Luisa Castagnoli, Bridget Currell, Somasekar Seshagiri, Haiyuan Yu, Barbara Winsor, Marc Vidal, Mark B Gerstein, Gary D Bader, Rudolf Volkmer, Gianni Cesareni, David G Drubin, Philip M Kim, Sachdev S Sidhu, Charles Boone
Published 2009-10-01