Going beyond clustering in MD trajectory analysis: an application to villin headpiece folding.

by Aruna Rajan, Peter L Freddolino, Klaus Schulten
Published 2010-04-01

Fitness landscape transformation through a single amino acid change in the rho terminator.

by Peter L Freddolino, Hani Goodarzi, Saeed Tavazoie
Published 2012-05-01

Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry

by Peter L Freddolino, Jamie Yang, Amir Momen-Roknabadi, Saeed Tavazoie
Published 2018-04-01

Dynamic landscape of protein occupancy across the Escherichia coli chromosome.

by Peter L Freddolino, Haley M Amemiya, Thomas J Goss, Saeed Tavazoie
Published 2021-06-01

An intrinsically disordered linker controlling the formation and the stability of the bacterial flagellar hook

by Clive S. Barker, Irina V. Meshcheryakova, Alla S. Kostyukova, Peter L. Freddolino, Fadel A. Samatey
Published 2017-10-01

Bacterial adaptation through loss of function.

by Alison K Hottes, Peter L Freddolino, Anupama Khare, Zachary N Donnell, Julia C Liu, Saeed Tavazoie
Published 2013-01-01

Rapid metabolic shifts occur during the transition between hunger and satiety in Drosophila melanogaster

by Daniel Wilinski, Jasmine Winzeler, William Duren, Jenna L. Persons, Kristina J. Holme, Johan Mosquera, Morteza Khabiri, Jason M. Kinchen, Peter L. Freddolino, Alla Karnovsky, Monica Dus
Published 2019-09-01

Uncovering Transcriptional Regulators and Targets of sRNAs Using an Integrative Data-Mining Approach: H-NS-Regulated RseX as a Case Study

by Mia K. Mihailovic, Alyssa M. Ekdahl, Angela Chen, Abigail N. Leistra, Bridget Li, Javier González Martínez, Matthew Law, Cindy Ejindu, Éric Massé, Peter L. Freddolino, Lydia M. Contreras
Published 2021-07-01

High Dietary Sugar Reshapes Sweet Taste to Promote Feeding Behavior in Drosophila melanogaster

by Christina E. May, Anoumid Vaziri, Yong Qi Lin, Olga Grushko, Morteza Khabiri, Qiao-Ping Wang, Kristina J. Holme, Scott D. Pletcher, Peter L. Freddolino, G. Gregory Neely, Monica Dus
Published 2019-05-01

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

by Naihui Zhou, Yuxiang Jiang, Timothy R. Bergquist, Alexandra J. Lee, Balint Z. Kacsoh, Alex W. Crocker, Kimberley A. Lewis, George Georghiou, Huy N. Nguyen, Md Nafiz Hamid, Larry Davis, Tunca Dogan, Volkan Atalay, Ahmet S. Rifaioglu, Alperen Dalkıran, Rengul Cetin Atalay, Chengxin Zhang, Rebecca L. Hurto, Peter L. Freddolino, Yang Zhang, Prajwal Bhat, Fran Supek, José M. Fernández, Branislava Gemovic, Vladimir R. Perovic, Radoslav S. Davidović, Neven Sumonja, Nevena Veljkovic, Ehsaneddin Asgari, Mohammad R.K. Mofrad, Giuseppe Profiti, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Florian Boecker, Heiko Schoof, Indika Kahanda, Natalie Thurlby, Alice C. McHardy, Alexandre Renaux, Rabie Saidi, Julian Gough, Alex A. Freitas, Magdalena Antczak, Fabio Fabris, Mark N. Wass, Jie Hou, Jianlin Cheng, Zheng Wang, Alfonso E. Romero, Alberto Paccanaro, Haixuan Yang, Tatyana Goldberg, Chenguang Zhao, Liisa Holm, Petri Törönen, Alan J. Medlar, Elaine Zosa, Itamar Borukhov, Ilya Novikov, Angela Wilkins, Olivier Lichtarge, Po-Han Chi, Wei-Cheng Tseng, Michal Linial, Peter W. Rose, Christophe Dessimoz, Vedrana Vidulin, Saso Dzeroski, Ian Sillitoe, Sayoni Das, Jonathan Gill Lees, David T. Jones, Cen Wan, Domenico Cozzetto, Rui Fa, Mateo Torres, Alex Warwick Vesztrocy, Jose Manuel Rodriguez, Michael L. Tress, Marco Frasca, Marco Notaro, Giuliano Grossi, Alessandro Petrini, Matteo Re, Giorgio Valentini, Marco Mesiti, Daniel B. Roche, Jonas Reeb, David W. Ritchie, Sabeur Aridhi, Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, Da Chen Emily Koo, Richard Bonneau, Vladimir Gligorijević, Meet Barot, Hai Fang, Stefano Toppo, Enrico Lavezzo, Marco Falda, Michele Berselli, Silvio C.E. Tosatto, Marco Carraro, Damiano Piovesan, Hafeez Ur Rehman, Qizhong Mao, Shanshan Zhang, Slobodan Vucetic, Gage S. Black, Dane Jo, Erica Suh, Jonathan B. Dayton, Dallas J. Larsen, Ashton R. Omdahl, Liam J. McGuffin, Danielle A. Brackenridge, Patricia C. Babbitt, Jeffrey M. Yunes, Paolo Fontana, Feng Zhang, Shanfeng Zhu, Ronghui You, Zihan Zhang, Suyang Dai, Shuwei Yao, Weidong Tian, Renzhi Cao, Caleb Chandler, Miguel Amezola, Devon Johnson, Jia-Ming Chang, Wen-Hung Liao, Yi-Wei Liu, Stefano Pascarelli, Yotam Frank, Robert Hoehndorf, Maxat Kulmanov, Imane Boudellioua, Gianfranco Politano, Stefano Di Carlo, Alfredo Benso, Kai Hakala, Filip Ginter, Farrokh Mehryary, Suwisa Kaewphan, Jari Björne, Hans Moen, Martti E.E. Tolvanen, Tapio Salakoski, Daisuke Kihara, Aashish Jain, Tomislav Šmuc, Adrian Altenhoff, Asa Ben-Hur, Burkhard Rost, Steven E. Brenner, Christine A. Orengo, Constance J. Jeffery, Giovanni Bosco, Deborah A. Hogan, Maria J. Martin, Claire O’Donovan, Sean D. Mooney, Casey S. Greene, Predrag Radivojac, Iddo Friedberg
Published 2019-11-01