(* indicates co-corresponding authors)


High Dietary Sugar Reshapes Sweet Taste to Promote Feeding Behavior in Drosophila melanogaster. 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, and Monica Dus. Cell Reports, in press. [html]

Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas. Adam E. Dolan, Zhonggang Hou, Yibei Xiao, Max J. Gramelspacher, Jaewon Heo, Sara E. Howden, Peter L. Freddolino, Ailong Ke, and Yan Zhang. Molecular Cell, in press. [html]

Applications of molecular modeling to flavoproteins: Insights and challenges. Emil Sjulstok, Ilia A. Solov'yov, and Peter L. Freddolino. Methods in Enzymology, 620:277-314, 2019. [html]

High-Resolution Mapping of the Escherichia coli Chromosome Reveals Positions of High and Low Transcription. Scott A. Scholz, Rucheng Diao, Michael B. Wolfe, Elayne M. Fivenson, Xiaoxia Nina Lin*, and Peter L. Freddolino*. Cell Systems 8:212-225, 2019. [html]

Global analysis of RNA metabolism using bio-orthogonal labeling coupled with next-generation RNA sequencing. Michael B. Wolfe, Aaron C. Goldstrohm*, and Peter L. Freddolino*. Methods, 155:88-103, 2019. [html]

Escherichia coli Lrp regulates one-third of the genome via direct, cooperative, and indirect routes. Grace M. Kroner, Michael B. Wolfe, and Peter L. Freddolino. Journal of Bacteriology, 201:e00411-18, 2019. [html]


The structure of human Nocturnin reveals a conserved ribonuclease domain that represses target transcript translation and abundance in cells. Elizabeth Abshire, Jennifer Chasseur, Jennifer Bohn, Paul Del Rizzo, Peter Freddolino, Aaron Goldstrohm, and Raymond Trievel. Nucleic Acids Research, 46(12):6257-6270, 2018. [html]

Cellular Adaptation Through Fitness-Directed Transcriptional Tuning. Peter L. Freddolino, Jamie Yang, Amir Roknabadi, and Saeed Tavazoie. eLife, 7:e31867, 2018.  [html]

MetaGO: Predicting Gene Ontology of non-homologous proteins through low-resolution protein structure prediction and protein-protein network mapping. Chengxin Zhang, Wei Zheng, Peter L. Freddolino, and Yang Zhang. Journal of Molecular Biology430(15):2256-2265, 2018. [html]

Identification of diverse target RNAs that are functionally regulated by human Pumilio proteins. Jennifer A. Bohn, Jamie L. Van Etten, Trista L. Schagat, Brittany M. Bowman, Richard C. McEachin, Peter L. Freddolino*, and Aaron C. Goldstrohm*. Nucleic Acids Research, 46:362-386, 2018. [html]


Structure of FlgK reveals the divergence of the bacterial Hook-Filament Junction of Campylobacter. Paula V. Bulieris, Nausad H. Shaikh, Peter L. Freddolino, and Fadel A. Samatey. Scientific Reports, 7:15743, 2017. [html]

An intrinsically disordered linker controlling the formation and the stability of the bacterial flagellar hook. Clive Barker, Irina Meshcheryakova, Alla Kostyukova, Peter Freddolino, and Fadel Samatey. BMC Biology, 15:97, 2017. [html]

COFACTOR: Improved protein function prediction by combining structure, sequence, and protein-protein interaction information. Chengxin Zhang, Peter L Freddolino*, and Yang Zhang*. Nucleic Acids Research, W1:W291-W299, 2017. [html]

Deficiencies in molecular dynamics simulation-based prediction of protein-DNA binding free energy landscapes. Morteza Khabiri and Peter L. Freddolino. Journal of Physical Chemistry B, 121:5151-5161, 2017. [html]

QwikMD—Integrative Molecular Dynamics Toolkit for Novices and Experts. João V Ribeiro, Rafael C Bernardi, Till Rudack, John E Stone, James C Phillips, Peter L Freddolino, and Klaus Schulten. Scientific Reports, 6: 26536, 2016. [html]

Interfacial activation of Candida antarctica lipase B: combined evidence from experiment and simulation. Themistoklis Zisis, Peter L Freddolino, Petri Turunen, Muriel CF van Teeseling, Alan E Rowan, and Kerstin G Blank. Biochemistry, 54:5969-5979, 2015. [html]

Representative examples of older work

Revealing the genetic basis of natural bacterial phenotypic divergence. Peter L. Freddolino, Hani Goodarzi, and Saeed Tavazoie. Journal of Bacteriology, 196:825-839, 2014. [html]

Bacterial Adaptation through Loss of Function. Alison K. Hottes, Peter L. Freddolino, Anupama Khare, Zachary N. Donnell, Julia C. Liu, and Saeed Tavazoie. PLoS Genetics, 9(7): e1003617, 2013. [html]

The Dawn of Virtual Cell Biology. Peter L. Freddolino and Saeed Tavazoie. Cell, 150:248-250, 2012. [html]

Beyond Homeostasis: A Predictive-Dynamic Framework for Understanding Cellular Behavior. Peter L. Freddolino and Saeed Tavazoie. Annual Review of Cell and Developmental Biology, 28:363-384, 2012. [html]

Fitness Landscape Transformation through a Single Amino Acid Change in the Rho Terminator. Peter L. Freddolino, Hani Goodarzi, and Saeed Tavazoie. PLoS Genetics, 8(5):e1002744, 2012. [html]

Challenges in protein-folding simulations. Peter L. Freddolino, Christopher B Harrison, Yanxin Liu, Klaus Schulten. Nature Physics, 6:751-758, 2010. [html]

Common structural transitions in explicit-solvent simulations of villin headpiece folding. Peter L. Freddolino and Klaus Schulten. Biophysical Journal, 97:2338-2347, 2009. [html]

Force field bias in protein folding simulations. Peter L. Freddolino, Sanghyun Park, Benoit Roux, and Klaus Schulten. Biophysical Journal, 96:3772-3780, 2009. [html]

Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Peter L. Freddolino, Anton S. Arkhipov, Steven B. Larson, Alexander McPherson, and Klaus Schulten. Structure, 14:437-449, 2006. [html]