Publications

(* indicates co-corresponding authors)

bioRxiv preprints
(we post a subset of our papers to bioRxiv at the time that they are submitted to a journal)

The Polycomb Repressive Complex 2.1 Links the Food Environment to a Persistent Neural State. Anoumid Vaziri, Morteza Khabiri, Brendan T. Genaw, Christina E. May, Peter L. Freddolino, and Monica Dus. [doi]

Dynamic landscape of protein occupancy across the Escherichia coli chromosome. Peter L. Freddolino*, Thomas J. Goss, Haley M. Amemiya, and Saeed Tavazoie*. [doi]

Differential processing and localization of human Nocturnin controls metabolism of mRNA and nicotinamide dinucleotide metabolites. Elizabeth T. Abshire, Kelsey Hughes, Rucheng Diao, Sarah Pearce, Raymond C. Trievel, Joanna Rorbach, Peter L. Freddolino,  and Aaron C. Goldstrohm. [doi]

Genome-wide Prediction of Potential Polycomb Response Elements and their Functions. Morteza Khabiri and Peter L. Freddolino. [doi]

2020

Principles of mRNA control by human PUM proteins elucidated from multi-modal experiments and integrative data analysis. Michael B. Wolfe, Trista L. Schagat, Michelle T. Paulsen,  Brian Magnuson, Mats Ljungman, Daeyoon Park, Chi Zhang,  Zachary T Campbell,  Aaron C Goldstrohm*,  and Peter L Freddolino*. RNA, in press. [preprint doi]

A Thermosensitive Phase-variable Epigenetic Switch: pap Revisited. Mario Zamora, Christine A. Ziegler, Peter L. Freddolino, and Alan J. Wolfe. Microbiology and Molecular Biology Reviews, in press.

Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons. Xiaoqiong Wei, Chengxin Zhang, Peter L. Freddolino*, and Yang Zhang*. Bioinformatics btaa548, 2020. [html]

A Well-Mixed E. coli Genome: Widespread Contacts Revealed by Tracking Mu Transposition. David M. Walker, Peter L. Freddolino*, and Rasika Harshey*. Cell 180:701-716, 2020. [html]

2019

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. The CAFA3 consortium (Naihui Zhou et al.). Genome Biology 20:1-23, 2019. [html]

Unique repression domains of Pumilio utilize deadenylation and decapping factors to accelerate destruction of target mRNAs. René M Arvola, Chung-Te Chang, Joseph P Buytendorp, Yevgen Levdansky, Eugene Valkov, Peter L Freddolino, and Aaron C Goldstrohm. Nucleic Acids Res. gk71187, 2019. [html]

Rapid metabolic shifts occur during the transition between hunger and satiety in Drosophila melanogaster. Daniel Wilinski, Jasmine Winzeler, William Duren, Jenna L. Persons, Kristina J. Holme, Johan Mosquera, Morteza Khabiri, Jason M. Kinchen, Peter L. Freddolino, Alla Karnovsky and Monica Dus. Nature Comm. 10:4052, 2019. [html]

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, 27:1675-1685, 2019. [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, 74:936-950, 2019. [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]


2018

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]


2015-2017

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]