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Author Details

Peter L Freddolino
University of Michigan ann arbor
2002
91
36
PMIDPaper TitleJournal TitlePublished Year
37522378BioLiP2: an updated structure database for biologically relevant ligand-protein interactions.Nucleic Acids Res2024
36786566Escherichia coli Leucine-Responsive Regulatory Protein Bridges DNA In Vivo and Tunably Dissociates in the Presence of Exogenous Leucine.mBio2023
38013998A large-scale assessment of sequence database search tools for homology-based protein function prediction.bioRxiv2023
37650367Integrating deep learning, threading alignments, and a multi-MSA strategy for high-quality protein monomer and complex structure prediction in CASP15.Proteins2023
37506321VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations.J Chem Inf Model2023
37693497Regulation of the Drosophila transcriptome by Pumilio and CCR4-NOT deadenylase.bioRxiv2023
37980570Deep mutational scanning highlights a role for cytosolic regions in Hrd1 function.Cell Rep2023
37494439RNase H genes cause distinct impacts on RNA:DNA hybrid formation and mutagenesis genome wide.Sci Adv2023
37493353Protein target highlights in CASP15: Analysis of models by structure providers.Proteins2023
36951889Nutrigenomic regulation of sensory plasticity.Elife2023
37214986RNase H genes cause distinct impacts on RNA:DNA hybrid formation and mutagenesis genome-wide.bioRxiv2023
36945633Tracking live-cell single-molecule dynamics enables measurements of heterochromatinassociated protein-protein interactions.bioRxiv2023
37066402Deep mutational scanning highlights a new role for cytosolic regions in Hrd1 function.bioRxiv2023
34961960Distinct heterochromatin-like domains promote transcriptional memory and silence parasitic genetic elements in bacteria.EMBO J2022
35476699Correction: Dynamic landscape of protein occupancy across the Escherichia coli chromosome.PLoS Biol2022
35662463PEPPI: Whole-proteome Protein-protein Interaction Prediction through Structure and Sequence Similarity, Functional Association, and Machine Learning.J Mol Biol2022
35568117TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction.Genomics Proteomics Bioinformatics2022
35420129LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation.Nucleic Acids Res2022
36279294Intracellular acidification is a hallmark of thymineless death in E. coli.PLoS Genet2022
36134716Genetic context effects can override canonical cis regulatory elements in Escherichia coli.Nucleic Acids Res2022
35876515Escherichia coli YigI is a Conserved Gammaproteobacterial Acyl-CoA Thioesterase Permitting Metabolism of Unusual Fatty Acid Substrates.J Bacteriol2022
35132244CR-I-TASSER: assemble protein structures from cryo-EM density maps using deep convolutional neural networks.Nat Methods2022
35289643Epistasis at the SARS-CoV-2 Receptor-Binding Domain Interface and the Propitiously Boring Implications for Vaccine Escape.mBio2022
33393786Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome.J Proteome Res2021
34936433Polyphosphate drives bacterial heterochromatin formation.Sci Adv2021
34499567Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom.Transcription2021
34758301The hepatic compensatory response to elevated systemic sulfide promotes diabetes.Cell Rep2021
34494024Epistasis at the SARS-CoV-2 RBD Interface and the Propitiously Boring Implications for Vaccine Escape.bioRxiv2021
34327153Uncovering Transcriptional Regulators and Targets of sRNAs Using an Integrative Data-Mining Approach: H-NS-Regulated RseX as a Case Study.Front Cell Infect Microbiol2021
34151666The leucine-responsive regulatory proteins/feast-famine regulatory proteins: an ancient and complex class of transcriptional regulators in bacteria and archaea.Crit Rev Biochem Mol Biol2021
34170902Dynamic landscape of protein occupancy across the Escherichia coli chromosome.PLoS Biol2021
34111031TNFRSF13B polymorphisms counter microbial adaptation to enteric IgA.JCI Insight2021
29741907Expression of Concern for "Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes".J Phys Chem B2020
32059782A Well-Mixed E. coli Genome: Widespread Contacts Revealed by Tracking Mu Transposition.Cell2020
31863588Unique repression domains of Pumilio utilize deadenylation and decapping factors to accelerate destruction of target mRNAs.Nucleic Acids Res2020
33236911Correction to "Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes".J Phys Chem B2020
33177090Persistent epigenetic reprogramming of sweet taste by diet.Sci Adv2020
32727743A Thermosensitive, Phase-Variable Epigenetic Switch: <i>pap</i> Revisited.Microbiol Mol Biol Rev2020
32753408Principles of mRNA control by human PUM proteins elucidated from multimodal experiments and integrative data analysis.RNA2020
32839274Differential processing and localization of human Nocturnin controls metabolism of mRNA and nicotinamide adenine dinucleotide cofactors.J Biol Chem2020
30529548Global analysis of RNA metabolism using bio-orthogonal labeling coupled with next-generation RNA sequencing.Methods2019
31744546The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.Genome Biol2019
31492856Rapid metabolic shifts occur during the transition between hunger and satiety in Drosophila melanogaster.Nat Commun2019
31072491Applications of molecular modeling to flavoproteins: Insights and challenges.Methods Enzymol2019
31067455High Dietary Sugar Reshapes Sweet Taste to Promote Feeding Behavior in Drosophila melanogaster.Cell Rep2019
30975459Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas.Mol Cell2019
30904377High-Resolution Mapping of the Escherichia coli Chromosome Reveals Positions of High and Low Transcription.Cell Syst2019
30420454<i>Escherichia coli</i> Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes.J Bacteriol2019
29165587Identification of diverse target RNAs that are functionally regulated by human Pumilio proteins.Nucleic Acids Res2018
29860338The structure of human Nocturnin reveals a conserved ribonuclease domain that represses target transcript translation and abundance in cells.Nucleic Acids Res2018
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Collaborators

Chengxin Zhang
University of Michigan ann arbor
Co-authored papers 7
Yang Zhang
University of Michigan ann arbor
Co-authored papers 6
Rebecca L Hurto
University of Michigan Medical School ann arbor
Co-authored papers 4
Wei Zheng
University of Michigan ann arbor
Co-authored papers 4
Feng Zhang
Massachusetts Institute of Technology, USA Broad Institute
Co-authored papers 2
Yanxin Liu
University of California san francisco
Co-authored papers 2
Gilbert S Omenn
and School of Public Health, University of Michigan ann arbor
Co-authored papers 2
Kevin H Gardner
CUNY Advanced Science Research Center
Co-authored papers 2
Naihui Zhou
The First Affiliated Hospital of Soochow University
Co-authored papers 1
Md Nafiz Hamid
Iowa State University
Co-authored papers 1
Larry Davis
Co-authored papers 1
Radoslav Davidovic
Institute of Nuclear Sciences Vinca, University of Belgrade
Co-authored papers 1
Mohammad R K Mofrad
University of California Berkeley
Co-authored papers 1
Sa??o D??eroski
Jozef Stefan Institute
Co-authored papers 1
Domenico Cozzetto
Imperial College London
Co-authored papers 1
Marco Mesiti
Universita degli Studi di Milano
Co-authored papers 1
David A Case
Rutgers University
Co-authored papers 1
Neven Sumonja
Institute of Nuclear Sciences VINCA, University of Belgrade
Co-authored papers 1
Magdalena Kotlicka-Antczak
Medical University of Lodz
Co-authored papers 1
Alan J Medlar
Co-authored papers 1
Rui Fa
University College London
Co-authored papers 1
Sabeur Aridhi
Universite de Lorraine, CNRS
Co-authored papers 1
Qizhong Mao
Temple University
Co-authored papers 1
Owen R Davies
Institute of Cell Biology, University of Edinburgh
Co-authored papers 1
Krzysztof Fidelis
University of California davis
Co-authored papers 1
Fabio Fabris
University of Kent
Co-authored papers 1
Wei-Cheng Tseng
Taipei Veterans General Hospital
Co-authored papers 1
Christophe Dessimoz
University of Lausanne
Co-authored papers 1
Gage S Black
Brigham Young University
Co-authored papers 1
Suyang Dai
Fudan University
Co-authored papers 1
Release 1.2