Peter L Freddolino (P Lydia Freddolino, P Lydia Freddolino, Lydia Freddolino)

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 87

Top Topics

Escherichia Coli

Convolutional Neural Network

Gene Expression

Top Venues

bioRxiv : the preprint server for biology

RNA (New York, N.Y.)

This page only lists publications with an associated author ORCID identifier.

Publications

Yulduz Rakibova, Drew T Dunham, Kimberley D Seed, Peter L Freddolino
Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae . mSphere (2024)
Chengxin Zhang, Peter L Freddolino
FURNA: A database for functional annotations of RNA structures. PLoS biology 22 (7) (2024)
Yulduz Rakibova, Drew T Dunham, Kimberley D Seed, Peter L Freddolino
Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae . bioRxiv : the preprint server for biology (2024)
Rebecca J Haugen, Catherine Barnier, Nathan D Elrod, Hua Luo, Madeline K Jensen, Ping Ji, Craig A Smibert, Howard D Lipshitz, Eric J Wagner, Peter L Freddolino, Aaron C Goldstrohm
Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex. RNA (New York, N.Y.) 30 (7) (2024)
Chengxin Zhang, Peter L Freddolino
FURNA: A database for functional annotations of RNA structures. PLoS biology 22 (7) (2024)
Chengxin Zhang, Peter L Freddolino
A large-scale assessment of sequence database search tools for homology-based protein function prediction. Briefings in bioinformatics 25 (4) (2024)
Rebecca J Haugen, Catherine Barnier, Nathan D Elrod, Hua Luo, Madeline K Jensen, Ping Ji, Craig A Smibert, Howard D Lipshitz, Eric J Wagner, Peter L Freddolino, Aaron C Goldstrohm
Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex. RNA (New York, N.Y.) (2024)
Rebecca J Haugen, Catherine Barnier, Nathan D Elrod, Hua Luo, Madeline K Jensen, Ping Ji, Craig A Smibert, Howard D Lipshitz, Eric J Wagner, Peter L Freddolino, Aaron C Goldstrohm
Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex. RNA (New York, N.Y.) (2024)
Rebecca J Haugen, Catherine Barnier, Nathan D Elrod, Hua Luo, Madeline K Jensen, Ping Ji, Craig A Smibert, Howard D Lipshitz, Eric J Wagner, Peter L Freddolino, Aaron C Goldstrohm
Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex. RNA (New York, N.Y.) 30 (7) (2024)
Yulduz Rakibova, Drew T Dunham, Kimberley D Seed, Peter L Freddolino
Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae . bioRxiv : the preprint server for biology (2024)
Yulduz Rakibova, Drew T Dunham, Kimberley D Seed, Peter L Freddolino
Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae . bioRxiv : the preprint server for biology (2024)
Yulduz Rakibova, Drew T Dunham, Kimberley D Seed, Peter L Freddolino
Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae . mSphere 9 (7) (2024)
Yulduz Rakibova, Drew T Dunham, Kimberley D Seed, Peter L Freddolino
Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae. bioRxiv : the preprint server for biology (2024)
Ziying Zhang, Yaxian Cai, Biao Zhang, Wei Zheng, Peter L Freddolino, Gui-Jun Zhang, Xiao-Gen Zhou
DEMO-EM2: assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting. Briefings in bioinformatics 25 (2) (2024)
Wei Zheng, Qiqige Wuyun, Yang Li, Chengxin Zhang, Peter L Freddolino, Yang Zhang
Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data. Nature methods (2024)
Chengxin Zhang, Peter L Freddolino
A large-scale assessment of sequence database search tools for homology-based protein function prediction. Briefings in bioinformatics 25 (4) (2024)
Alyssa M Ekdahl, Tatiana Julien, Sahana Suraj, Judith F Kribelbauer, Saeed Tavazoie, Peter L Freddolino, Lydia M Contreras
Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs. bioRxiv : the preprint server for biology (2024)
Chengxin Zhang, Peter L Freddolino
FURNA: A database for functional annotations of RNA structures. PLoS biology 22 (7) (2024)
Yulduz Rakibova, Drew T Dunham, Kimberley D Seed, Peter L Freddolino
Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae . mSphere 9 (7) (2024)
Chengxin Zhang, Peter L Freddolino
FURNA: A database for functional annotations of RNA structures. PLoS biology 22 (7) (2024)
Yulduz Rakibova, Drew T Dunham, Kimberley D Seed, Peter L Freddolino
Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae. bioRxiv : the preprint server for biology (2024)
Rebecca J Haugen, Catherine Barnier, Nathan D Elrod, Hua Luo, Madeline K Jensen, Ping Ji, Craig A Smibert, Howard D Lipshitz, Eric J Wagner, Peter L Freddolino, Aaron C Goldstrohm
Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex. RNA (New York, N.Y.) 30 (7) (2024)
Wei Zheng, Qiqige Wuyun, Yang Li, Chengxin Zhang, Peter L Freddolino, Yang Zhang
Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data. Nature methods 21 (2) (2024)
Yulduz Rakibova, Drew T Dunham, Kimberley D Seed, Peter L Freddolino
Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae. bioRxiv : the preprint server for biology (2024)
Wei Zheng, Qiqige Wuyun, Yang Li, Chengxin Zhang, Peter L Freddolino, Yang Zhang
Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data. Nature methods 21 (2) (2024)
Rebecca J Haugen, Catherine Barnier, Nathan D Elrod, Hua Luo, Madeline K Jensen, Ping Ji, Craig A Smibert, Howard D Lipshitz, Eric J Wagner, Peter L Freddolino, Aaron C Goldstrohm
Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex. RNA (New York, N.Y.) 30 (7) (2024)
Wei Zheng, Qiqige Wuyun, Yang Li, Chengxin Zhang, Peter L Freddolino, Yang Zhang
Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data. Nature methods 21 (2) (2024)
Aathmaja Anandhi Rangarajan, Jeremy W Schroeder, Rebecca L Hurto, Geoffrey B Severin, Macy E Pell, Meng-Lun Hsieh, Christopher M Waters, Peter L Freddolino
Negative feedback of cyclic di-GMP levels optimizes switching between sessile and motile lifestyles in Vibrio cholerae . bioRxiv : the preprint server for biology (2024)
Ziyuan Chen, Melissa Seman, Yekaterina Fyodorova, Ali Farhat, Amanda Ames, Alexander Levashkevich, Saikat Biswas, Fengting Huang, Peter L Freddolino, Julie S Biteen, Kaushik Ragunathan
Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein-protein interactions. Nucleic acids research (2024)
Yulduz Rakibova, Drew T Dunham, Kimberley D Seed, Peter L Freddolino
Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae . bioRxiv : the preprint server for biology (2024)
Yulduz Rakibova, Drew T Dunham, Kimberley D Seed, Peter L Freddolino
Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae . bioRxiv : the preprint server for biology (2024)
Rebecca J Haugen, Catherine Barnier, Nathan D Elrod, Hua Luo, Madeline K Jensen, Ping Ji, Craig A Smibert, Howard D Lipshitz, Eric J Wagner, Peter L Freddolino, Aaron C Goldstrohm
Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex. RNA (New York, N.Y.) (2024)
Yulduz Rakibova, Drew T Dunham, Kimberley D Seed, Peter L Freddolino
Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae . mSphere 9 (7) (2024)
Alyssa M Ekdahl, Tatiana Julien, Sahana Suraj, Judith F Kribelbauer, Saeed Tavazoie, Peter L Freddolino, Lydia M Contreras
Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs. bioRxiv : the preprint server for biology (2024)
Alyssa M Ekdahl, Tatiana Julien, Sahana Suraj, Judith F Kribelbauer, Saeed Tavazoie, Peter L Freddolino, Lydia M Contreras
Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs. bioRxiv : the preprint server for biology (2024)
Ziying Zhang, Yaxian Cai, Biao Zhang, Wei Zheng, Peter L Freddolino, Gui-Jun Zhang, Xiao-Gen Zhou
DEMO-EM2: assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting. Briefings in bioinformatics 25 (2) (2024)
Sonya K Royzenblat, Peter L Freddolino
Spatio-temporal organization of the E. coli chromosome from base to cellular length scales. EcoSal Plus (2024)
Wei Zheng, Qiqige Wuyun, Yang Li, Chengxin Zhang, Peter L Freddolino, Yang Zhang
Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data. Nature methods 21 (2) (2024)
Yulduz Rakibova, Drew T Dunham, Kimberley D Seed, Peter L Freddolino
Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae . mSphere (2024)
Ziyuan Chen, Melissa Seman, Yekaterina Fyodorova, Ali Farhat, Amanda Ames, Alexander Levashkevich, Saikat Biswas, Fengting Huang, Peter L Freddolino, Julie S Biteen, Kaushik Ragunathan
Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein-protein interactions. Nucleic acids research (2024)
Chengxin Zhang, Peter L Freddolino
FURNA: A database for functional annotations of RNA structures. PLoS biology 22 (7) (2024)
Chengxin Zhang, Peter L Freddolino
A large-scale assessment of sequence database search tools for homology-based protein function prediction. Briefings in bioinformatics 25 (4) (2024)
Jeremy W Schroeder, Rebecca L Hurto, Justin R Randall, Katherine J Wozniak, Taylor A Timko, Taylor M Nye, Jue D Wang, Peter L Freddolino, Lyle A Simmons
RNase H genes cause distinct impacts on RNA:DNA hybrid formation and mutagenesis genome-wide. bioRxiv : the preprint server for biology (2023)
Chengxin Zhang, Peter L Freddolino
FURNA: a database for function annotations of RNA structures. bioRxiv : the preprint server for biology (2023)
Chengxin Zhang, Peter L Freddolino
FURNA: a database for function annotations of RNA structures. bioRxiv : the preprint server for biology (2023)
Chengxin Zhang, Xi Zhang, Peter L Freddolino, Yang Zhang
BioLiP2: an updated structure database for biologically relevant ligand-protein interactions. Nucleic acids research (2023)
Ziyuan Chen, Melissa Seman, Ali Farhat, Yekaterina Fyodorova, Saikat Biswas, Alexander Levashkevich, Peter L Freddolino, Julie Suzanne Biteen, Kaushik Ragunathan
H3K9 methylation enhances HP1-associated epigenetic silencing complex assembly and suppresses off-chromatin binding. bioRxiv : the preprint server for biology (2023)
Yang Li, Chengxin Zhang, Chenjie Feng, Robin Pearce, Peter L Freddolino, Yang Zhang
Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction. Nature communications 14 (1) (2023)
Jeremy W Schroeder, Rebecca L Hurto, Justin R Randall, Katherine J Wozniak, Taylor A Timko, Taylor M Nye, Jue D Wang, Peter L Freddolino, Lyle A Simmons
RNase H genes cause distinct impacts on RNA:DNA hybrid formation and mutagenesis genome wide. Science advances 9 (30) (2023)
Brian G Peterson, Jiwon Hwang, Jennifer E Russ, Jeremy Schroeder, Peter L Freddolino, Ryan D Baldridge
Deep mutational scanning highlights a new role for cytosolic regions in Hrd1 function. bioRxiv : the preprint server for biology (2023)
Chengxin Zhang, Peter L Freddolino
FURNA: a database for function annotations of RNA structures. bioRxiv : the preprint server for biology (2023)
Chengxin Zhang, Peter L Freddolino
FURNA: a database for function annotations of RNA structures. bioRxiv : the preprint server for biology (2023)
Leila Tamara Alexander, Janani Durairaj, Andriy Kryshtafovych, Luciano Andrés Abriata, Yusupha Bayo, Gira Bhabha, Cécile Breyton, Simon G Caulton, James Chen, Séraphine Degroux, Damian C Ekiert, Benedikte S Erlandsen, Peter L Freddolino, Dominic Gilzer, Chris Greening, Jonathan M Grimes, Rhys W Grinter, Manickam Gurusaran, Marcus D Hartmann, Charlie J Hitchman, Jeremy Russell Keown, Ashleigh Kropp, Petri Kursula, Andrew Lee Lovering, Bruno Lemaître, Andrea Lia, Shiheng Liu, Maria Logotheti, Shuze Lu, Sigurbjörn Markússon, Mitchell D Miller, George Minasov, Hartmut H Niemann, Felipe Opazo, George N Philips, Owen Richard Davies, Samuel Rommelaere, Monica Rosas-Lemus, Pietro Roversi, Karla J F Satchell, Nathan Smith, Mark A Wilson, Kuan-Lin Wu, Xian Xia, Han Xiao, Wenhua Zhang, Z Hong Zhou, Krzysztof Fidelis, Andriy Kryshtafovych, John Moult, Torsten Schwede
Protein target highlights in CASP15: Analysis of models by structure providers. Proteins (2023)
Ha Yeon Sung, Anoumid Vaziri, Daniel Wilinski, Riley K R Woerner, Peter L Freddolino, Monica Dus
Nutrigenomic regulation of sensory plasticity. eLife 12 (2023)
Chengxin Zhang, Peter L Freddolino
A large-scale assessment of sequence database search tools for homology-based protein function prediction. bioRxiv : the preprint server for biology (2023)
Mariano Spivak, John E Stone, João Ribeiro, Jan Saam, Peter L Freddolino, Rafael C Bernardi, Emad Tajkhorshid
VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations. Journal of chemical information and modeling (2023)
Chengxin Zhang, Peter L Freddolino
FURNA: a database for function annotations of RNA structures. bioRxiv : the preprint server for biology (2023)
Christine A Ziegler, Peter L Freddolino
Escherichia coli Leucine-Responsive Regulatory Protein Bridges DNA In Vivo and Tunably Dissociates in the Presence of Exogenous Leucine. mBio (2023)
Rebecca J Haugen, Catherine Barnier, Nathan D Elrod, Hua Luo, Madeline K Jensen, Ping Ji, Craig A Smibert, Howard D Lipshitz, Eric J Wagner, Peter L Freddolino, Aaron C Goldstrohm
Regulation of the Drosophila transcriptome by Pumilio and CCR4-NOT deadenylase. bioRxiv : the preprint server for biology (2023)
Ziyuan Chen, Melissa Seman, Ali Farhat, Yekaterina Fyodorova, Saikat Biswas, Alexander Levashkevich, Peter L Freddolino, Julie Suzanne Biteen, Kaushik Ragunathan
H3K9 methylation enhances HP1-associated epigenetic silencing complex assembly and suppresses off-chromatin binding. bioRxiv : the preprint server for biology (2023)
Chengxin Zhang, Peter L Freddolino
FURNA: a database for function annotations of RNA structures. bioRxiv : the preprint server for biology (2023)
Ha Yeon Sung, Anoumid Vaziri, Daniel Wilinski, Riley K R Woerner, Peter L Freddolino, Monica Dus
Nutrigenomic regulation of sensory plasticity. eLife 12 (2023)
Ha Yeon Sung, Anoumid Vaziri, Daniel Wilinski, Riley K R Woerner, Peter L Freddolino, Monica Dus
Nutrigenomic regulation of sensory plasticity. eLife 12 (2023)
Chengxin Zhang, Peter L Freddolino
FURNA: a database for function annotations of RNA structures. bioRxiv : the preprint server for biology (2023)
Scott A Scholz, Chase D Lindeboom, Peter L Freddolino
Genetic context effects can override canonical cis regulatory elements in Escherichia coli. Nucleic acids research 50 (18) (2022)
Xi Zhang, Biao Zhang, Peter L Freddolino, Yang Zhang
CR-I-TASSER: assemble protein structures from cryo-EM density maps using deep convolutional neural networks. Nature methods 19 (2) (2022)
Michael Schmidt, Theresa Proctor, Rucheng Diao, Peter L Freddolino
Escherichia coli YigI is a Conserved Gammaproteobacterial Acyl-CoA Thioesterase Permitting Metabolism of Unusual Fatty Acid Substrates. Journal of bacteriology 204 (8) (2022)
Nash D Rochman, Guilhem Faure, Yuri I Wolf, Peter L Freddolino, Feng Zhang, Eugene V Koonin
Epistasis at the SARS-CoV-2 Receptor-Binding Domain Interface and the Propitiously Boring Implications for Vaccine Escape. mBio 13 (2) (2022)
Alexandra Ketcham, Peter L Freddolino, Saeed Tavazoie
Intracellular acidification is a hallmark of thymineless death in E. coli. PLoS genetics 18 (10) (2022)
Wei Zheng, Qiqige Wuyun, Xiaogen Zhou, Yang Li, Peter L Freddolino, Yang Zhang
LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation. Nucleic acids research (2022)
Saikat Biswas, Ziyuan Chen, Joshua D Karslake, Ali Farhat, Amanda Ames, Gulzhan Raiymbek, Peter L Freddolino, Julie Suzanne Biteen
HP1 oligomerization compensates for low-affinity H3K9me recognition and provides a tunable mechanism for heterochromatin-specific localization. Science advances 8 (27) (2022)
Francois Beaufay, Haley M Amemiya, Jian Guan, Joseph Basalla, Ben A Meinen, Ziyuan Chen, Rishav Mitra, James C A Bardwell, Julie Suzanne Biteen, Anthony G Vecchiarelli, Peter L Freddolino, Ursula Jakob
Polyphosphate drives bacterial heterochromatin formation. Science advances 7 (52) (2021)
Chengxin Zhang, Wei Zheng, Micah Cheng, Gilbert S Omenn, Peter L Freddolino, Yang Zhang
Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome. Journal of proteome research 20 (2) (2021)
Haley M Amemiya, Jeremy Schroeder, Peter L Freddolino
Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom. Transcription 12 (4) (2021)
Peter L Freddolino, Haley M Amemiya, Thomas J Goss, Saeed Tavazoie
Dynamic landscape of protein occupancy across the Escherichia coli chromosome. PLoS biology 19 (6) (2021)
Nash D Rochman, Guilhem Faure, Yuri I Wolf, Peter L Freddolino, Feng Zhang, Eugene V Koonin
Epistasis at the SARS-CoV-2 RBD Interface and the Propitiously Boring Implications for Vaccine Escape. bioRxiv : the preprint server for biology (2021)
Haley M Amemiya, Thomas J Goss, Taylor M Nye, Rebecca L Hurto, Lyle A Simmons, Peter L Freddolino
Distinct heterochromatin-like domains promote transcriptional memory and silence parasitic genetic elements in bacteria. The EMBO journal 41 (3) (2021)
Christine A Ziegler, Peter L Freddolino
The leucine-responsive regulatory proteins/feast-famine regulatory proteins: an ancient and complex class of transcriptional regulators in bacteria and archaea. Critical reviews in biochemistry and molecular biology 56 (4) (2021)
Anoumid Vaziri, Morteza Khabiri, Brendan T Genaw, Christina E May, Peter L Freddolino, Monica Dus
Persistent epigenetic reprogramming of sweet taste by diet. Science advances 6 (46) (2020)
Mario Zamora, Christine A Ziegler, Peter L Freddolino, Alan J Wolfe
A Thermosensitive, Phase-Variable Epigenetic Switch: pap Revisited. Microbiology and molecular biology reviews : MMBR 84 (3) (2020)
Morteza Khabiri, Peter L Freddolino
Correction to "Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes". The journal of physical chemistry. B 124 (49) (2020)
Michael B Wolfe, Trista L Schagat, Michelle T Paulsen, Brian R Magnuson, Mats Ljungman, Daeyoon Park, Chi Zhang, Zachary T Campbell, Aaron C Goldstrohm, Peter L Freddolino
Principles of mRNA control by human PUM proteins elucidated from multimodal experiments and integrative data analysis. RNA (New York, N.Y.) 26 (11) (2020)
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
Rapid metabolic shifts occur during the transition between hunger and satiety in Drosophila melanogaster. Nature communications 10 (1) (2019)
Grace M Kroner, Michael B Wolfe, Peter L Freddolino
Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes. Journal of bacteriology 201 (3) (2019)
Morteza Khabiri, Peter L Freddolino
Expression of Concern for "Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes". The journal of physical chemistry. B 124 (6) (2018)
Peter L Freddolino, Jamie Yang, Amir Momen-Roknabadi, Saeed Tavazoie
Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry. eLife 7 (2018)
Morteza Khabiri, Peter L Freddolino
Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes. The journal of physical chemistry. B 121 (20) (2017)