Philip Bevilacqua

Co-Director, Center for RNA Molecular Biology; Distinguished Professor of Chemistry and of Biochemistry and Molecular Biology

Philip Bevilacqua

Research Summary

RNA folding in vivo and genome-wide; RNA regulation of gene expression; Ribozyme Mechanism; roles RNA may have played in the emergence of life on early earth

Huck Graduate Students

Huck Affiliations

Links

Most Recent Publications

VariantFoldRNA: a flexible, containerized, and scalable pipeline for genome-wide riboSNitch prediction

Kobie J. Kirven, Philip C. Bevilacqua, Sarah M. Assmann, 2025, NAR Genomics and Bioinformatics

CHiTA: A scarless high-throughput pipeline for characterization of ribozymes

Lauren N. McKinley, Philip C. Bevilacqua, 2025, ImmunoMethods on p. 120-130

A new reagent for in vivo structure probing of RNA G and U residues that improves RNA structure prediction alone and combined with DMS

Catherine A. Douds, Paul Babitzke, Philip C. Bevilacqua, 2024, RNA on p. 901-919

Single-cell probing of RNA structure

Elizabeth Jolley, Philip C. Bevilacqua, 2024, Nature Methods on p. 377-378

Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections

Lauren McKinley, McCauley Meyer, Aswathy Sebastian, Benjamin Chang, Kyle Messina, Istvan Albert, Philip C. Bevilacqua, 2024, Nucleic Acids Research on p. 14133--14153

In vivo-like nearest neighbor parameters improve prediction of fractional RNA base-pairing in cells

Jacob P. Sieg, Elizabeth A. Jolley, Melanie J. Huot, Paul Babitzke, Philip C. Bevilacqua, 2023, Nucleic Acids Research on p. 11298-11317

In vivo structure probing of RNA in Archaea: novel insights into the ribosome structure of Methanosarcina acetivorans

Allison M. Williams, Elizabeth A. Jolley, Michel Geovanni Santiago-Martínez, Cheong X.I.N. Chan, Robin R. Gutell, James Gregory Ferry, Philip C. Bevilacqua, 2023, RNA on p. 1610-1620

MeltR software provides facile determination of nucleic acid thermodynamics

Jacob P. Sieg, Sebastian J. Arteaga, Brent M. Znosko, Philip C. Bevilacqua, 2023, Biophysical Reports

Rock, scissors, paper: How RNA structure informs function

Sarah Assmann, H Chou, Philip C. Bevilacqua, 2023, Plant Cell on p. 1671-1707

Transcriptome-wide probing reveals RNA thermometers that regulate translation of glycerol permease genes in Bacillus subtilis

Elizabeth Jolley, Helen Yakhnin, E Yakhnin, David Tack, Paul Babitzke, Philip C. Bevilacqua, 2023, RNA on p. 1365-1378

Most-Cited Papers

Template-directed RNA polymerization and enhanced ribozyme catalysis inside membraneless compartments formed by coacervates

Raghav R. Poudyal, Rebecca M. Guth-Metzler, Andrew J. Veenis, Erica A. Frankel, Christine D. Keating, Philip C. Bevilacqua, 2019, Nature Communications on p. 490

Genome-Wide Analysis of RNA Secondary Structure

Philip C. Bevilacqua, Laura Ritchey, Zhao Su, Sarah M. Assmann, 2016, Annual Review of Genetics on p. 235--266

Physical Principles and Extant Biology Reveal Roles for RNA-Containing Membraneless Compartments in Origins of Life Chemistry

Raghav Poudyal, Fatma Cakmak, Christine Keating, Philip Bevilacqua, 2018, Biochemistry on p. 2509-2519

Polyamine/Nucleotide Coacervates Provide Strong Compartmentalization of Mg<sup>2+</sup>, Nucleotides, and RNA

Erica A. Frankel, Philip C. Bevilacqua, Christine D. Keating, 2016, Langmuir on p. 2041-2049

The RNA structurome: Transcriptome-wide structure probing with next-generation sequencing

Chun Kit Kwok, Yin Tang, Sarah M. Assmann, Philip C. Bevilacqua, 2015, Trends in Biochemical Sciences on p. 221-232

Prebiotically-relevant low polyion multivalency can improve functionality of membraneless compartments

Fatma Pir Cakmak, Saehyun Choi, McCauley C.O. Meyer, Philip C. Bevilacqua, Christine D. Keating, 2020, Nature Communications

Genome-wide RNA structurome reprogramming by acute heat shock globally regulates mRNA abundance

Zhao Su, Yin Tang, Laura E. Ritchey, David C. Tack, Mengmeng Zhu, Philip C. Bevilacqua, Sarah M. Assmann, 2018, Proceedings of the National Academy of Sciences of the United States of America on p. 12170-12175

Phase-specific RNA accumulation and duplex thermodynamics in multiphase coacervate models for membraneless organelles

Saehyun Choi, M Meyer, Philip C. Bevilacqua, Christine D. Keating, 2022, Nature Chemistry on p. 1110-1117

Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq

Yiliang Ding, Chun Kit Kwok, Yin Tang, Philip C. Bevilacqua, Sarah M. Assmann, 2015, Nature Protocols on p. 1050-1066

Modeling RNA secondary structure folding ensembles using SHAPE mapping data

Aleksandar Spasic, Sarah M. Assmann, Philip Bevilacqua, David H. Mathews, D Matthews, 2017, Nucleic Acids Research on p. 314-323

News Articles Featuring Philip Bevilacqua

Jul 15, 2025

Optical tweezers help elevate single-molecule research at Penn State

The instrument, supported by a new NIH infrastructure grant, uses laser light to ‘tweeze’ tiny objects like DNA molecules and proteins.

Full Article

Jun 30, 2025

Lab Bench to Commercialization program broadens its scope

Eberly College of Science seed grant program to shift emphasis to earlier development of research, focusing on societal impact and career readiness.

Full Article

Nov 27, 2024

Heard on Campus: Launch of new center in molecular and cellular sciences, NCEMS

Reception celebrates new NSF-funded National Synthesis Center for Emergence in the Molecular and Cellular Sciences at Penn State.

Full Article

Nov 05, 2024

Testing thousands of RNA enzymes helps find first ‘twister ribozyme’ in mammals

A new method, developed by Penn State researchers, can test the activity of thousands of predicted ribozymes in a single experiment.

Full Article

Feb 15, 2024

Penn State chemist Eric Nacsa receives 2024 NSF CAREER Award

Eric Nacsa, assistant professor of chemistry, has been honored with a Faculty Early Career Development (CAREER) award from the U.S. National Science Foundation (NSF)

Full Article

Feb 15, 2024

Committee advances plan to rename Chemistry Building as 'Benkovic Building'

The Chemistry Building at the University Park campus will be renamed in honor of the careerlong scholarly impact of Stephen Benkovic, Atherton Professor of Chemistry

Full Article

Feb 14, 2024

Penn State biochemist Carsten Krebs named distinguished professor

Carsten Krebs, professor of chemistry and of biochemistry and molecular biology at Penn State, has been selected to receive the title of Distinguished Professor of Chemistry and Biochemistry and Molecular Biology

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Sep 26, 2023

Could RNA folding play a role in the origin of life?

New research in model protocells reveals naturally occurring chemical modifications to RNA molecules help them properly fold into functional structures.

Full Article

Jul 06, 2023

Penn State chemist Stephen Benkovic named Atherton Professor

Stephen Benkovic, Evan Pugh Professor and Holder of the Eberly Family Chair in Chemistry at Penn State, has been honored by Penn State with the title of Atherton Professor.

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Apr 20, 2023

Grad Students in Huck Labs Win Awards for Innovative Research

Two graduate students—one in the Huck's Neuroscience program and the other in the Eberly College of Science's BMMB program—have been named recipients of an award available to those working in Biochemistry and Molecular Biology labs. Both PIs are also part of the Huck.

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Apr 17, 2023

Structured Nucleic Acids Day, Robert Simpson and Sons Lecture set for April 18

A half-day symposium on structured (noncanonical) nucleic acids will be held on Tuesday, April 18, in Foster Auditorium, Paterno Library, Penn State University Park.

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Feb 23, 2023

Nobel Prize-winning Penn State alumnus Paul Berg dies

Penn State alumnus Paul Berg, who received the 1980 Nobel Prize in chemistry, died Feb. 15 at his home in Stanford, California, surrounded by loved ones. He was 96.

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Aug 31, 2022

Boal recieves Early Career Award from Society of Biological Inorganic Chemistry

Amie Boal, professor of chemistry and of biochemistry and molecular biology, has been named a recipient of the 2022 Early Career Award from the International Society for Biological Inorganic Chemistry (SBIC), an organization dedicated to advancing research and promoting understanding of biological inorganic chemistry within academia, industry, and the general public

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Jun 13, 2022

Climate-associated genetic switches found in plants

Genetic variants that can act as switches directing structural changes in the RNA molecules that code for proteins in plants have been experimentally validated in plants for the first time. The changes to RNA structure can affect the molecule’s stability, how it interacts with other molecules, and how efficiently it can be translated into protein — all of which can impact its function and the traits of the plant.

Full Article

Aug 20, 2019

Penn State Chemistry Alum Recognized with Young Scientists Award

Kathleen Leamy has been awarded the 2019 Gordon Hammes Scholar Award, based on a 2018 article she co-authored with the Huck Institutes' Neela Yennawar and Phillip Bevilacqua.

Full Article

Apr 19, 2019

NIH Trainees Juan Cerda and Catherine Douds Receive NSF-GRFP Honorable Mentions

Juan Cerda and Catherine Douds, both members of NIH-sponsored training programs overseen by the Huck Institutes, were recognized for their promising research ideas.

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