People

James M. Berger

jmberger@jhmi.edu

My laboratory’s research is focused on understanding how multi-subunit assemblies use ATP for overcoming topological challenges within the chromosome and controlling the flow of genetic information.  We are particularly interested in developing mechanistic models that explain how macromolecular machines transduce chemical energy into force and motion, and in determining how cells exploit these complexes and their activities for regulating the initiation of DNA replication, chromosome superstructure, and other essential nucleic acid transactions.  Our principal approaches rely on a variety of structural, biochemical, and biophysical methods to define the architecture, function, evolution, and regulation of biological complexes. We also have extensive interests in mechanistic enzymology and the study of small-molecule inhibitors of therapeutic potential, the development of chemical approaches to trapping weak protein/protein and protein/nucleic acid interactions, and in using microfluidics for biochemical investigations of protein dynamics and structure.

Awards/ Honors

• Jane Coffin Childs Postdoctoral Fellowship –  James Keck
• Damon Runyon Postdoctoral Fellowship – Scott Gradia
• Berkeley Miller Postdoctoral Fellowship –  Erin Dueber, Franziska Bleichert
• EMBO Postdoctoral Fellowship – Alessandro Costa, Timothy Blower
• Spanish Ministry of Science Postdoctoral Fellowship – Ernesto Arias-Palomo
• Life Sciences Research Foundation Postdoctoral Fellowship – Philip Kranzusch
• American Cancer Society Postdoctoral Fellowship – Scott Classen, Jeff Lerman, Artem Lyubimov
• Swiss National Postdoctoral Fellowship – Frédéric Stanger
• Kirschstein-NRSA Predoctoral Fellowship – Joyce Lee, Arman Siddiqui
• Kirschstein-NRSA Postdoctoral Fellowship – Valerie O’Shea, Matthew Parker, Dan Richman
• NSF Graduate Research Fellowship – Rachel Fennell-Fezzie, Kevin Corbett, Allyn Schoeffler, Melissa Mott, Seychelle Vos, Michael Lawson, Tim Wendorff, Michael Lawson, Amy Fernandez
• DOE Graduate Research Fellowship – Iris Hood
• Berkeley Outstanding GSI Award – Jan Erzberger, Kevin Corbett, Allyn Schoeffler, Nathan Thomsen, Melissa Mott, Bryan Schmidt, Michael Lawson
• Alan Bearden Graduate Award – Kevin Corbett, Nathan Thomsen
• Harold Weintraub Graduate Award – Jacob Corn
• Carpenter Award for Academic Excellence (Undergraduate) – David Mai
• HHMI Biology Fellows Award (Undergraduate) – Heather McFarlane, David Mai, Clement Chu, Francisco Solorio
• Fullbright Scholar – Michael Lawson

Alumni (Has your present status changed? Let me know!)

Post-doctoral fellows:

• Dr. Deborah Fass –  Present position: Full Professor at the Weizmann Institute, Israel
• Dr. Jinyu Liu – Present position: Senior Scientist,  Genzyme Corporation.
• Dr. James L. Keck – Present position: Full Professor, University of Wisconsin, Madison
• Dr. Scott Gradia – Present position: Director of Research and Development, Caribou Biosciences
• Dr. Emmanuel Skordalakes – Present position: Full Professor, Wistar Institute
• Dr. David Akey – Present position: Research Investigator, Life Sciences Institute, University of Michigan
• Dr. Scott Classen – Present position: Staff Scientist, Advanced Light Source, Lawrence Berkeley National Laboratory
• Dr. Jeff Lerman – Present position: Ontology Engineer, Ingenuity Systems, Inc.
• Dr. Erin Cunningham – Present position: Group Leader, Genentech Inc.
• Dr. Marcelo Nollmann – Present position: Charge de Research, CNRS Montpelier, France
• Dr. Imsang Lee – Present position: Senior Scientist, CJ Cheil Jedang, South Korea
• Dr. Kevin Jude – Present position: Staff Research Scientist, Stanford University
• Dr. Artem Lyubimov – Present position: Staff Research Scientist, Stanford Synchrotron Radiation Lightsource Laboratory
• Dr. Valerie O’Shea – Present position: Patent Agent, Montgomery McCracken
• Dr. Alessandro Costa – Present position: Group Leader, Crick Institute, London
• Dr. Ernesto Arias-Palomo – Present position: Group Leader, Centro de Investigaciones Biológicas (CIB), Madrid.
• Dr. Franziska Bleichert – Present position: Assistant Professor, Yale University.
• Dr. Philip Kranzusch – Present position: Assistant Professor, Harvard Medical School
• Dr. Timothy Blower – Present position: Associate Professor, Durham University, UK
• Dr. Matthew Parker – Present position: Assistant Professor, University of Texas South Western Medical School.
• Dr. Frédéric Stanger – Present position: Bioinformatician/Computational Biologist, Novartis
• Dr. Neha Puri – Present position: Group Leader – FogPharma

Graduate students:

• Rachel Fennell-Fezzie – Present position: biodefense consultant.
• Jan Erzberger – Present position: Assistant Professor, UT Southwest.
• Kevin Corbett – Present position: Full Professor, UC San Diego.
• Jacob Corn – Present position: Group Leader, ETH, Zurich.
• Allyn Schoeffler – Present position: Assistant Professor, Loyola University New Orleans.
• Ken Dong – Present position: Staff Research Scientist, UC Berkeley
• Andy Antczak – Present position: Patent Agent at Morgan, Lewis & Bockius LLP
• Melissa Mott  – Present position: Independent practicing physician, Salt Lake City, UT.
• Nathan Thomsen – ‎Present position: Research Scientist, Gilead Sciences.
• Karl Duderstadt – Present position: Max Planck Fellow, Max Planck Institute at Munich.
• Shellie Weisfield Freedman – Present position: Associate in the New York office of Gibson, Dunn & Crutcher
• Richard Rymer – Present position: Principal Data Scientist with Verizon Media Group
• Melania Strycharska – Present position: Oxford Nanopore
• Bryan Schmidt – Present position: Assistant Professor, Davidson College
• Elsa Tretter – Present position: Scientist and Alliance Management/Business Development Manager, Nurix, Inc.
• Seychelle Vos – Present position: Assistant Professor, Massachusetts Institute of Technology.
• Iris Hood – Present position: Biology and Chemistry Faculty, The Chapin School, NYC.
• Thomas Murray – Present position: Patent Technical Specialist at LeClairRyan.
• Timothy Wendorff – Present position: Senior Scientific Researcher, Genentech.
• Michael Lawson – Present position: post-doctoral fellow, Dr. Joseph Puglisi, Stanford University.
• Andrew Eller –  Present position: Research Associate, FLIR Systems
• Matthew Hobson – Present position: Senior Analyst, Catalio Capital Management.

Research Associates:

• Anette Bruun
• Stephanie Capaldi
• Nancy Crisona
• Mary Coons
• Kristen DeAngelis
• Dorothy Kim

Undergraduates/Post-baccalaureates:

• Diego Ramos – PREP Scholar
• Francisco Solorio – HHMI Undergraduate Fellowship recipient
• Kevin Cheung
• Matt Krietzberg
• Song Qu
• Esther Choi
• Chih-Yih (Andy) Liao – Honors thesis, MCB Outstanding Poster Award
• David Mai -Honors thesis, HHMI Undergraduate Fellowship recipient, Jesse Rabinowitz  Prize in Biochemistry
• Noopur Batsha Heather McFarlane ‘“ HHMI Undergraduate Fellowship recipient
• Jamie Lo
• Anobel Odisho
• Clement Chu – HHMI Undergraduate Summer Fellowship recipient; NSF pre-doctoral fellowship recipient
• Stuart Sievers – Honors thesis
• Ray Nagatani – Honors thesis
• Vikas Mehta
• Eric Cheung
• Matthew Nichols