Matthew Rossi, PhD

• Professional Background

  Education

  • 2011 - Doctor of Philosophy - Biochemistry - Drexel University College of Medicine, Philadelphia, PA
  • 2005 - Master of Science - Biology - East Stroudsburg University, East Stroudsburg, PA
  • 2003 - Bachelor of Science - Biochemistry & Cell Biology - Bucknell University, Lewisburg, PA

  Training

  • 2017 - Postdoctoral Fellow - Biochemistry & Cell Biology - Penn State University, University Park, PA-Advisor: B. Franklin Pugh

  Highlights

  Amedeo Bondi Award Winner Graduating Students, Drexel Univ. College of Medicine 11

  For excellence in research-Biomedical Graduate Studies

  Amedeo Bondi Fellowship Award Winner, Drexel Univ. College of Medicine 08

  For excellence in research-Biomedical Graduate Studies

  First Place Award-Poster Presentation Jr Graduate Student 06

  Drexel Univ. College of Medicine Annual Research Day

  Magna Cum Laude, B. S., Biochemistry & Cell Biology, Bucknell University 03

  Appointments

  • 2020 - Assistant Research Professor - Penn State University, University Park, PA
  • August 2020 - Research Assistant Professor - Drexel University College of Medicine, Philadelphia, PA
  • 2021-April - Assistant Professor - UTHSA, Dept. of Biochemistry and Structural Biology

• Research & Grants

  Research profile

• Service

  Institutional

  Professor:  Model Systems & Approaches in Cell Biology BMB 448   Fall semester 2017 – 2019

  Department of Biochemistry & Molecular Biology

  Penn State University

  Guest Lecturer:    Communities of Practice in Biochemistry & Molecular Biology   Spring semester 2018

  BMB 488, Department of Biochemistry & Molecular Biology

  Penn State University

  Tutor: graduate and undergraduate students in biochemistry,  2003 – 2007

  molecular biology, and introductory biological science courses.

  Drexel University College of Medicine & East Stroudsburg University

  Teaching assistant:  introduction to molecular biology lab course 2004 – 2005

  Service to the Profession

  CONFERENCE PRESENTATIONS

  Cold Spring Harbor Laboratory Meeting – Mechanisms of Eukaryotic Transcription. Cold Spring Harbor, NY, 2019.

  38th Penn State Summer Symposium in Molecular Biology: Chromatin and Epigenetic Regulation of Transcription. University Park, PA, 2019.

  34th Penn State Summer Symposium in Molecular Biology: Chromatin and Epigenetic Regulation of Transcription. University Park, PA, 2015.

  American Society of Biochemistry and Molecular Biology Meeting: Transcriptional Regulation: Chromatin and RNA polymerase II. Snowbird, UT, 2014.

  Cold Spring Harbor Laboratory Meeting – Mechanisms of Eukaryotic Transcription. Cold Spring Harbor, NY, 2013.

• Publications

  1. Matthew J. Rossi, Prashant K. Kuntala, William K.M. Lai, Guray Kuzu, Naomi Yamada, Nitika Badjatia, Chitvan Mittal, Kylie Bocklund, Nina Farrell, Joshua D. Mairose, Thomas R. Blanda, Kate S. Mistretta, David J. Rocco, Emily S. Perkinson, Gretta D. Kellogg, Shaun Mahony, B. Franklin Pugh. A high-resolution protein architecture of the budding yeast genome. under review at Nature. 2021. v592 no7853. pg 309-14. doi: 10.1038/s41586-021-03314-8.
  2. William K. M. Lai, Luca Mariani, Gerson Rothschild, Edwin R. Smith, Bryan J. Venters, Thomas R. Blanda, Prashant K. Kuntala, Kylie Bocklund, Joshua Mairose, Sarah N Dweikat, Katelyn Mistretta, Matthew J. Rossi, Daniela James, James T. Anderson, Sabrina K. Phanor, Wanwei Zhang, Avani P. Shaw, Katherine Novitzky, Eileen McAnarney, Michael-C. Keogh, Ali Shilatifard, Uttiya Basu, Martha L. Bulyk, B. Franklin Pugh. Screening of PCRP transcription factor antibodies in biochemical assays. in preparation.
  3. Nitika Badjatia, Matthew J. Rossi, Alain R. Bataille, Chitvan Mittal, William K.M. Lai, B. Franklin Pugh. Acute stress drives global repression through two independent RNA polymerase II stalling events in Saccharomyces. 2021. Cell Reports. v34 no3. pg 108640 doi: 10.1016/j.celrep.2020.108640.
  4. Naomi Yamada, Matthew J. Rossi, Nina Farrell, B. Franklin Pugh, Shaun Mahony. Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein-DNA complexes. Nucleic Acids Research. 2020. v48 no 20. pg 11215-26. doi: 10.1093/nar/gkaa618.
  5. Matthew J. Rossi, William K.M. Lai, and B. Franklin Pugh. Simplified ChIP-exo assays. 2018. Nature Communications. 2018. v9 n1. 2842. doi: 10.1038/s41467-018-05265-7.
  6. Matthew J. Rossi, William K.M. Lai, and B. Franklin Pugh. Genome-wide determinants of sequence-specific DNA binding of general regulatory factors. Genome Research. 2018. v28 n4. pg 497-508. doi: 10.1101/gr.229518.117.
  7. Vinesh Vinayachandran, Rohit Reja, Matthew J. Rossi, Bongsoo Park, Lila Rieber, Chitvan Mittal, Shaun Mahony, and B. Franklin Pugh. Widespread and precise epigenomic reprogramming of yeast protein-genome interactions in response to heat shock. Genome Research. 2018. v28 n3. pg 357-66. doi: 10.1101/gr.226761.117
  8. Nadish Goyal, Matthew J. Rossi, Olga M. Mazina, Yong Chi, Robert L. Moritz, Bruce E Clurman, and Alexander V. Mazin. RAD54 N-terminal domain: a DNA sensor that couples ATP hydrolysis with branch migration of Holliday junctions. Nature Communications. 2018. v9 n1. 34. doi: 10.1038/s41467-017-02497-x.
  9. Matthew J. Rossi, William K.M. Lai, and B. Franklin Pugh. Correspondence: DNA Shape is insufficient to explain binding. Nature Communications. v8 pg15643. 2017.
  10. Olga M. Mazina, Matthew J. Rossi, Julianna S. Deakyne, Fei Huang, and Alexander V. Mazin. Polarity and bypass of DNA heterology during branch migration of Holiday junctions by human RAD54, BLM, and RECQ1. Journal of Biological Chemistry. v287 n15. pg 11820-11832. 2012.
  11. Matthew J. Rossi and Alexander V. Mazin. DNA Repair and Recombination. Encyclopedia of Biophysics. In press. 2012. updated 2021.
  12. Matthew J. Rossi, Dmitry V. Bugreev, Olga M. Mazina, and Alexander V. Mazin. Reconstituting key steps of the DNA double-strand break repair in vitro. Methods in Molecular Biology: DNA Recombination. v745. pg 407-420. 2011.
  13. Matthew J. Rossi, Olga M. Mazina, Dmitry V. Bugreev, and Alexander V. Mazin. RecA/RAD51 drives migration of Holliday junctions via polymerization on DNA. Proceedings of the National Academy of Sciences. v108 n16. pg 6432-6437. 2011
  14. Dmitry V. Bugreev, Matthew J. Rossi, and Alexander V. Mazin. Cooperation of RAD51 and RAD54 in DNA lesion bypass via the template switch mechanism. Nucleic Acids Research. v39 n6. pg 5134-5146. 2010. *This article was rated a “must read” by Faculty of 1000.
  15. Alexander V. Mazin, Olga M. Mazina, Dmitry V. Bugreev, and Matthew J. Rossi. Rad54, the Motor of Homologous Recombination. DNA Repair. v9 n3. pg 286-302. 2010.
  16. Matthew J. Rossi, Olga M. Mazina, Dmitry V. Bugreev, and Alexander V. Mazin. Analyzing the Branch Migration Activities of Eukaryotic Proteins. Methods. v51 pg 336-346. 2010.
  17. L. Sangeetha Vedula, Grace Brannigan, Nicoleta J. Economou, Jin Xi, Michael A. Hall, Renyu Liu, Matthew J. Rossi, William P. Dailey, Kimberly C. Grasty, Michael L. Klein, Roderic G. Eckenhoff, Patrick J. Loll. A Unitary Anesthetic-Binding Site at High Resolution. Journal of Biological Chemistry. v284 n36. pg 24176-24184. 2009.
  18. Matthew J. Rossi and Alexander V. Mazin. Rad51 Protein Stimulates the Branch Migration Activity of Rad54 Protein. Journal of Biological Chemistry. v283 n36. pg 24698-24706. 2008.
  19. Dmitry V. Bugreev, Matthew J. Rossi, Olga M. Mazina, and Alexander V. Mazin. The Late Step of Homologous Recombination: Branch Migration of Holliday Junction. pg 141-158. Bresler Memorial Lectures II Molecular Genetics Biophysics and Medicine Today. Russian Academy of Sciences. St. Petersburg. 2007.
  20. Olga M. Mazina, Matthew J. Rossi, Nicolas H. Thomä, and Alexander V. Mazin. Interactions of hRad54 protein with branched DNA molecules. Journal of Biological Chemistry. v282 n29. pg 21068-21080. 2007.
  21. Jin Xi, Renyu Liu, Matthew J. Rossi, Jay Yang, Patrick J. Loll, William P. Dailey, and Roderic G. Eckenhoff. Photoactive Analogues of the Haloether Anesthetics Provide High-Resolution Features from Low-Affinity Interactions. ACS Chemical Biology. v1 n6. pg 377-384. 2006.