Spotlights

April 2024

Kara Bernstein Awarded PA Breast Cancer Coalition Grant 

Please join us in congratulating primary faculty member Kara Bernstein for being awarded a $100,000 grant from the PA Breast Cancer Coalition in support of her research on triple negative breast cancer. This funding will go towards continued research that could lead to developing therapies for those fighting the disease. View the NBC Philadelphia coverage of this event here.

Kathy Liu and Kenji Murakami Promoted with Tenure as Associate Professors 

We are excited to share that both Kathy Liu and Kenji Murakami have been fully approved by the Provost office for promotion with Tenure as Associate Professors! Kathy Liu has built a world-class research program to uncover fundamental mechanisms of enzyme-mediated RNA processing – with impact in cancer, sex-biased disease, and metabolism. Kenji Murakami has served as a leader in the Cryo-EM field and has also built an outstanding research program revealing critical insights into the mechanisms of transcriptional initiation and DNA repair. We are incredibly thankful for their contributions to the department and cannot wait to see what they do next!

March 2024

Black Lab Published in Science

The Black Lab recently published a paper in Science, "Efficient formation of single-copy human artificial chromosomes." The paper highlights a significant breakthrough in the field of human artificial chromosomes (HACs) that could lead to more efficient laboratory research and better engineered cell therapies, including gene therapies for diseases like cancer. This work was done in collaboration with researchers from the J. Craig Venter Institute, the University of Edinburgh, and the Technical University Darmstadt. For more information, see the press release published by Penn Medicine News here. 

Sgourakis Lab Awarded 2024 Cancer Grand Challenges Funding 

The Sgourakis Lab has been chosen to join a global team that is being awarded Cancer Grand Challenges funding to find treatments for some of the most impenetrable childhood cancers. Co-founded by the National Cancer Institute (NCI) and Cancer Research UK, the initiative selected five teams — chosen from 176 initial applicants — to receive grants of up to $25 million. The Sgourakis Lab is investigating T-cell receptors as part of Team MATCHMAKERS. They will contribute their structural biology expertise and enhance their work using the university's new, state-of-the-art spectrometer. Read more about the CHOP researchers participating in the Cancer Grand Challenges here. 

February 2024

Mark Sellmyer, MD, PhD

Dr. Mark A. Sellmyer is an Assistant Professor in the Radiology Department with a secondary appointment in the Department of Biochemistry & Biophysics at the University of Pennsylvania (UPenn) Perelman School of Medicine (PSOM). Since 2018, he has been an attending physician in the Nuclear Medicine Imaging and Therapy Division at UPenn in the tenure track. His lab works on chemical tool development for basic biologic research as well as translational imaging, including nuclear imaging strategies for gene and cell therapies, oncologic imaging, and infectious diseases. Recently his group developed the eDHFR/trimethoprim positron emission tomography (PET) reporter gene and radiopharmaceutical probe pair. In addition to imaging, they have further developed proteolysis targeted chimeric small molecules (PROTACs) based on the potential uses of eDHFR as a genetic tag. Technologies from his lab have been licensed commercially and recent radiopharmaceutical probes from his lab have been applied in human patients. He is a recipient of the NIH Director’s DP5 award, the Burrough’s Wellcome Fund Career Award for Medical Scientists, and R01 support from the NIH. He is the Co-Director of the Center for Translational Chemical Biology (CTCB) at UPenn with Dr. Ronen Marmorstein. The CTCB is a collaborative effort between the Departments of Biochemistry & Biophysics and Radiology, with the support of Dr. Kristin Lynch, and is growing synthetic and translational chemistry research at PSOM.

January 2024

Mirna El Khatib, PhD Selected for Emerging Leaders in Biochemistry Seminar Series 

Congratulations to Mirna El Khatib, a research assistant professor in the Vinogradov Lab, for being selected for the Emerging Leaders in Biochemistry seminar series at the Emory University School of Medicine! The Department of Biochemistry at Emory has reserved slots in their departmental seminar series for mid- and senior-level postdoctoral researchers who are considering academic careers. This is an opportunity for postdocs in biochemistry to present their cutting-edge research, meet faculty and trainees, and expand their network.

Sgourakis Lab Featured in Penn Medicine's Benchmarks 

A recent paper by the Sgourakis Lab, "Structural principles of peptide-centric chimeric antigen receptor recognition guide therapeutic expansion," has been featured in the December issue of Penn Medicine's Benchmarks newsletter. The newsletter highlights how the lab, in collaboration with John M. Maris, a professor of Pediatrics, recently devised a PC-CAR that, in preclinical work, enabled T cells to wipe out tumors from neuroblastoma. Read the full newsletter here. 

December 2023

Sergei Vinogradov Awarded NEMO Prize

The Nemirovsky Engineering and Medicine Opportunity (NEMO) Prize, funded by Penn Health-Tech, awards $80,000 to a collaborative team of researchers from the University of Pennsylvania’s Perelman School of Medicine and the School of Engineering and Applied Science for early-stage, interdisciplinary ideas. This year, the award was given to Biochemistry & Biophysics faculty member Sergei Vinogradov, along with Daeyeon Lee and Oren Friedman. Together, they are developing a new therapy that improves the survival and success of soft-tissue grafts used in reconstructive surgery. Read more about the award here. 

November 2023

New Website for the Johnson Foundation

The Department of Biochemistry and Biophysics is home to the Johnson Research Foundation. Founded in 1929, The Foundation has an 94-year record of instrumental invention and physical biochemical and medical application. Recently, a new website for the foundation and the Biophysics and Structural Biology core was published. Check out the new site and read more about the foundation and its related programs here.

October 2023

First Annual Meyerhof-Matschinsky Lecture

The department recently hosted our first annual Meyerhof-Matschinsky Lecture on September 18th, 2023. This lecture series highlights research in metabolism that has contributed to human health, and honors the memory of past leaders in metabolic research Drs. Franz Matschinsky and Otto Meyerhof. We were thrilled to host Dr. Michael Brown C'62 M'66 as our inaugural speaker. Thank you to all involved in putting on this event. We are already excited for the next one!

September 2023

Installation of New Equipment: Zeiss Crossbeam 550 

We are excited to share that we have recently begun the installation of a brand new piece of equipment, the Zeiss Crossbeam 550. This can perform volume imaging on cryogenic samples using the scanning electron microscopy (SEM) module without the need for extraneous contrast enhancing reagents, thus preserving the native cellular architecture for biological samples. Additionally, its focused ion beam milling (FIB) component can be used to make thin samples from thicker biological specimens, rendering them imageable by cryo-electron tomography (cryo-ET; a high resolution 3-dimensional imaging method) under a transmission electron microscope (TEM). The SEM and FIB processes are precisely guided by a fluorescence module that is integrated into the microscope.

Congratulations Mildred Cohn Distinguished Postdoctoral Award Winners

We are happy to announce the winners of The Mildred Cohn Distinguished Postdoctoral Awards: Vladimir Kolyadko (Krishnaswamy Lab), JiaBei Lin (Shorter Lab), and Ruchao Peng (Chang Lab). These awards are designed to spark innovative and collaborative research led by post-docs in the Department of Biochemistry and Biophysics. Research can be in any area of Biochemistry and Biophysics. 

August 2023

Kushol Gupta

Kushol Gupta is a Research Assistant Professor in the department, a member of the BMB graduate group, and directs the Johnson Foundation Biophysics and Structural Biology Core (JFBSB), a departmental resource that serves Penn and the greater region. His group is currently focused on two specific topics:  

1. The structural biology of HIV Integrase, including a rising class of drugs that has recently entered human trials known as the Allosteric Inhibitors of Integrase (ALLINIs) (recent publication) and  

2. The structural biology of Phenylalanine Hydroxylase, the enzyme that underlies the condition phenylketonuria (PKU) (recent publication).   

More recently, as an affiliated member of the Institute for RNA, he has been developing emerging methods in the JFBSB to serve the RNA community at Penn, including the application of multiwavelength analytical ultracentrifugation, SEC-MALS, and synchrotron SEC-SAXS to the characterization of mRNA lipid nanoparticles in collaboration with the Mitchell group at Penn.  

June 2023

Greg Bowman Featured in Penn Bioengineering Blog

Greg Bowman, Louis Heyman University Professor and PIK Professor in the Department of Biochemistry and Biophysics, was recently featured by the Penn Bioengineering Blog. The blog highlighted Dr. Bowman's work directing the Folding@Home program, which is a distributed computing program that allows individuals to sign up and run simulations at home and then report the results back to the network hub at Penn. Read more about Dr. Bowman's involvement with the Folding@Home here. 

George Burslem

George Burslem is an Assistant Professor in the Departments of Biochemistry and Biophysics, and Cancer Biology. The Burslem lab aims to bring the tools provided by synthetic chemistry to bear on problems in biomedical sciences, particularly in cancer biology and epigenetics. Specifically, we are interested in post-translational modifications, changes to a protein after it’s produced, which add an incredible level of diversity to the underlying proteins within a cell and can control a diverse array of processes, including protein stability, interactions, and activity. For example, some favorite modifications can lead to the protein being degraded which provides a mechanism to get rid of proteins which cause disease. Our hope is that through our work, we will not only provide insight into the processes underlying disease, but also provide new therapeutic strategies which can be used in a clinical setting to ultimately improve patient outcomes. For example, several of our projects have provided new drug-like molecules to address liabilities in lung cancers and leukemia. 

May 2023

Announcing New Institute for Structural Biology

The Perelman School of Medicine (PSOM) has announced the establishment of the Penn Institute for Structural Biology (ISB), which will be led by Dr. Vera Moiseenkova-Bell, Professor in the Department of Systems Pharmacology and Translational Therapeutics and Secondary faculty in the Department of Biochemistry and Biophysics.

The ISB will catalyze novel advances in the areas of structural biology, provide access to expertise and technology to support cryo-EM, Xray crystallography, NMR, molecular dynamics simulations and more, and promote collaborative studies across the biomedical community. 

The creation of the ISB highlights the recognition and value PSOM places on the impact of structural biology in biomedical discovery and therapeutic development and will empower our community to achieve even greater success!

April 2023

Mark Sellmyer

Mark Sellmyer is an Assistant Professor and physician-scientist in the Departments of Radiology and Biochemistry & Molecular Biophysics. The Sellmyer Lab aims to develop molecular and cellular solutions to address challenges in the biomedical sciences and clinical medicine, particularly in the areas of imaging and diagnostics. They make small molecules, engineered proteins and cell-based tools that can "light up" and control in vivo biology using principles of chemical and synthetic biology. These molecules have diverse applications in broad fields of investigation including cancer biology, immunology, and infectious disease. Mark also serves as the Co-Director for the Center for Translational Chemical Biology.

March 2023

Greg Bowman Appointed Penn Integrates Knowledge (PIK) Professor 

Greg Bowman, one of the departments newest faculty members, has been named a Penn Integrated Knowledge (PIK) professor. The announcement was made on March 28th by President Liz Magill and Interim Provost Beth A. Winkelstein. Penn Integrates Knowledge (PIK) Professors hold joint appointments in two or more schools and exemplify excellence in multidisciplinary scholarship and learning. Read the full announcement here.  

Rahul Kohli

Rahul Kohli is a physician-scientist with appointments in both the Department of Medicine and the Department of Biochemistry and Biophysics. The Kohli lab is focused on the study of enzymes that modify and mutate DNA, given the central role that genome dynamics play in epigenetics and in host-pathogen interactions. These processes are open to interrogation by enzymology and chemical biology approaches. The lab also aims to harness the biotechnological or therapeutic potential of DNA altering enzymes and pathways, with applications that include new sequencing methodologies, targeted genome editing, and combating the evolution of antibiotic resistance. Dr. Kohli is passionate about supporting pathways that meld fundamental science and medicine, and in this spirit, also serves as an Associate Program Director for Penn’s MD/PhD program. 

February 2023

Welcoming Blanton Tolbert

Exciting News -  Blanton Tolbert will be joining the Department of Biochemistry and Biophysics and the Institute for RNA Innovation at Penn starting in July! Blanton is a leader in RNA Structural Biology with particular emphasis on using NMR to study viral RNAs and their complexes. He is also the Vice President for Science Leadership and Culture at HHMI. Blanton’s recruitment will greatly enhance RNA structural biology expertise at Penn and promote critical mass in the area of NMR. We are excited for the collaborative impact he will have across the RNA, virology and biophysics communities at Penn. Welcome to Blanton and his lab!

January 2023

Yi-Wei Chang

Yi-Wei Chang is an Assistant Professor of Biochemistry and Biophysics. The Chang lab is specialized in utilizing cryo-electron tomography to image microbial pathogens in 3 dimensions at molecular resolution, thereby resolving the detail structures and mechanisms driving their infection of human. Such new understanding can pave the way for designing new medicines or strategies to fight against many important infectious diseases, such as malaria. To learn more about Yi-Wei's work, you can visit his lab website here. 

December 2022

Aaron Timperman

Aaron Timperman is a Research Professor with appointments in both Bioengineering and Biochemistry & Biophysics. The Timperman Lab at Penn develops next-generation microfluidic and nanofluidic technologies to improve the analysis the biochemical components within cells and intact cells. For the analysis of individual cells, they emphasize the measurement of surface charge which plays a major role in interactions with other cells and the general external environment. In the future, this technology could be used to interrogate cell-cell interactions and binding events at cell surface receptors. For the analysis of cellular components, the Timperman lab focuses on proteins and develop improved methods for comprehensive mass spectrometry-based proteomics. Additionally, they develop multiplexed microfluidic systems that couple individual cell culture chambers with improved biomimicry of in vivo systems and on-chip gradient generators to dose cells with a range of concentrations of one or two soluble factors. Currently, they are also developing new methods for detecting many viruses from saliva, and determining factors that make some corals more resilient than others using traditional proteomic methods.

November 2022

Ben Black

Ben Black and his team are answering some of the most pressing questions in chromosome biology, such as: How does genetic inheritance actually work? How was epigenetic information transmitted to our parents? How do enzymes signal to the cell when chromosome damage has occurred? The Black lab has made seminal discoveries regarding the physical basis for how CENP-A-containing nucleosomes epigenetically mark and maintain centromere location on the chromosome. Recently, they have hijacked the pathways for chromosome inheritance to design and create new types of artificial chromosomes. They also discovered a tunable aspect in a class of cancer therapeutics, called PARP inhibitors, and have now assembled a collaborative team to create new versions that will improve their efficacy and expand their utility.

October 2022

Sergei Vinogradov

Sergei Vinogradov is a Professor in the Department of Biochemistry and of Chemistry. His lab works at the intersection of synthetic chemistry and optical spectroscopy, developing probes for optical biological imaging. On a fundamental level, the lab is interested in chemistry and spectroscopy of porphyrins and related pyrrolic dyes, optical energy upconversion, multiphoton absorption and magnetic field effects on luminescence. One central research topic has been the imaging of oxygen in biological tissues, including chemistry of phosphorescent imaging probes, design of imaging instrumentation as many applications of phosphorescence. Currently, the Vinogradov Lab operates a national research resource for Oxygen Imaging by Phosphorescence Quenching, which is funded by the National Institute of Biomedical Imaging and Bioengineering (NIBIB). 

Future Leaders in Biochemistry & Biophysics

Our department hosted the second iteration of our Future Leaders in Biochemistry & Biophysics Symposium on Friday, October 7th. Building on the success of last years event, we yet again set about identifying those we believe to be rising stars in the fields of biochemistry and biophysics and inviting them to Penn for an afternoon symposium highlighting them and their science, as they transition to independence. 

We were thrilled to welcome such a talented group of speakers from a variety of outside institutions, such as Scripps Research Translation Institute, Princeton, Stanford, and more. Our visiting speakers had the chance to meet with faculty members from the department one-on-one and later presented their research to an audience of faculty, students, postdocs, and other department affiliates. We were thrilled with the turnout for this event, and appreciate everyone who helped make it possible. More photos from the event can be found on our Instagram account. For information about more upcoming seminars, please visit our seminars page. 

September 2022

Mirna El Khatib

Dr. Mirna El Khatib is one of the recent recipients of the Johnson Foundation (JF) Fellowship in the Department of Biochemistry and Biophysics, which supports individuals in their transition to faculty positions. She is also an NIH K25 fellow working on the development of molecular probes for biological imaging in the Vinogradov lab. Specifically, she is interested in the development of various membrane-anchored probes, e.g. for oxygen and other small-molecule analytes.

Mirna is a synthetic organic chemist by training. She received her PhD in organic chemistry working under the direction of Alan R. Katritzky at the University of Florida, then moved to the University of Pennsylvania to conduct her post-doctoral work under the direction of Gary A. Molander, exploring various cross-coupling methodologies. Later, she transitioned to the Perelman School of Medicine at Penn to gain first-hand experience in imaging probes development and applications in the laboratory of Dr. Sergei Vinogradov, where she currently works.  

Penn FERBS

Students from the Penn First-Year Exposure to Research in Biomedical Sciences (FERBS) program attended the Center for Undergraduate Research and Fellowships (CURF) Fall Expo on September 19^th. The Expo, which was open to undergraduates doing research in all fields,  featured 15 FERBS students across the second and third-year cohorts from a variety of labs in BGS. Mentors, faculty and even some family members came out to support the FERBS students who presented impressive work from only one or two summers' worth of research in a lab.  

FERBS seeks to support students from underrepresented backgrounds and foster their growth as researchers. The program was started in conjunction with the School of Arts and Sciences Biology Department and involves getting undergraduate students into labs, pairing them with PhD students or postdocs as mentors, and providing other training. Any lab within BGS & BMB can apply to become a PennFERBS lab. Information about the program can be found here. 

Greg Bowman

Greg Bowman is the Louis Heyman University Professor and one of the newest members of the Department of Biochemistry and Biophysics, as well as Bioengineering. His lab devises new ways to interpret genetic variation and combat global health threats by understanding/exploiting protein dynamics using a combination of biophysical experiments, machine learning, physics-based simulations, and the world’s largest distributed computer. To achieve their goals, the lab seeks to: 1) Develop new computational and experimental methods for mapping out the ensemble of structures that a protein adopts instead of settling for a single static snapshot; 2) Understand how proteins function an malfunction in the context of global health threats like Alzheimer’s disease and COVID-19 by iteratively using simulations to gain mechanistic insight, conducting experimental tests of these models, and refining them based on feedback from experiments; and, 3) Exploit computational models to predict the impact of genetic variations on phenotype and to design new proteins and drugs.  

August 2022

Kara Bernstein

Kara Bernstein is one of our newest arrivals and is a Professor in the Department of Biochemistry and Biophysics, who also has affiliations with the Basser Center for BRCA, Penn Center for Genome Integrity and Abramson Cancer Center. Dr. Bernstein’s research focuses on proteins that contribute to cancer development and studies how accurate repair of DNA double-strand breaks is regulated using the budding yeast and mammalian systems. The Bernstein lab has been focusing on the DNA repair genes, the RAD51 paralogs, which when mutated lead to increased breast and ovarian cancer risk using genetic biochemical, and cell biological approaches. By understanding RAD51 paralog molecular function, the Bernstein lab aims to determine individuals who are at risk for cancer development and to uncover more effective targeted treatment strategies for these patients.

Natoya Peart - Postdoc Spotlight

Dr. Natoya Peart has been a postdoc and Johnson Foundation Fellow in the Lynch Lab since July 2021. She started her postdoc work at the University of Pennsylvania with Carstens Lab working on identifying the in vivo RNA targets of the RNA binding protein, ESRP1. Natoya has had a longstanding interest in the RNA research, and as a graduate student at the MD Anderson UTHealth Graduate School of Biomedical Sciences she worked on identifying the regulatory elements required to produce Dux4 mRNA, the leading candidate gene for FSHD. Since joining the Lynch lab she has continued her work on ESRP1 and is focused on exploring and defining the regulatory network mediated by ESRP1 in governing mRNA metabolism. Natoya is one of the inaugural fellows for the Johnson Foundation Fellowship in the department of Biochemistry and Biophysics, which seeks to support senior postdocs in the transition to faculty. While at UPenn she has served on the Biomedical Postdoctoral Council in several capacities including co-editor of the BPC Newsletter, founding member of the Du Bois Postdoctoral Council, co-chair of the PR committee and on the diversity committee. Outside of UPenn, Natoya is a member of the RNA Society Diversity Equity and Inclusion Committee, where she leads efforts to build a more inclusive RNA community regardless of race, sex, nationality, sexuality and religion.

March 2022

Elizabeth Rhoades is a professor in the Department of Chemistry with a secondary appointment in Biochemistry & Biophysics, as well as co-PI of the Structural Biology and Molecular Biophysics Training Grant. Research in her lab focuses on determining functional mechanisms of intrinsically disordered proteins, with a particular interest in two proteins involved in neurodegenerative disorders, alpha-synuclein and tau. The lab uses a variety of biophysical and cell biological approaches, with special expertise in single molecule fluorescence. Recent efforts from the lab  have focused on identifying cellular binding partners of alpha-synuclein (publication) and determining molecular mechanisms of tau-mediated polymerization of tubulin (publication).

January 2022

Cornelius Taabazuing is an Assistant Professor in the Department of Biochemistry and Biophysics and our newest faculty member. The focus of his lab is to understand molecular mechanisms of cell death. The lab utilizes microscopy, cell biology, and biochemical approaches to study the molecular regulation of the innate immune system, and the response to DNA damage. Specifically, Dr. Taabazuing and his lab are interested in understanding the activation mechanism of proteases termed caspases that induce cell death. Their goal is to leverage this knowledge to develop treatments for human diseases.  

November 2021

James Shorter is a Professor in the Department. The Shorter lab uses diverse techniques to pioneer protein disaggregases, small-molecule drugs, and RNAs to counter deleterious phase transitions in neurodegenerative disease. In an exciting study published in eLife, Dr. Shorter and colleagues discovered a human mitochondrial protein disaggregase, Skd3 (human ClpB), which is a AAA+ protein related to Hsp104. Skd3 maintains the solubility of several critical mitochondrial proteins. Importantly, Skd3 variants linked to 3-methylglutaconic aciduria, a severe mitochondrial disorder, display diminished disaggregase activity, which predicts disease severity. Moreover, in a recent study published in Blood, dominant-negative mutations in Skd3 were connected to severe congenital neutropenia. Thus, Skd3 is a potent protein disaggregase critical for human health.

August 2021

Ronen Marmorstein
Dr. Marmorstein is the George W. Raiziss Professor, Vice-Chair in the Department of Biochemistry and Biophysics, Adjunct Professor of Chemistry, Director of the University of Pennsylvania Chemistry-Biology Interface training program, and oversees the ‘Structural Talk’ interest group seminar series. The laboratory studies the molecular mechanisms of (1) protein post- and co-translational protein acetylation and acetyl-CoA metabolism, (2) gene expression and epigenetic regulation, and (3) MAPK signaling. They use a broad range of biochemical, biophysical and structural research tools (X-ray crystallography and cryo-EM) to determine macromolecular structure and mechanism of action and use high-throughput small molecule screening and structure-based design strategies to develop protein-specific small molecule probes to interrogate protein function and for preclinical studies. Recent studies include elucidating the molecular mechanism of the multimeric NatB (publication) and  NatC (publication) N-terminal acetyltransferases and determining the molecular basis for acetyl-CoA production by ATP citrate-lyase (publication).

May 2021

Viridiana Herrera - Postdoc Spotlight
Dr. Viridiana Herrera has been a postdoc in the Black lab since October of 2019. She did her graduate studies at the University of Oklahoma, where she worked on determining the structure of hemeprotein-nitroso complexes. Viridiana is now fascinated by centromere biology and currently interrogates the recruitment of the Chromosome Passenger Complex on to the chromosome for proper segregation. As part of the NIH/IRACDA sponsored PennPORT Program, she serves as an adjunct faculty member at Lincoln University, the first degree-granting HBCU. She also established a monthly Journal Club to champion social-justice and diversity in academia. Outside of UPenn, she serves as the Future Chair for the 2022 National Organization for the Professional Advancement of Black Chemists and Chemical Engineers Conference. In her free time, Viridiana enjoys listening to true crime podcasts and hiking.

March 2021

Nikolaos Sgourakis
Welcome our newest Associate Professor, Nikolaos Sgourakis, also an Associate Professor in the Center for Computational & Genomic Medicine at CHOP. His laboratory investigates molecular mechanisms which drive adaptive responses and maintain immune homeostasis. To do this, they integrate NMR with computational modeling and functional immunoassays. One direction focuses on the selection of peptide antigens displayed by the proteins of the Major Histocompatibility Complex for surveillance by T cells and Natural Killer cells. Their detailed characterization of peptide editing by molecular chaperones has recently enabled a powerful platform for analyzing T cell repertoires relevant in immuno-oncology and immunotherapy. In a synergistic direction, the lab characterizes neuroblastoma-associated antigens to guide CAR T cell therapies in close collaboration with the lab of Cancer Biologist and Pediatric Oncologist John Maris. (Publication highlights)

February 2021
Kathy Fange Liu
Kathy F. Liu is an Assistant Professor of Biochemistry and Biophysics at the University of Pennsylvania. The Liu lab is focused on the function of modifications in coding and non-coding RNAs in human diseases. Specifically, they use kinetics, structural biology methods, mass spectrometry, RNA biology techniques, combined with next-generation high-throughput sequencing techniques to investigate the crosstalk of modifications across RNA species in neuronal development. (Recent publication here.) Another research focus of the lab is on sex-specific features in the physiology and pathology in the neuronal system. An area of particular interest is the functions of sex-chromosome encoded RNA binding proteins in regulating protein translation and stress granule formation.

January 2021

E. James Petersson
E. James Petersson, Ph.D. is a Professor of Chemistry at the University of Pennsylvania with a secondary appointment in our Department. His laboratory develops tools, such as novel chromophores and protein semi-synthesis, to investigate how peptides and proteins mediate cellular communication and how changes in the cellular environment catalyze protein misfolding and disfunction. Studies in the lab range from computational modeling, to detailed in vitro folding studies, to tracking protein aggregation in neurons, to the analysis of the role of post-translational modifications in controlling protein misfolding. An area of particular interest is the introduction of thioamide modifications to the peptide backbone, which can serve as protein folding probes, or stabilizers for improved therapeutic peptides or in vivo imaging reagents.

November 2020

Hana Odeh - Postdoc Spotlight 
Dr. Hana Odeh has been a postdoc in the Shorter lab since November of 2018. Prior to coming to the Department, she worked on SUMO regulation in the lab of Dr. Michael Matunis at Johns Hopkins. In the Shorter lab, Hana works on strategies to prevent TDP-43 aggregation and dipeptide-repeat toxicity in C9-ALS/FTD. Her most recent findings on the effects of poly(GR) on TDP-43 aggregation were published in Science Translational Medicine (co-first author). In addition to her research, Hana has a passion for mentoring students and a strong commitment to social justice. She serves on the Diversity, Equity and Inclusion committee in our Department, and leads efforts of anti-racism work in her lab and beyond. In her free time, Hana enjoys long-distance hiking and rock climbing. 

September 2020

Yale Goldman
Prof. Yale E. Goldman, MD, PhD, is Professor of Physiology at the University of Pennsylvania and former Director of the Pennsylvania Muscle Institute. 

His lab investigates muscle contraction, molecular motors, protein synthesis, and develops advanced methods in optical microscopy and single molecule biophysics. Novel biophysical techniques that lead to striking research findings have included laser photolysis of caged ATP, stable isotope oxygen exchange, polarized total internal fluorescence microscopy for single molecule structural dynamics, ultra-high speed optical traps, “parallax view” 3D tracking of single molecules, and alternating laser excitation (ALEX) microscopy for single molecule FRET measurements. The lab is currently investigating cardiac muscle contraction, including hypertrophic cardiomyopathies, mechano-biology of cellular gene expression and termination and read-through at premature mRNA stop codons that lead to truncated proteins in diseases such as muscular dystrophy and cystic fibrosis.

July 2020

Nicolai Doliba
Nicolai Doliba is a Research Associate Professor and Technical Director of the Islet Cell Biology Core, which serves academic and industry partners in the functional characterization of pancreatic islets as part of the Diabetes Research Center at Penn's Institute for Diabetes, Obesity and Metabolism.

Dr. Doliba currently oversees the islet physiology arm of the Human Pancreas Analysis Program, the multi-institutional initiative to characterize the cellular and molecular events which lead to dysfunction in Type 1 and Type 2 Diabetes. He develops bioenergetic methods to understand stimulus-secretion coupling and neuro-endocrine regulation, as well as their changes during diabetes mellitus. Together with his colleagues in the department, Dr. Doliba established the relationship between energy production and insulin secretion using novel phosphorescence methods for measuring oxygen consumption. In partnership with Hua Medicine, Dr. Doliba is studying the reparative effects of dorzagliatin, a novel antidiabetic drug that is currently in phase III clinical trials.

May 2020

Kushol Gupta
Kushol Gupta is a Research Assistant Professor in the department, a member of the BMB graduate group, and directs the Johnson Foundation Structural Biology and Biophysics Core, a departmental resource that serves Penn and the greater region. 

He is a structural biologist with expertise in both X-ray crystallography and solution biophysical methods, including small-angle X-ray and neutron scattering, light scattering, and analytical ultracentrifugation. His ongoing research focuses on retroviral integrases, their interaction with host factors, and a new class of drugs known as allosteric inhibitors of integrase (ALLINIs), which are potent antivirals against HIV. His research also includes other projects in the areas of phenylketonuria, RNA splicing, and site-specific recombination, highlighting the collaborative nature of research at Penn.

March 2020

Mark Sellmyer
Mark Sellmyer is an assistant professor with appointments in the Department of Radiology and in Biochemistry & Biophysics. He is a rising-star in chemical biology and molecular imaging and has received many awards including the Burroughs Welcome Fund Career Award for Medical Scientists (CAMS) and the NIH Director’s Early Independence Award (DP5). Dr. Sellmyer’s lab works onthe development of small molecule, engineered protein, and immune cell technologies that can be leveraged to understand cancer and infection pathogenesis as well as to monitor therapeutic efficacy. His group has experience in chemical synthesis, molecular biology, and preclinical animal models of disease and apply these to tool development for a range of basic science and clinical applications. Most recently, his group developed radiotracers based on the small-molecule antibiotic trimethoprim for imaging infection and engineered immune cells. These radiotracers are now in first-in-human studies.

February 2020
George Burlem
Welcome to our newest faculty member, George Burslem. Dr. Burslem is an Assistant Professor in the Department of Biochemistry and Biophysics with a secondary appointment in Cancer Biology and affiliations to the Penn Epigenetics Institute and the Basser Center. George joined the department in January 2020 after a postdoctoral fellowship at Yale University with Prof. Craig Crews.

The Burslem Lab is interested in understanding and modulating lysine post-translational modifications, particularly ubiquitination and acetylation. To do this they employ a wide variety of techniques including synthetic organic chemistry, biochemistry, molecular biology and cell biology to gain new insights as well as develop new chemical biology tools and potential therapeutic approaches. George’s recruitment to Penn strengthens our presence in Chemical Biology and highlights the collaborative nature of research across the Penn campus.

January 2020
Sara Cherry
Sara Cherry is a Professor with appointments in the Departments of Pathology and Laboratory Medicine, Microbiology, and Biochemistry and Biophysics. She is also a Faculty Director for the High Throughput Screening Core and the Director of the Program for Chemogenomics Discovery. 
    Dr. Cherry’s laboratory has pioneered the use of RNAi technology and other cell-based screening approaches to discover mechanisms by which diverse viral pathogens hijack cellular machinery while evading defenses. Her laboratory has discovered new factors involved in viral entry, translation, RNA replication and RNA stability. She has discovered new antiviral innate defenses against these emerging viruses and uncovered connections between metabolic regulation, the microbiota and immune defense. Recently, Dr. Cherry has expanded her interests to cancer where she has developed a functional precision pipeline as part of the Chemogenomics Discovery Program to screen acute leukemia cells for their sensitivities to drugs, with an eye toward guiding precision medicine patient therapy.

December 2019
Kim Sharp
Kim Sharp studies protein and nucleic acid structure and function using theoretical methods, computational and computer graphics tools. He currently splits his time between research, teaching, writing and BMB Graduate Group activities. Kim's current research includes work on development of virtual drug design tools and the mechanism of viral genome packing. In his role as BMB Graduate Group Chair, he is updating the graduate biostatistics curriculum and teaching Ph.D students Bayesian Statistics. Kim’s book, “Entropy and the Tao of Counting: A Brief Introduction to Statistical Mechanics and the Second Law of Thermodynamics,” will be published by Springer in January 2020. In his spare time, he collaborates with Franz Matschinsky on translating Ludwig Boltzmann’s papers on statistical mechanics intoEnglish.

November 2019
Vera Moiseenkova-Bell
Vera Moiseenkova-Bell is an Associate Professor with appointments in both the Department of Systems Pharmacology and Translational Therapeutics and the Department of Biochemistry and Biophysics. She is also a Faculty Director for the Electron Microscopy Resource Laboratory and Beckman Center for Cryo-Electron Microscopy. 
    The Moiseenkova-Bell laboratory is focused on understanding structure and function of Transient Receptor Potential (TRP) channels which have been implicated in a diverse range of cellular processes, including pain sensation, neuronal development, cardiovascular and renal pathophysiology, and cancer. Dr. Moiseenkova-Bell and her team utilize cryo-electron microscopy to determine the structural basis of TRP channel activation, inhibition and desensitization mechanisms. Structural information on TRP channels and their interaction with agonists/antagonists at the molecular level will establish a structural framework to enhance our understanding of their function at the molecular level, whereby improving therapeutic strategies and drug design.

October 2019
Franz M. Matschinsky
Franz M. Matschinsky, now on the way to retirement in 2021, continues to collaborate with a group of colleagues here at Penn and other institutions in the US and abroad. His efforts are focused on unraveling the molecular and physiological basis of glucose homeostasis in health and its defects in disease with particular emphasis on role of the glucose phosphorylating enzyme glucokinase. This enzyme, first discovered by Dr. Matschinsky, functions as the glucose sensing element of cells in the endocrine pancreas, the liver, the gut, the pituitary and neurons of different brain centers regulating fuel homeostasis. Over 600 inhibitory and activating mutations of have been discovered in this enzyme in humans. To combat these disease-causing mutations, allosteric glucokinase activator molecules are currently being assessed for their therapeutic potential in type II diabetics.

September 2019
Bohdana Discher
Bohdana Discher is a research associate professor in the Department of Biochemistry and Biophysics. The Discher laboratory utilizes biophysical and chemical tools to design synthetic water-soluble and membrane proteins. These non-natural proteins are based on a simple, functionally transparent 4-alpha-helical scaffold, which makes them an ideal test bed for ligand binding or electron transfer and catalysis.  These proteins have been exploited to study light harvesting, magnetic field sensing in bird navigation and for blood substitute development.  Their future promise lies in the development of rapid optical reporting of voltage sensing for neuroscience and mitochondrial research as well as for redox sensing within living cells to study metabolism.

August 2019
Kenji Murakami
The Murakami lab seeks to understand the mechanisms of RNA polymerase II transcription activation in response to stress and its regulations in the context of chromatin. The lab is also interested in the mechanism of nucleotide excision repair (NER). In particular, we focus on the mechanism of how a set of factors serve dual functions in NER and transcription and how they are regulated.  In all of these projects we use primarily structural (cryo-EM and cross-linking mass spectrometry) and biochemical approaches to dissect the architecture and function of the macromolecular complexes we study.

July 2019
Greg Van Duyne
The Van Duyne laboratory studies the mechanistic biochemistry of site-specific recombination and retroviral integration.  Site-specific recombinases such as phage integrases and resolvases are widely used in genome engineering and in vitro DNA applications. Cre recombinase, an enzyme that the Van Duyne laboratory has studied extensively, is a well-known example. The integrase from HIV, which inserts a cDNA copy of the viral RNA into the host genome, is the focus of much of our current work. The laboratory uses a broad range of structural, biochemical, and cell-based approaches to study these systems. Our HIV program involves close collaborations with researchers from Penn and from the pharmaceutical industry to study the mechanism of action of a new class of integrase inhibitors.

June 2019
Rahul Kohli
Rahul Kohli is a physician-scientist with appointments in both the Department of Medicine and the Department of Biochemistry and Biophysics. The Kohli lab is focused on the study of enzymes that modify and mutate DNA, given the central role that genome dynamics play in epigenetics and in host-pathogen interactions. These processes are open to interrogation by enzymology and chemical biology approaches. The lab also aims to harness the biotechnological or therapeutic potential of DNA altering enzymes and pathways, with applications that include new sequencing methodologies, targeted genome editing, and combating the evolution of antibiotic resistance. Dr. Kohli is passionate about supporting pathways that meld fundamental science and medicine, and in this spirit, also serves as an Associate Program Director for Penn’s MD/PhD program.

May 2019
Mitch Lewis
Mitch Lewis has long been a leader in understanding the biophysical parameters that determine how proteins respond to metabolites and regulate transcription. In recent years, the Lewis lab has used this knowledge to generate tunable transgene expression in gene therapy vectors. This work has tremendous promise to reduce toxicity and improve our ability to use gene therapy to cure disease. Dr. Lewis’s interest in metabolic regulation of transcription is also manifest in his commitment to teaching medical students, as he serves as director of the Metabolism course that is central to the first year medical school curriculum.

April 2019
Jeremy Wilusz
The Wilusz lab aims to reveal new insights into how RNAs are generated, regulated, and function. By combining high-throughput approaches with detailed biochemical studies, the laboratory has revealed new mechanisms controlling transcription, pre-mRNA processing, and translation of many protein-coding genes. Ongoing efforts are focused on circular RNAs, which have covalently linked ends, and a novel role for the Integrator complex in transcription termination. Congratulations to two postdoctoral fellows in the Wilusz lab who have successfully obtained NIH Pathway to Independence (K99/R00) Awards in the past year!

March 2019
Kristen Lynch
Kristen Lynch is Chair of the Department and a Professor of Biochemistry and Biophysics with a secondary appointment in Genetics. Kristen’s laboratory studies regulation of RNA processing, namely alternative splicing and polyadenylation, and how these processes are controlled during immune responses. For example, a recent study focused on the role of alternative splicing in host-viral interactions. Additional areas of interest are how signaling pathways influence the activity of RNA binding proteins, the variation of splicing in cancer and in T cell biology, and the coordination of splicing with polyadenylation and epigenetics. Kristen also oversees the Penn RNA Group.

Febuary 2019
S. Walter Englander
Walter Englander is the emeritus Gershon-Cohen Professor of Biophysics and Medical Science and a member of the National Academy of Sciences and The American Academy of Arts and Sciences. His lab led the development of the hydrogen exchange field for protein biophysical studies, discovered the role of cooperative foldon units in protein structure and folding, developed the defined pathway model to explain how proteins fold, and invented and developed the leading-edge technology of hydrogen exchange mass spectrometry (HX/MS). His lab is actively involved in protein folding studies and in the function of large energy-driven protein machines like heat shock protein 104.

January 2019
Yi-Wei Chang
WELCOME to our newest member of the faculty, Dr. Yi-Wei Chang!  The Chang Lab is devoted to understanding biology from a structural perspective. Based on the notion that the best way to understand the function of a molecule is to understand its structure in its native environment, the Chang lab utilizes Electron Cryotomography (ECT), an emerging powerful cryo-electron microscopy imaging technique, to study the structure and mechanism of macromolecular nanomachines directly inside cells. ECT reveals not only native conformations and assemblies of the nanomachines as they are conducting functions, but also their distribution, orientations and interactions to other cellular components – thus enabling studies of Structural Cell Biology and Molecular Sociology. We are excited to have Dr. Chang and ECT as part of our growing cryo-EM community.

December 2018
Ben Garcia
Ben Garcia is the John McCrea Dickson M.D. Presidential Professor of Biochemistry and Biophysics, as well as vice-chair of the Biochemistry and Molecular Biophysics Graduate Group and Director of the Quantitative Proteomics Resource Center. The Garcia Lab utilizes high-resolution mass spectrometry to explore cellular signaling, epigenetic mechanisms and chromatin regulation; with particular interest in understanding how protein and nucleic acid modifications regulate nuclear processes. Recent discoveries include understanding the structural dynamics of histone tails, uncovering connections between histone acetylation in metabolism, and identifying lncRNAs in ant brains. The Garcia lab also is a leader in the development of mass spectrometry methods, enabling new applications of mass spectrometry throughout the scientific community.

November 2018
Ronen Marmorstein
The Marmorstein laboratory studies the molecular mechanisms of protein post- and co-translational modification with a particular focus on protein acetylation and phosphorylation and chromatin regulation.  The laboratory uses a broad range of molecular, biochemical and biophysical research tools centered on macromolecular structure determination.  The laboratory is particularly interested in gene regulatory proteins and their upstream signaling kinases that are aberrantly regulated in cancer and other age-related disorders, and the use of high-throughput small molecule screening and structure-based design strategies towards the development of protein-specific small-molecule probes to be used to further interrogate protein function and for development into therapeutic agents.

October 2018
Sergei Vinogradov
Sergei Vinogradov's research is focused on the development of optical probes for biological microscopy and imaging. The laboratory has long-standing interest in metalloporphyrins, which can be used as sensors for oxygen, pH, metal ions and other environmental parameters of biological systems. Two-photon phosphorescence lifetime microscopy (2PLM) of oxygen, developed by the lab, is now broadly used in neuroscience and stem cell biology. Recently, the group theoretically predicted a new class of porphyrins with exceptionally high two-photon absorption cross-sections, and using them developed probes for 2PLM with 100 times higher performance. The current focus is on exploration of higher order optical non-linearity, such as in three-photon absorption, to gain deeper insight at the energy metabolism in the brain.

September 2018
Ben Black
Ben Black, newly promoted Professor, and his team are answering some of the most pressing questions in chromosome biology, such as: How does genetic inheritance actually work? How was epigenetic information transmitted to our parents? And can building new artificial chromosomes help us understand how natural chromosomes work?The Black lab has made seminal discoveries regarding the physical basis for how CENP-A-containing nucleosomes epigenetically mark and maintain centromere location on the chromosome. Recently they have also discovered how amplified centromeric DNA repeats act as selfish elements in female meiosis to explain rapid centromere evolution.

August 2018
Jim Shorter
Congratulations to Jim Shorter, one of the newly promoted Professors in the Department. The Shorter lab is a leader in the study of protein aggregation and disaggregation. His laboratory uses techniques ranging from biophysics to yeast genetics to identify novel ways to dissociate toxic protein phases that are common in many neurodegenerative diseases. In a recent exciting study published in Cell, Dr. Shorter and colleagues discovered that nuclear-import receptors can dissociate toxic phase separated states of several RNA-binding proteins connected to neurodegenerative diseases. These findings open the way to urgently needed therapeutics for amyotrophic lateral sclerosis and frontotemporal dementia.

July 2018
Kathy (Fange) Liu
Welcome to the newest faculty in the Department, Dr. Kathy Fange Liu!  Dr. Liu joins us from U Chicago, where she was a post-doctoral fellow with Chuan He and Tao Pan.  She brings expertise in enzymology and RNA modifications to the Department. The rapidly growing Liu Lab studies the roles of RNA epigenetics in the regulation of human energy homeostasis using a broad spectrum of research tools including of RNA biochemistry, structural biology, and Next-Gen sequencing. Topics of study in the Liu Lab currently include: regulation of mRNA and tRNA modifications; identification and function of new types of modifications in messenger RNA; and the relationship between tRNA modification, tRNA fragmentation and disease.

June 2018
Gideon Dreyfuss
Gideon Dreyfuss is a Howard Hughes Medical Institute Investigator and the Isaac Norris Professor of Biochemistry and Biophysics.  The Dreyfuss Lab focuses on RNA-binding proteins and small nuclear ribonuclear protein complexes (snRNPs), their roles in the life of messenger RNAs (mRNAs) and their links to disease. Recently his group uncovered a new gene regulation mechanism in metazoan cells termed Telescripting, in which the U1 snRNP suppresses cleavage and polyadenylation signals, thereby protecting nascent transcripts from premature transcription termination. Telescripting is crucial for full-length mRNA synthesis, especially for large genes, and also determines mRNA length. A recent study from the lab demonstrates the importance of Telescripting for regulating size-function-stratified genomes.