Director

Matteo Pellegrini, Ph.D.

Matteo Pellegrini, Ph.D.

Director

Dr. Matteo Pellegrini is a biophysicist who has served on the UCLA Life Sciences Division faculty since he joined the Department of Molecular, Cell and Developmental Biology in 2005. Dr. Pellegrini earned his B.A. in Physics at Columbia University and his Ph.D. in Physics at Stanford. He was a postdoctoral fellow at UCLA, where he worked on computational biology. Following his postdoctoral studies Dr. Pellegrini co-founded a start-up company and later worked for the pharmaceutical company Merck before returning to UCLA. His laboratory research centers on the development of novel computational approaches to reverse engineer biomolecular networks. Professor Pellegrini is also a member of the California NanoSystems Institute (CNSI). Email: matteop@mcdb.ucla.edu + Website: https://www.pellegrini.mcdb.ucla.edu/people/

Support Staff

Eloy Lopez

Eloy Lopez

Programs Manager

Eloy Lopez provides academic, administrative and analytic support for the Institute for Quantitative and Computational Biosciences (QCBio) and the QCBio Collaboratory. His role includes overseeing marketing, recruitment, hiring, and inter-departmental financial support the QCBio Collaboratory postdoctoral fellows; as well facilitating an inclusive learning environment for our postdoc fellows who teach the latest next-generation sequencing techniques. Additionally, Eloy establishes interactive workshop scheduling, online and in-person enrollment, and programs expenses.

Over his career, Eloy worked similar capacities at USC, UCLA Graduate Division, the LA Galaxy and LAFC of Major League Soccer. Eloy earned his B.A. degree in American Studies at the California State University, Fullerton, and his M.Ed. degree in Educational Counseling at the University of Southern California.
Email: eloylopez@lifesci.ucla.edu

Current Fellows

Ibraheem Ali, Ph.D.

Ibraheem Ali, Ph.D.

Collaboratory Fellow

Dr. Ibraheem Ali is the Sciences Data Librarian based in the UCLA Louise M. Darling Biomedical Library. Ibraheem earned is B.S. in Biology at Fresno State University and his PhD Biomedical Sciences at University of California, San Francisco. His research background is in virology, regulation of gene expression and epigenetics in mammalian systems. In the library, Ibraheem is currently developing tools in R for interactive, reproducible scholarly communication and data analysis. He currently works closely with the UCLA Library Data Science Center and a number of other campus partners to organize and streamline computation support services across UCLA. Outside the lab, Ibraheem enjoys cooking, biking, dancing, collecting music and creating art. Email: ibraheemali@library.ucla.edu

Maria Izabel Cavassim Alves, Ph.D.

Maria Izabel Cavassim Alves, Ph.D.

Collaboratory Fellow

Dr. Cavassim Alves is a Postdoctoral Fellow at the Lohmueller lab in the Department of Ecology and Evolutionary Biology. Her interests are in using comparative genomics to deepen our understanding of the evolutionary mechanisms that give rise to and maintain genetic variation. Currently, Izabel is investigating the impact of dominance on the distribution of fitness effects in human populations. Dr. Cavassim Alves earned her Bachelor in Agriculture Engineering from University of Sao Paulo (Brazil), Masters and Ph.D. in Bioinformatics from Aarhus University (Denmark).

Email: izabelcavassim@gmail.com

Arjun Bhattacharya, Ph.D.

Arjun Bhattacharya, Ph.D.

Collaboratory Fellow

Dr. Arjun Bhattacharya is a Postdoctoral Fellow in the Department of Pathology and Laboratory Medicine with Prof. Bogdan Pasaniuc and Prof. Michael Gandal. Arjun’s research focuses on integrative methods for statistical genetics and genetic epidemiology to study complex traits, mainly cancer, neuropsychiatric disorders, and neonatal traits. He received his BS in Biology and Statistics at the University of North Carolina at Chapel Hill and a PhD in Biostatistics at the Gillings School of Global Public Health at the University of North Carolina at Chapel Hill. Email: abtbhatt@ucla.edu

Shawn Cokus, Ph.D.

Shawn Cokus, Ph.D.

Collaboratory Fellow

Dr. Shawn Cokus is an Associate Researcher in the Department of Molecular, Cell, and Developmental Biology. Dr. Cokus has been doing bioinformatics at UCLA since 2002, and his interests include methods for BS-Seq, RNA-Seq, Hi-C, and protein-protein interaction prediction. His recent work focuses on de novo genome assembly and annotation. Dr. Cokus earned a Ph.D. in Mathematics from the University of Washington.
Email: cokus@ucla.edu

Giorgia Del Vecchio, Ph.D.

Giorgia Del Vecchio, Ph.D.

Collaboratory Fellow

Dr. Del Vecchio is currently a postdoctoral fellow in Dr. Sherin U. Devaskar laboratory in the Department of Pediatrics, Devid Geffen School of Medicine at UCLA. Before joining UCLA, she earned a PhD in Genetics and Molecular Biology from Sapienza University of Rome, working on the microRNA-target interaction mechanism and demonstrating how miR-200a together with the binding protein HuR could have a stabilizing effect on their target c-Jun. Her current research focus on circulating cell-free nucleic acids isolated from maternal samples (plasma and urine), trying to understand their function and diagnostic potential early in pregnancy.
Email: giodelv@g.ucla.edu

Amandine Gamble, Ph.D.

Amandine Gamble, Ph.D.

Collaboratory Fellow

Dr. Gamble is a postdoc in the Lloyd-Smith lab in the Department of Ecology and Evolutionary Biology. Her research focuses on the biological mechanisms driving infectious disease dynamics, from the cellular to the species community scale. In particular, she develops mechanistic models aiming at identifying the molecular and ecological drivers of pathogen transmission and virulence across animal species from laboratory and field data. Dr. Gamble earned her D.VM. from Alfort National Veterinary School, her M.S. in Ecophysiology and Animal Behavior from Strasbourg University, and her Ph.D. in Ecology and Population Biology from Montpellier University in France. Outside the lab, Amandine enjoys sharing her research with the public and exploring the Los Angeles area through photography and food tasting.
Email: amandinegamble@g.ucla.edu

Wenbin Guo

Wenbin Guo

Collaboratory Fellow

Wenbin came from biological and computer science backgrounds and is currently a Ph.D. student in the Bioinformatics IDP at UCLA. His current research focuses on using methylation and transcriptomic data in disease status prediction and biomarker discovery. He is experienced in building bioinformatics pipelines, analyzing high-throughput (genetics/epigenetics/transcriptomics) data as well as applying machine learning methods to biological problems. Aside from research, Wenbin enjoys hiking, sightseeing, and playing sports with friends.
Email: wbguo@g.ucla.edu

Daniel Ha, Ph.D.

Daniel Ha, Ph.D.

Collaboratory Fellow

Dr. Daniel (Sung-min) Ha is a Postdoctoral Fellow at the Xia Yang Lab in the Department of Integrative Biology and Physiology. Dr. Ha research focuses on Bacterial Genomics and Epidemiology and interest involves host-microbiome interaction using multi-omics systems biology approach. He earned a Bachelor in Mathematics and Genetics & Biotechnology at the University of Toronto in Canada, and a Ph.D. at Seoul National University in South Korea.

Email: smha118@ucla.edu

Karolina Kaczor-Urbanowicz, Ph.D; D.M.D.

Karolina Kaczor-Urbanowicz, Ph.D; D.M.D.

Collaboratory Fellow

Dr. Karolina E. Kaczor-Urbanowicz, DMD, Phd, MSc is an Assistant Project Scientist in Prof. David Wong’s laboratory of UCLA Center for Oral/Head & Neck Oncology Research and Salivary Diagnostics, Section of Oral Biology, UCLA School of Dentistry. She is a dentist-scientist who graduated from the Faculty of Dental Medicine at the Medical University of Warsaw, Poland. She did her residency in orthodontics simultaneously with the international studies in Bio-Medical Sciences at the Hebrew University of Jerusalem, Israel, working in the Prof. Aaron Palmon’s Laboratory of Proteomics and Salivary Diagnostics, Institute of Dental Sciences. After earning her Ph.D. title, she was awarded the UCLA’s R90 NIH/NIDCR Postdoctoral Dentist-Scientist Scholarship and AACR-DDF postdoctoral fellowship in developing salivary H.pylori exRNA biomarkers for early detection of gastric cancer. At the UCLA, she developed her immense interests in salivary RNA Sequencing, bioinformatics and biomarker development for many oral and systematic diseases including cancer. Email: kkaczor@ucla.edu

Seyoon Ko, Ph.D

Seyoon Ko, Ph.D

Collaboratory Fellow

Dr. Seyoon Ko is a Postdoctoral Fellow at Hua Zhou’s laboratory in the Department of Biostatistics. Dr. Ko’s research interests include large-scale computational methods in biostatistics and bioinformatics using parallel and distributed computing. His current projects include developing scalable software for genome-wide associational study modeling within-subject variability and identifying ancestry-informative markers at the biobank scale. He earned a Ph.D. degree in Statistics from Seoul National University in South Korea, as well as a M.S. degree in Computational Sciences and a B.S. degree in Physics, Mathematical Sciences, and Computational Science.
Email: kos@g.ucla.edu

Sergey Knyazev, Ph.D

Sergey Knyazev, Ph.D

Collaboratory Fellow

Dr. Knyazev is a postdoctoral fellow from Dr. Pasaniuc‘s Lab at UCLA. Before joining UCLA, Sergey developed, bench-marked, and applied NGS data processing software for viral and metagenomic data at Dr. Zelikovsky’s lab at GSU and Dr. Swithzer’s lab at the Centers for Disease Control and Prevention. He received M.S. in Applied Mathematics at Saint Petersburg Academic University and Ph.D. in Computer Science at Georgia State University (GSU).
Email: sergey.n.knyazev@gmail.com

Lukasz Salwinski, Ph.D.

Lukasz Salwinski, Ph.D.

Collaboratory Fellow

Dr. Lukasz Salwinski is currently an assistant researcher in the laboratory of Professor David Eisenberg who, for over a decade, has been responsible for development and maintenance of The Database of Interacting Proteins (https://dip.doe-mbi.ucla.edu). He received his master degree in biology at the Jagiellonian University, Krakow (Poland) and earned Ph.D. at UCLA, in the group of Professor Wayne Hubbell where he applied EPR spectroscopy to study structure of pore-forming bacterial toxins. Email: lukasz@mbi.ucla.edu

Breanne Sparta, Ph.D.

Breanne Sparta, Ph.D.

Collaboratory Fellow

Dr. Breanne Sparta is a postdoctoral fellow at UCLA, in the lab of Professor Eric Deeds. Breanne’s research explores theories of biological organization and variation. Their current research centers questions of how cellular identities are realized. Breanne completed her B.S. in Biochemistry at Northeastern University and her Ph.D. at the University of California, Davis, where she studied the coordination of growth and metabolism in single, living cells. Email: bsparta@ucla.edu

Don Vaughn, Ph.D.

Don Vaughn, Ph.D.

Collaboratory Fellow

Dr. Don Vaughn is a neuroscience postdoctoral fellow at UCLA. His research has included functional Magnetic Resonance Imaging (fMRI), perceptual psychophysics, and sensory substitution. Don uses fMRI to research neural correlates of freewill and how social dynamics modulate empathy. In psychophysics, Don investigated how information, before and after an event has occurred, influences perception of the event - an effect dubbed peri-diction. Don now applies multivariate classification and non-parametric statistics to bioinformatics datasets. Email: donaldavaughn@gmail.com

Weihong Yan, Ph.D.

Weihong Yan, Ph.D.

Galaxy Administrator

Dr. Weihong Yan is the system administrator of Galaxy. She constructs and maintains software and hardware needed for bioinformatics application. Dr. Wang provides consultation services on microarray, proteomic and genomic data analysis. Email: wyan@chem.ucla.edu

Xinjun Zhang, Ph.D.

Xinjun Zhang, Ph.D.

Collaboratory Fellow

Dr. Xinjun Zhang (Jun) is a Postdoctoral Fellow at the Lohmueller lab in the Department of Ecology and Evolutionary Biology. Jun’s research lies at the intersection of empirical population genetics and statistical methods development, where she is particularly interested in the dynamics between admixture and selection. Currently, she is working on developing machine learning-based methods for the inference of adaptive introgression and dominance on the human genome. Jun earned a Ph.D. in Anthropological Genetics from UC Davis. Email: xinjunzhang@g.ucla.edu

Collaboratory Guest

Robert Kuhn, Ph.D.

Robert Kuhn, Ph.D.

Guest Collaboratory Instructor

Robert Kuhn received his PhD at the University of California, Santa Barbara in Biochemistry and Molecular Biology, where he studied the centromeres of yeast. Following a postdoctoral at UC Berkeley/USDA Plant Gene Expression Center, he taught biochemistry, molecular biology and genetics at UC Santa Cruz. He joined the UCSC Genome Browser project in 2003, where he is now Associate Director, with a particular interest in clinical genetics. The Genome Browser is a widely used visualization tool giving access to the genomes of human and more than one hundred other animals. Dr. Kuhn’s responsibilities include identifying important datasets for inclusion into the Browser, enabling researchers through teaching the Genome Browser in workshops and seminars and learning from them how to improve the Browser. Email: kuhn@soe.ucsc.edu

Roberto Spreafico, Ph.D.

Roberto Spreafico, Ph.D.

Current Position: Senior Manager Data Scientist, GSK.

Michael Weinstein, Ph.D.

Michael Weinstein, Ph.D.

Guest Collaboratory Instructor

Current Position: Scientist, Zymo Research

Alumni

Robert Brown, Ph.D.

Robert Brown, Ph.D.

Dr. Rob Brown is a post-doctoral researcher working with Sriram Sankararaman and Eleazar Eskin. He completed is BA in astrophysics from Columbia University and his Ph.D. in bioinformatics from UCLA while advised by Bogdan Pasaniuc. As a graduate student, he developed new methods for finding non-linear genetic associations with phenotypes. His current post-doctoral work has two main focuses. The first is to develop surgery outcome predictors using the electronic health records and genotype data from individuals in the UC system. Second, he is interested in understanding how interactions between deleterious coding and regulatory variation shape the genetic architectures and association signals for complex phenotypes.

Alex Brummer, Ph.D.

Alex Brummer, Ph.D.

Dr. Alex Brummer is a postdoctoral scholar in Dr. Van Savage’s group through the Depts. of Biomathematics and of Ecology and Evolutionary Biology. Alex is working with the lab software Angicart to digitally reconstruct and analyze vascular tissues from medical images spanning multiple modalities (e.g. MRI, CT, and micro-CT) to search for geometric signatures of disease and recovery. Concurrent with this, Alex is developing and testing new models for asymmetric branching in vascular networks that relate the degree or pattern of asymmetry to biological scaling exponents that encapsulate how metabolic rate, heart rate, and lifespan change with body size across species. Alex earned B.S. degrees in physics and mathematics at Oregon State University, and his M.S. and Ph.D. degrees in physics at the University of Arizona.

Renaud Dessalles, Ph.D.

Renaud Dessalles, Ph.D.

Dr. Renaud Dessalles is a Post-Doctoral researcher at the laboratory of Biomathematics currently working on the modeling of the immune responses to antigens. His main interested consist in mathematical and computational modeling applied to biology, using mainly (but not exclusively) stochastic models. During his PhD in applied mathematics at INRA and INRIA (France), he worked on the stochastic modeling of protein production inside bacteria. Renaud’s main skills consist of the analysis of stochastic and deterministic models and the use of several computational language (Python, C++, Matlab, Julia) for simulations.

Sorel Fitz-Gibbon, Ph.D.

Sorel Fitz-Gibbon, Ph.D.

Dr. Sorel Fitz-Gibbon is an assistant researcher in the laboratory of Dr. Matteo Pellegrini. Dr. Fitz-Gibbon did her undergraduate work in Molecular, Cell and Developmental Biology at UCLA and also received her Ph.D. there, in Microbiology and Molecular Genetics. Her QCB research is on the bioinformatics aspect of a project to sequence and analyze the genomes of C. reinhardtii laboratory strains.

Catherine Grasso, Ph.D.

Catherine Grasso, Ph.D.

Current Position: Associate Director, Parker Institute for Cancer Immunotherapy at UCLA

Rob Foreman, Ph.D.

Rob Foreman, Ph.D.

Dr. Rob Foreman is a postdoctoral scholar in the lab of Dr. Roy Wollman, Department of Chemistry and Biochemistry. Rob is developing a multiplexed smFISH measurement technique. He wants to use this technique to observe how cells are distributed in a joint gene expression state-space in order to pose questions about these distributions.

Marcus Gallagher-Jones, Ph.D.

Marcus Gallagher-Jones, Ph.D.

Dr. Marcus Gallagher-Jones is a postdoctoral fellow working in the Rodriguez lab at UCLA. He received his BS in Biochemsitry from Durham University and his PhD in Biophysics from University of Liverpool before working for 2 years in the department of Physics at UCLA. His main interests are in structural analysis across many length-scales (atomic to whole cell) using electron and x-ray diffraction. His expertise include: structural biology, algorithm design, digital image processing, phase retrieval and tomographic reconstruction.

Yerbol Kurmangaliev, Ph.D.

Yerbol Kurmangaliev, Ph.D.

Dr. Yerbol Kurmangaliev is currently a postdoctoral researcher in the laboratory of Professor S. Lawrence Zipursky. He earned a M.S. degree in Biochemistry at Lomonosov Moscow State University in 2006. He earned a Ph.D. degree in Bioinformatics at Kharkevich Institute for information transmission problems of the Russian Academy of Sciences in 2011 under the supervision of Professor Mikhail S. Gelfand. Before joining to UCLA he was a postdoctoral researcher in the laboratory of Professor Sergey V. Nuzhdin at USC. His previous research interests have been primarily focused on genetic basis of gene expression.

Fides Lay, Ph.D.

Fides Lay, Ph.D.

Dr. Fides Lay is a postdoctoral fellow in the laboratory of Dr.Hanna Mikkola. Her current research focuses on elucidating the transcriptional machineries controlling fate commitment and self-renewal during normal hematopoiesis and understanding how these processes are hijacked during leukemogenesis. When not in lab, she enjoys running, kickboxing, going to concerts, eating unhealthy amount of chocolates, and basking in the warm Los Angeles sun.

Marina Linardic, Ph.D.

Marina Linardic, Ph.D.

Collaboratory Fellow

Dr. Marina Linardic was a Postdoctoral Scholar in Dr Siobhan A. Braybrook’s laboratory in the Department of Molecular, Cell and Developmental Biology. She received her bachelor and master degrees in Ecology and Nature Protection at the University of Zagreb during which she also received an ERASMUS scholarship to study at the University of Vienna. She received her PhD from the University of Cambridge where she focused on understanding cell wall-mediated expansion in the brown algal lineage. Using both experimental and computational approaches, she is currently investigating cellular and molecular mechanisms of abiotic stress adaptation in intertidal brown algae. Email: linardicm@ucla.edu

Nicholas Mancuso, Ph.D.

Nicholas Mancuso, Ph.D.

Dr. Nicholas Mancuso is currently a post-doctoral researcher in computational/statistical genetics in Bogdan Pasaniuc’s lab. My research interests include developing computational methods to infer population parameters from low-coverage sequencing data, fine-mapping associations between complex trait and gene expression, and elucidating the role of rare genetic variation in complex traits.

Igor Mandric, Ph.D.

Igor Mandric, Ph.D.

Dr. Igor Mandric was a postdoctoral fellow in the labs of Bogdan Pasaniuc and Eran Halperin at UCLA. He completed his M.S in Applied Mathematics at Moldova State University. Before joining UCLA, he earned Ph.D in Bioinformatics under the supervision of Alex Zelikovsky at Georgia State University. His main research interest lays in the area of single-cell RNA sequencing. In particular, he is interested in inferring cell-type specific expression profiles in the settings of low sequencing coverage. Additionally, Igor is also interested in statistical fine-mapping for large-scale genotype-phenotype data.

Serghei Mangul, Ph.D.

Serghei Mangul, Ph.D.

Dr. Mangul is currently a Postdoctoral Fellow with Eleazar Eskin (Department of Computer Science) at UCLA. Serghei holds a Collaboratory Fellowship from Institute for Quantitative and Computational Biosciences (QCB). His research focuses on developing bioinformatics methods to leverage large-scale high-throughput genomics datasets to better understand the biology of disease. His flagship product is Read Origin Protocol (ROP), a tool for discovering the source of all RNA-Seq reads originated from complex RNA molecules recombined T and B cell receptors and microbial communities. ROP was applied across 1 trillion reads across 10641 samples. Serghei is also interested in bioinformatics education and pedagogy. He is leading an undergraduate research group, focused on genomic research. His philosophy on how to engage undergraduates in genomic research is presented here.

Simon Mitchell, Ph.D.

Simon Mitchell, Ph.D.

Simon Mitchell is a postdoc in computational systems biology working with Professor Alexander Hoffmann. He is working in constructing mathematical simulations of immune systems and cancer. Prior to joining UCLA, his undergraduate studies in computer science and math led him to a PhD investigating the computational modeling of human iron metabolism at the University of Manchester. Dr. Mitchell’s general interests lie in programming, computational biology, mathematical modeling, sensitivity analyses and translational research.

Marco Morselli, Ph.D.

Marco Morselli, Ph.D.

Dr. Marco Morselli was a post-doc in the Lab of Professor Matteo Pellegrini. He received his bachelor and master degrees in Molecular Biotechnology at the University of Parma, Italy. He earned his PhD at UCLA focusing on the crosstalk between histone modifications and DNA methylation. Outside of the lab, Marco enjoys cooking, running, cycling and playing soccer.

Thiago Mosqueiro, Ph.D.

Thiago Mosqueiro, Ph.D.

Dr. Thiago S. Mosqueiro is a Post-Doctoral researcher at the Pinter-Wollman lab (UCLA), primarily working with data analysis and simulations involving learning and behavior of honey bees. His main research interests are mathematical and computational modeling applied to systems biology, especially neuroscience. He received his BS and Ph.D. in Physics from the University of São Paulo (USP). During his Ph.D., he was a visiting graduate student at the BioCircuits Institute (BCI) and the Rady School of Management, at University of California San Diego (UCSD). Thiago has also contributed to research in applied fields, such as Machine Learning, Data Analysis of Chemical Sensors, and Cloud Computing.

Alice Mouton, Ph.D.

Alice Mouton, Ph.D.

Dr Alice Mouton is an Assistant Project Scientist in Robert Wayne laboratory in the department of Ecology and Evolutionary Biology. Her current researches focus on applying gene expression methodologies (RNA-seq and RRBS) to study non model organisms (bobcat, island fox) in a context of conservation.

Diane Lefaudeux

Diane Lefaudeux

Diane Lefaudeux was currently an assistant specialist in the Signaling Systems lab with Professor Alexander Hoffmann. Diane’s research focus on understanding and modeling RNA expression and main expertise is in computational biology, mathematical modeling and transnational research. She obtained a double engineering degree in 2013 from École Centrale Paris in France and Universität Stuttgart in Germany. Diane’s research focus on understanding and modeling RNA expression.

Alon Oyler-Yaniv, Ph.D.

Alon Oyler-Yaniv, Ph.D.

Dr. Alon Oyler-Yaniv Alon was a postdoctoral researcher in the lab of Dr. Roy Wollman. Alon earned his BS.c., M.Sc., and Ph.D. in Physics from Ben-Gurion University of the Negev. Alon is interested in the effects of the spatial structure of living tissue on cell to cell communication. Using advanced optical tools to image molecular interactions, he studies how cells move and communicate during the process of wound healing in living organs. Email: alonyan@ucla.edu

Nicolas Rochette, Ph.D.

Nicolas Rochette, Ph.D.

Dr. Nicolas C. Rochette was a postdoc in the laboratory of Dr. Shane Campbell-Staton in the Department of Ecology and Evolutionary Biology and the Institute for Society and Genetics. His research intersects population genomics and evolutionary physiology, with the goal of understanding the dynamics of adaptation in quantitative traits. His current projects include work on the genetic architecture of high-altitude adaptation in the North American Deer Mouse, and local adaptation in Caribbean Anole lizards. He was previously a postdoc in the laboratory of Dr. Julian Catchen at the University of Illinois, developing new analytical tools for RADseq data and population genomics in non-model organisms. He received his PhD in Comparative Genomics and MS in Evolutionary Genomics from the University of Lyon and Ecole Normale Superieure de Lyon, in France.

Peter Scott, Ph.D.

Peter Scott, Ph.D.

Dr. Peter Scott was a postdoctoral researcher in the laboratory of Dr. Brad Shaffer. He received his PhD in Ecology and Evolutionary Biology from the University of Alabama. Peter’s primary research interests lie in applying genomic methods to understand species limits and diversification, hybrid zone dynamics, and landscape and conservation genomics in reptiles and amphibians. Additionally, he is interested in investigating how to best apply and adapt modern genomic methods to non-model systems that are representative of difficult evolutionary questions (e.g. resolving relationships in recent, rapid radiations), or that push the limits of these technologies (e.g. organisms with very large genomes).

Baochen Shi, Ph.D.

Baochen Shi, Ph.D.

Baochen Shi was a former postdoc working with Dr. Huiying Li in the department of Molecular and Medical Pharmacology. By studying genomes and transcriptomes of the microorganisms living inside and on the humans, he aims to understand how human microbiome play a role in health and disease. Prior to joining UCLA, he completed his Ph.D. in the bioinformatics lab of Prof. Runsheng Chen in the Institute of Biophysics, Chinese Academy of Sciences.

Trent Su, Ph.D.

Trent Su, Ph.D.

Trent Su is a postdoctoral fellow at Dr. Siavash Kurdistani lab in the Department of Biological Chemistry. In collaboration with Dr. Arnie Berk lab, his research focus on using high-throughput genomics methods to study genome-wide epigenetic changes induced by Adenoviral oncoprotein e1a which upon expression forces stationary host cells into S phase. Dr. Su received his B.S. in Molecular and Cell Biology at UC Berkeley. Afterwards, he received his M.S. in Computer Science at UC Irvine where he co-written a java web application for Systems Biology pathway modeling. He completed his PhD training in the Kurdistani lab and received his PhD in Oral Biology at UCLA School of Dentistry. His current interests include writing custom python scripts for high-throughput sequencing analysis and mining cancer mutation databases.

Ying Tang, Ph.D.

Ying Tang, Ph.D.

Dr. Ying Tang was a postdoc in signaling systems laboratory working with Professor Alexander Hoffmann. His research interest is to develop quantitative understanding on immune systems through mathematical modeling, from the level of intracellular information transmission to cell population dynamics. Prior to joining UCLA, he did PhD study in Shanghai Jiao Tong University and University of California, San Deigo. During PhD, he worked on stochastic process, nonequilibrium statistical physics, and mathematical modeling of E. coli chemotaxis.

Michael Thompson, Ph.D.

Michael Thompson, Ph.D.

Dr. Michael Thompson received a BA in physics from Boston University, a PhD in biophysics from the University of Michigan. Over his research career, Michael has invented quantitative methods for predicting protein structure from evolutionary information, prion proteins from sequence determinants, and gene function from co-evolution. Michael is currently working with Prof. Pellegrini and Prof. Horvath to illuminate the role of DNA methylation in cancer and aging.

Anela Tosevska, Ph.D.

Anela Tosevska, Ph.D.

Dr. Anela Tosevska was a postdoctoral fellow in the lab of Dr. Matteo Pellegrini at UCLA. She completed her master degree in Pharmacy at Ss. Cyril and Methodius University of Skopje. Before joining UCLA, she earned a PhD in Life Sciences from the University of Vienna, working as a part of the research platform Active Aging. Dr. Tosevska is interested in the role of DNA methylation in aging and age-associated disease progression. She is also working with circulating cell-free nucleic acids from liquid biopsies, trying to understand their function and diagnostic potential in health and disease.

Bridgett vonHoldt, Ph.D.

Bridgett vonHoldt, Ph.D.

Current Position: Assistant Professor, Princeton University’s Ecology and Evolutionary Biology

Emily Wu, Ph.D.

Emily Wu, Ph.D.

Dr. Emily Wu is currently an assistant project scientist in the laboratory of Dr. Weizhe Hong in the Department of Biological Chemistry. Her current research interest focuses on applying and developing single-cell RNA sequencing methods and circuit manipulation for the molecular and functional dissection of neural circuitry underlying animal behaviors. She received her B.S. in Biology from Peking University, China. She then earned her Ph.D. from Stanford University where her graduate research focused on molecular and cellular mechanisms governing synapse formation and axonal transport in neurons. Afterwards, she worked as a postdoctoral fellow in Dr. Daniel Geschwind’s lab at UCLA where she investigated the neural mechanisms of autism spectrum disorders through functional genomic and animal behavioral studies.

Asli Yildirim, Ph.D.

Asli Yildirim, Ph.D.

Asli Yildirim was a postdoctoral researcher in Dr. Frank Alber’s lab at the University of California, Los Angeles. She received her Ph.D. in Chemistry from Michigan State University and B.S. and M.S. degrees in Chemistry from Bogazici University, Turkey. Her research focuses on developing computational methods to build 3D genome structures and understanding the relationship between genome structure and function.

Nathan Zemke, Ph.D.

Nathan Zemke, Ph.D.

Dr. Nathan Zemke was a post-doc in the Lab of Professor Arnie Berk in the Microbiology, Immunology, & Molecular Genetics department at UCLA. He received his bachelor’s degree in molecular biology at UCSD. He earned his PhD from the Molecular Biology Interdepartmental program at UCLA researching the adenovirus oncoprotein e1a and its regulation of chromatin, innate immune responses, and differentiation.

Ying Zhen, Ph.D.

Ying Zhen, Ph.D.

Dr. Ying Zhen is a postdoc working with Kirk Lohmueller and Tom Smith. Her research focuses on using NGS data to study the demographic history and natural selection of non-model species from Central Africa. Ying was a postdoc with Peter Andolfatto at Princeton University, working on convergent evolution in insects and gene expression evolution in Drosophila. She received her Ph.D. from Kansas State University where she worked on evolution of freezing tolerance.