Luca Pinello, Ph.D. Associate Professor
Luca is an Associate Professor at Massachusetts General Hospital and Harvard Medical School. He received his BA, MA and Phd in Computer Science and Mathematics from the University of Palermo in Italy. He had the good fortune to be part of the “omics” revolution and the opportunity to work on many computationally-challenging problems since he was an undergraduate student. During his postdoctoral research with Prof. Guo-Cheng Yuan at Dana-Farber Cancer Institute/Harvard School of Public health he studied the role of chromatin structure in gene regulation and developed computational methods for single cell analysis and epigenomics. He has a background in computer science and extensive experience in machine learning, data mining and web technologies. His research program uses computational approaches to systematically analyze the sources of variation that affect gene regulation: epigenetic variation, genetic variation and (single-cell) gene expression variability. In his free time he likes to hike, to cook and roast green coffee and to do photography.
Basheer Becerra, Ph.D. Student
Basheer is a Ph.D. student at Harvard University in the Bioinformatics and Integrative Genomics program in both the Pinello and Bauer lab. He grew up in El Paso, IL and graduated from Illinois State University ’19 with a double major in Computer Science and Statistics. His research focuses on performing CRISPR screens to identify regulators of blood cell traits as well as developing statistical models to analyze and interpret single-cell CRISPR screens. In his spare time, Basheer enjoys training for triathlons and reading.
Lucas Ferreira, Ph.D. Research Fellow
Lucas Ferreira received his Ph.D. in Bioinformatics in 2017 from Universidade de São Paulo, Brazil. Between 2017 and 2020, he worked as a postdoctoral researcher at the University of Miami, studying and developing biocomputational analysis to elucidate the role of the integrator complex in different transcriptional contexts. He is currently developing analyses and new methods to integrate epigenetic data (PRO-Seq, HICHIP, ATAC-Seq, CHiP-Seq) and single-cell assays with CRISPR perturbations. In his free time, he enjoys activities such as volleyball, salsa, drawing, homemade music, and visiting new places.
Kendell Clement, Ph.D. Instructor
Kendell Clement joined the lab in July 2017 after completing his PhD in the Harvard-MIT Division of Health Sciences and Technology where he studied epigenetics in the contexts of pluripotency, embryonic development, and oncogenesis. He is interested in using computational algorithms to understand and interpret biological data, with particular interest in applications to genome modification and human disease.
Jonathan Y. Hsu, Ph.D. Student
Jonathan is a Ph.D. student in the MIT Biological Engineering department and received his BS in Bioengineering: Biotechnology from UCSD. He is currently co-advised by Professors Luca Pinello, Keith Joung, and Jim Collins and his research interests lie at the intersection of genome editing, epigenome engineering, and computational biology. Outside of research, he enjoys exploring the local Boston restaurant scene and exercising in order to keep in shape for the pipetting and coding he must do to graduate.
Jiecong Lin, Visiting Ph.D. Student
Jiecong Lin is a visiting PhD student in the Pinello lab. He is a third-year PhD student at City University of Hong Kong in the Department of Computer Science. His research interest lies in developing deep-learning-based methods to predict and interpret CRISPR off-targets and gene expression. Outside of research, he enjoys playing basketball, watching NBA and Netflix.
Qian Alvin Qin,Ph.D. Research Fellow
Qian Alvin Qin is a postdoc research fellow co-mentored by Professor Luca Pinello and Professor David Langenau. Alvin completed his Ph.D. in bioinformatics from Tongji University, where he developed Cistrome Data Browser and related tools under the supervision of Professor Xiaole Shirley Liu. Before he joined the lab, he was an assistant researcher at Children’s Hospital of Fudan University, where he integrated multi-modal MRI datasets for neonatal encephalopathy diagnosis with deep learning. His current interest lies in single-cell data integration across species to construct the gene regulatory network and detect functional cis-elements underlying the mechanisms of oncogenesis and development. In his spare time, he enjoys reading, swimming and playing badminton.
Jayoung Ryu, Ph.D. Student
Jayoung is a graduate student in Bioinformatics & Integrative Genomics PhD program at Harvard University. Her research interest is in devloping methods that reliably model single cell and CRISPR screen analysis to draw conclusions on gene regulation. Outside the lab she’s into exploring nature, drawing/painting, and taking walks.
Justine Shih
Justine Shih is a research technician in the Pinello and Joung lab. She grew up in Texas and graduated from Cornell University with a BS in Biometry & Statistics and Biological Sciences in 2020. Outside of research, she loves to optimize recipes, explore new places and cultures, listen to soundtracks, and hike.
Maya Talukdar, MD-PhD rotation student
Maya is a MD-PhD rotation student in the Harvard-MIT Health Sciences and Technology Program. She is from Buffalo, NY and graduated with dual degrees in Computer Science and Biology from Columbia University in 2020. She is broadly interested in developing methods for analyzing single-cell epigenomic and transcriptomic data, especially in regards to trajectory analysis and single-cell CRISPR screens. Outside of the lab, Maya enjoys running and biking along the Charles, volunteering with Best Buddies, and playing ukulele.
Nikolaos Trasanidis, Ph.D. Visiting Research Fellow
Nikolaos Trasanidis is a visiting research fellow at the Massachusetts General Hospital, who joined Prof. Pinello lab in March 2020. He recently received his PhD degree in biomedical research and cancer epigenomics from Imperial College School of Medicine (London, UK). He has developed expertise in execution and computational analysis of several -omics technologies (transcriptomics, epigenomics, 3D-genome), with particular interest in their applications in normal haemopoiesis and cancer. He is currently exploring novel machine-learning algorithms to construct gene regulatory networks using single-cell data. In his free time, he enjoys cooking, improvising piano songs and exercising in nature.
Michael Vinyard, Rotating Ph.D. Student
Michael Vinyard is a third-year PhD student at Harvard University in the Department of Chemistry and Chemical Biology. He grew up in Carmel, Indiana and graduated from the University of Iowa with a B.A. in Chemistry in the Spring of 2016. At Iowa, he did undergraduate research with Professor Hien Nguyen and competed for the University of Iowa Men’s Swimming and Diving Team. Michael completed the first two years of his PhD work under the guidance of Professor Brian Liau where he studied the mechanism of epigenetic regulators in cancer using CRISPR screens, ChIP-seq, and other functional genomics and molecular biology approaches. He is broadly interested in the biological mechanisms of physiological phenomena, at the molecular level. In his free time, he enjoys reading, writing, exploring concepts in philosophy, hiking, and more recently, snowboarding.
Qian Zhang
Qian Zhang is a bioinformatician in both the Pinello and Bauer lab. Her research interests are in applying the emerging CRISPR-cas9 based genetic editing or single cell transcriptomic approach to record lineage history and to reconstruct the differential trajectory. She is also looking to advance methods in single cell genomics through statistical and computational learning. In her free time, she likes swimming, hiking, playing pipa, and more recently, photography.
Lingfei Wang, Ph.D. Research Fellow
Lingfei joined the lab as a postdoctoral research fellow in August 2020. He obtained his Ph.D. in theoretical cosmology in Lancaster University. Lingfei is interested in reconstructing gene regulatory networks especially from single-cell multi-omic datasets. Outside of research, he likes musicals, racquet sports, cycling, and other healthy activities electronically.
Alumni
Nafiz Hamid Ph.D, Research Fellow
Michael Hu, high school intern
Huidong Chen Ph.D., Research Fellow
Rebecca Combs, high school intern
Qiuming Yao Ph.D., Research Fellow
Maria Izzi, high school intern
Arya Kaul, Rotating Ph.D. Student
Tommaso Andreani, Visiting Ph.D. Student
Matthew Canver, MD,Ph.D., Visiting Research Fellow
Samuele Cancellieri, Visiting undergraduate student
Rick Farouni Ph.D., Research Fellow
Giuseppe Ritrovato, Visiting undergraduate student