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.
Logan Blaine, Ph.D. Student
Logan is a Ph.D. candidate in the Bioinformatics and Integrative Genomics (BIG) program at Harvard Medical School. He grew up in several states across the Northeast and studied Molecular Biology at Princeton University. After graduating, he worked as an Associate Computational Biologist at Dana-Farber Cancer Institute studying genome instability using single-cell DNA sequencing. In the Pinello Lab, Logan is currently developing machine learning algorithms and statistical methods for analyzing large single-cell experiments, especially CRISPR screens. In his spare time, he enjoys running and cycling around Greater Boston and playing Super Smash Bros.
Eric Che, Research Assistant
Eric Che is a research assistant in the Pinello and Bauer labs. He grew up in New York and graduated from Columbia University ’23 under the pre-medical track, with a B.A. in Computer Science. His research focuses on developing pipelines and standards to facilitate the analysis of bulk CRISPR screens. He is also interested in natural language processing and the application of large language models within a genomic context. In his free time, he enjoys playing basketball, DJing, and trying out new recipes.
Justin Delano, Ph.D. Student
Justin is a graduate student in the Bioinformatics & Integrative Genomics Ph.D. program at Harvard University. He grew up in Weymouth, MA, and graduated from Northeastern University with a MS in Applied Mathematics, BS in Mathematics, and minors in Biology and Data Science. His current research involves creating generative models to analyze data from novel CRISPR screens. Outside of lab work, he likes to go bouldering, cook new recipes, play games online with friends, and hang out with his cats.
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.
Zhijian Li, Ph.D., Research Fellow
Zhijian joined Pinello Lab in January 2023 as a postdoctoral associate supported by Broad Institute of MIT and Harvard. He received his PhD in Bioinformatics at the RWTH Aachen University in Germany (2022), MSc at the Central China Normal University (2016) and BSc at the Jilin University in China (2012). During his PhD, Zhijian mainly focused on machine learning and statistical methods to analyze high throughput sequencing data measuring open chromatin data at both the bulk and single-cell level. In Pinello Lab, he will work on developing computational methods to analyze biological data from single-cell, spatial omics, and CRISPR genome editing experiments. Out of the lab, he enjoyed watching movies, reading books and playing games.
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.
Zain Patel, Ph.D., Research Fellow
I defended my Ph.D. recently. It has been a wonderful and kind of an insane journey. It would not have been possible without the constant advice and support of my supervisor, Tim Hughes, my committee members Fritz Roth and Phil Kim, the wonderful people in the Hughes lab and, lastly, my family and friends. As for the future, I have moved to Boston to start as a postdoctoral research fellow at Harvard Medical School and Mass General Hospital.
Jayoung Ryu, Ph.D. Student
Jayoung is a graduate student in Bioinformatics & Integrative Genomics PhD program at Harvard University. Her research interest is in developing 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.
Cameron Smith, Ph.D., Research Fellow
Cameron joined the lab as a research fellow in September 2022. Following his undergraduate education in biomedical engineering at Duke University, he received his M.D. and Ph.D. in systems & computational biology from the Albert Einstein College of Medicine in 2018. Cameron completed his medical residency in clinical pathology at Massachusetts General Hospital/Harvard Medical School in 2021. He has previously worked on the mathematical modeling of molecular crosstalk in bacterial quorum sensing systems and theoretical predictions of the impact of evolutionary constraints on the architectural features of gene regulatory networks. He has also applied symmetry methods to solving stochastic branching processes utilized in evolutionary dynamics and phylogenetic inference. He is motivated by the perspective adapted from statistical physics that molecular phenotypes are constrained in evolution and development to coherently coarse-grain into metastable macroscopic observables. He is developing tools for probabilistic inference of the relationship between genotype evolution and stochastic dynamic models of molecular phenotypes. He enjoys good coffee, jazz, basketball, philosophy, and hiking with his family.
Manuel Tognon, Visiting Ph.D. Student
Manuel Tognon joined the Pinello lab as visiting Ph.D. student in August 2022. He is a Ph.D. student in Bioinformatics at the Department of Computer Science at the University of Verona (Italy). He holds a BSc in Bioinformatics and an MSc in Medical Bioinformatics from the same university. His research interests cover the development of innovative computational methods to predict the impact of genetic variants on epigenetic elements and CRISPR genome editing. During his Ph.D., he is co-supervised by prof. Rosalba Giugno (University of Verona) and prof. Luca Pinello. In his free time, he enjoys visiting museums, playing soccer and watching NFL games.
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.
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
Kendell Clement Ph.D., Instructor
Huidong Chen Ph.D., Research Fellow
Rick Farouni Ph.D., Research Fellow
Nafiz Hamid Ph.D., Research Fellow
Qian Alvin Qin Ph.D., Research Fellow
Qiuming Yao Ph.D., Research Fellow
Qian Zhang, Bioinformatician
Jonathan Y. Hsu, Ph.D. Student
Arya Kaul, Rotating Ph.D. Student
Maya Talukdar, Rotating MD Ph.D. student
Justine Shih, Research Technician
Matthew Canver MD Ph.D., Visiting Research Fellow
Nikolaos Trasanidis Ph.D., Visiting Research Fellow
Tommaso Andreani, Visiting Ph.D. Student
Samuele Cancellieri, Visiting undergraduate student
Giuseppe Ritrovato, Visiting undergraduate student
Rebecca Combs, high school intern
Michael Hu, high school intern
Maria Izzi, high school intern