Difference between revisions of "Members"
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Shane Chu earned his PhD in computer science from Washington University in St. Louis, working with Gary Stormo. His PhD work focused on developing interpretable representation learning methods for addressing challenges in protein-DNA/RNA interactions. Outside of his academic pursuits, he finds relaxation and enjoyment in playing tennis and visiting the Peridance Center in NYC. | Shane Chu earned his PhD in computer science from Washington University in St. Louis, working with Gary Stormo. His PhD work focused on developing interpretable representation learning methods for addressing challenges in protein-DNA/RNA interactions. Outside of his academic pursuits, he finds relaxation and enjoyment in playing tennis and visiting the Peridance Center in NYC. | ||
| + | Web: https://kchu25.github.io | ||
Revision as of 07:26, 20 February 2024
 Zhang lab photo, 2023 @ Columbia University Irving Medical Center |
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Chaolin Zhang   Associate Professor, Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Motor Neuron Center Chaolin is currently an Associate Professor with joint appointments in Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, and Motor Neuron Center at Columbia University Irving Medical Center. Before he joined Columbia, he performed PhD studies at Cold Spring Harbor Laboratory in computational biology and then Postdoc work on computational and molecular biology at Rockefeller University. Before that he obtained bachelor's degree studying Automation at Tsinghua University (Beijing). As an engineer-converted biologist, he has a deep interest in understanding gene regulatory logics. From the beginning of his academic endeavor, he decided to tackle the RNA code, i.e., how specific protein-RNA interactions determine the gene output in health and disease conditions, which remains the focus of the lab. Chaolin is a winner of Pathway to Independence Award (K99/R00, 2011) and Maximizing Investigators' Research Award (MIRA/R35, 2022) from NIH, and Scientific Innovations Award from the Brain Research Foundation (2023).
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Current Lab Members
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Shah Alam (06/2023-), Postdoc Email: sa4354 (at) cumc (dot) columbia (dot) edu
Shah joined Zhang's lab in June 2023 as a postdoctoral research scientist. Prior to joining Columbia, he gained experience working as a postdoc at the LIMES Institute, University of Bonn, Germany, for over a year. He also completed his PhD at the same institute. During his PhD, he unraveled the signaling of sphingosine-1-phosphate (S1P) in primary neurons, microglia, and astrocytes of a neurodegenerative disease mouse model called neural-cell specific S1P-lyase (SGPL1) deficient mice. He earned his master's degree in molecular biotechnology from the University of Bonn and his bachelor's degree in biotechnology from VIT University, India. Shah's current research plans involve delving into the regulatory mechanisms and lineage-specific alternatively splicing events and their functional impacts on brain development and developmental disorders. Moreover, he is also interested in developing experimental systems that will strategically map and compare RBP binding sites and RBP-dependent splicing regulation in neurons. Beyond his academic pursuits, he is particularly passionate about cricket, running, and hiking.
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Shane Chu (01/2024-), Postdoc Email: sc5502 (at) cumc (dot) columbia (dot) edu
Shane Chu earned his PhD in computer science from Washington University in St. Louis, working with Gary Stormo. His PhD work focused on developing interpretable representation learning methods for addressing challenges in protein-DNA/RNA interactions. Outside of his academic pursuits, he finds relaxation and enjoyment in playing tennis and visiting the Peridance Center in NYC.
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Wangyang Dai (10/2023-), Master Student Email: wd2383 (at) columbia (dot) edu
Wangyang obtained her Bachelor's degree in Life Sciences from Fudan University in 2023. During her time as an undergraduate student, she conducted research on proline metabolism and its effects on ATF4 regulation. Later, she developed an interest in the RNA world (cool!), specifically focusing on alternative splicing and its correlation with neuron cell properties within and across cell types. Now in the Zhang lab, she is involved in a project about analysis of CLIP data using crosslink-induced mutation sites (CIMS) and aims to utilize it as a signature to better understand RBP binding specificity. Besides academics, she enjoys exploring good food, visiting museums, and building her own coffee map here in New York.
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Jessica Estrada (11/2022-), Technician Email: je2673 (at) cumc (dot) columbia (dot) edu
Jessica received her B.A from Stony Brook University in Chemistry and is a Technician in the Zhang Lab. She assists on various projects in the lab while developing a research focus, and plans on pursing a PhD in the biomedical sciences. In her free time, she likes to go on hikes and cook for friends and family.
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Brian Joseph (11/2021-), Postdoc (joint with Hynek Witchterle lab) Email: bj2468 (at) cumc (dot) columbia (dot) edu
Brian joined the Zhang and Wichterle labs as a postdoctoral fellow in November 2021 after a brief research experience in Kevin Eggan’s motor neuron lab at Harvard. He completed his PhD with Eric Lai at the Sloan Kettering Institute in NYC focusing on the biology of cotranscriptional RNA processing mechanisms. He plans to explore RNA metabolism in neurons and hopes to identify novel vulnerabilities that can be the basis for therapeutic intervention. Brian is currently an ALS scholar in therapeutics. A native Pakistani, Brian is obsessed with cricket and biryani. He is also an avid runner who still believes the PRs are yet to come.
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Suvrajit Maji (07/2022-), Postdoc Email:sm4073 (at) cumc (dot) columbia (dot) edu
Suvrajit is received his Bachelor's and Master's degree in Mathematics and Computing from the Indian Institute of Technology, Kharagpur, India. He then received his Ph.D. degree in computational biology from Carnegie Mellon University under the mentorship of his thesis advisor Dr. Marcel P. Bruchez. His thesis topic was single-molecule localization microscopy and super-resolution reconstruction of biological structures using generative models. He moved to Columbia University to continue his postdoctoral research work under the mentorship of Dr. Joachim Frank, when he focused on developing advanced mathematical, computer vision, and machine learning techniques for studying the structure and dynamics of molecular machines such as the Ribosomes and determining high-resolution 3D structures from 2D cryo-EM image datasets. His current research focuses on computational methods development, application, and analysis to study RNA-protein binding interactions using CLIP sequencing datasets. He is also involved in developing and applying machine learning & deep learning methods to study RNA-protein complex structures.
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Daniel Moakley (06/2018-), Graduate Student Email: dfm2129 (at) cumc (dot) columbia (dot) edu
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Paola Rinchetti (05/2022-), Postdoc Email: pr2485 (at) cumc (dot) columbia (dot) edu
Paola's research career started in 2014 in Prof. Stefania Corti's lab at University of Milan. During her studies in Italy, she maximized her knowledge in the field of cellular biology and in particular in the use of induced pluripotent stem cells (iPSCs) and 2D models to study neurodegenerative diseases such as SMA and ALS and the development of potential treatments. During her PhD, she mainly focused on the generation of new 3D models to investigate the pathological mechanism underlying SMA and ALS. During this time, she was also involved in exchange programs with the laboratory of Prof. Prezdborsky and Prof. Lotti at Columbia University where she was able to deepen her knowledge in the field of in vivo models. In the Zhang lab, she is working on RNA-based medicine for neurodevelopmental disorders.
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Ruchika (07/2023-), Postdoc Email: fr2563 (at) columbia (dot) edu
Ruchika completed her doctoral degree in molecular biology from Japan Advanced Institute of Science and Technology (JAIST) in Japan in 2022. During PhD, she worked on the identification and characterization of U-to-C RNA editing events in plants and used a plant-derived pentatricopeptide repeat (PPR) proteins to develop an artificial deamination system for C-to-U RNA editing in mammalian cells, and received an Excellent student award for her work. Thereafter, she joined Kyushu University in Fukuoka, Japan, as an assistant professor and she worked on designer PPR proteins to target long non-coding RNAs, especially related to neurodegenerative diseases and cancer. At the next step, Ruchika is excited for multiple projects related to programmable RNA targeting using different approaches at Columbia.
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Email: xw2006 (at) columbia (dot) edu
Before coming to work at Columbia, Xiaojian earned her Bachelor’s and Master’s degrees from Beijing Medical University and the Ohio State University, respectively. At CUIMC, she worked as supporting staff and lab manager in several labs. She joined the Zhang lab in 2016, and has been providing support on both molecular biology experiments and mouse work, as well as daily lab operations. In her free time, Xiaojian enjoys cooking, watching baseball games, and spending time with her family.
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Email: yw4291 (at) columbia (dot) edu
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Tim Yeh (09/2022-), Postdoc
Tim received his Ph.D. in Biological Sciences from Columbia University (2022). Throughout his scientific career, he has been interested in understanding how the brain works and developing treatment. His graduate research focused on auditory processing in the brain and sensorimotor interaction. As a postdoc in the Zhang lab, Tim hopes to investigate the roles of RNA splicing in normal brain functions and neurological diseases using novel research methods such as gene editing tools and sequencing technologies. When he is not doing science, he likes to play tennis and ping pong. He is also a foodie who enjoys eating pizza!
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Matthew Yuan (06/2023-), Visiting High School Student (remote) Matthew currently attends Lynbrook High School in San Jose, California as a rising Sophomore, and is passionate about Math and Science. Matthew is a two-time AIME qualifier, and has years of experience in Science Olympiad and Science Bowl. His favorite research area is Marine Biology. In his spare time, Matthew enjoys reading and writing, playing basketball as well as playing video games (Geometry Dash and Crossy Road are his favorites).
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Alumni
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Name/Position in the Lab |
Position When Exiting |
Current Position
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Email: yr2330 (at) cumc (dot) columbia (dot) edu
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Associate, Law firm. | |
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Email: gn2267 (at) cumc (dot) columbia (dot) edu
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Senior Scientist, Sanofi |
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Email: mmc2259 (at) cumc (dot) columbia (dot) edu
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Assistant Professor, UCSD |
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Email: hf2304 (at) columbia (dot) edu
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Associate Professor, Fudan University |
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Email: sb4045 (at) columbia (dot) edu
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Bioinformatics Manager, Regeneron |
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Email: du2145 (at) columbia (dot) edu
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Blavatnik Fellow in Life Science Entrepreneurship, Yale University |
Associate, Flagship Pioneering |
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Email: bp2563 (at) cumc (dot) columbia (dot) edu
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Medical Writer, Chrysalis Medical Communications |
Medical Writing Senior Manager, Amgen |
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Ph.D. student, Integrative Program, Columbia University
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Bioinformatics Scientist, Stoke Therapeutics. |
Principal Scientist, Bioinformatics, Fosun Pharma USA Inc. |
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Ph.D. student (joint with Wichterle lab), Department of Pathobiology & Molecular Medicine, Columbia University |
Postdoc, Alice Ting Lab, Stanford University |
CEO, Aperture Therapeutics |
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Scientist, Amgen |
CSO, Leverna Therapeutics |
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Yong Zhang (04/2013-11/2014), Postdoc
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Postdoc, Xuemei Chen lab, UC Riverside |
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Visiting Ph.D. student, Cold Spring Harbor Laboratory / Applied Maths and Statistics, Stony Brook University |
Bioinformatics Scientist, BioMicro Center, MIT |
Associate Director, Bioinformatics at Accent Therapeutics, Inc. |
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Qiyang Wu (01/2013-), Master Student Email:qw2388 (at) columbia (dot) edu
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Email: fp2409 (at) cumc (dot) columbia (dot) edu
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Email: amn2201 (at) cumc (dot) columbia (dot) edu
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Madeline (Maddie) Scanlon (06/2023-09/2023), Visiting High School Student
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Vivian Coraci (07/2023-09/2023), Visiting High School Student
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Yuchen Xu (02/2022-05/2023), Master Student
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Research Technician, Abbas Rizvi Lab, University of Wisconsin-Medison |
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Lily Wang (07/2020-09/2020), Undergraduate Research Assistant Undergraduate student, Mathematics/Statistics, Columbia University
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Meghna Gopalan (06/2022-08/2022), Undergrad Summer Research Assistant Email: mg4166 (at) barnard (dot) edu
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Lydia Wu (10/2021-06/2022), Undergrad Research Assistant
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Undergraduate student, Department of Engineering, Columbia University
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Medical School, Johns Hopkins School of Medicine |
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Undergraduate student, Department of Computer Science, Columbia University
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Graduate Student, UC Berkeley |
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Email: yq2139 (at) columbia (dot) edu
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Research Scientist, NYU Lagone Health |
Model Risk Management, Barclays |
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Helene Lovett (06/2017-08/2017), Undergraduate Research Assistant Undergraduate student, Department of Neurobiology, Harvard University
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Undergraduate student, Barnard College
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Graduate Student, University of Chicago |
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Jonah Lee (05/2015-01/2017), Volunteer Undergraduate student, Columbia College |
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Andrew Arditi (Volunteer, 09/2016-12/2016) |
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Jingxian You (Volunteer, 07/2016-09/2016) |
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MA in Biotechnology, Columbia University Volunteer |
Co-Founder, EleGo Education | |
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Technician |
MD program, UCSF |
Resident Physician, UCSF |
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Joy Pai ( 09/2013-05/2016)
Undergraduate Research Assistant |
Bioinformatics specialist, Michel Russenzweig lab, Rockefeller University |
Graduate Student, Stanford University |
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Kernyu Park (07/2015-10/2015) Undergraduate Research Assistant |
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