Team
Our team consists of dedicated scientists and researchers with solid background in genomics research.
Zhong Wang
Genome Analysis Group Lead, DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
Contact Information: Email
HomepageZhong Wang's research in the Analysis R&D group focuses on developing new bioinformatics solutions to support JGI in adopting new genomics technologies, scaling up genomics analysis to peta-bases, and enabling data-driven science. This is a group of computational biologists, bioinformaticians, computer scientists and biostatisticians. Through collaborations with internal and external scientists, the Wang group has developed customized data analyses and software to enable “grand-scale” scientific projects. These solutions include large-scale genome variants analyses, next-generation transcriptome de novo assembly, metagenome and metatranscriptome assembly, Hadoop based on sequence analysis framework, etc. For example, this group was responsible for the tera-base scale data analysis in the cow rumen and sheep rumen metagenome projects.
Han Liu
Orrington Lunt Professor of Computer Science, Northwestern University
Contact Information: Email
HomepageHan Liu directs the MAGICS (Modern Artificial General Intelligible and Computer Systems) lab at the Northwestern University. He has been the director of the deep reinforcement learning center at Tencent AI Lab and had been a professor at the Princeton University and Johns Hopkins University. He received a joint PhD in Machine Learning and Statistics from the Machine Learning Department at the Carnegie Mellon University, advised by John Lafferty and Larry Wasserman. His research lies at the intersection of artificial intelligence and computer systems, which deploys statistical machine learning methods on edges and clouds to achieve analytical advantages. Han Liu has received numerous research awards including the Alfred P Sloan Fellowship in Mathematics, the IMS Tweedie New Researcher Award, the ASA Noether Young Scholar Award, the NSF CAREER Award, the Howard B Wentz Award and the Umesh Gavaskar Memorial Best Dissertation Award. He is now serving as associate editors for the Journal of American Statistical Association, the Electronic Journal of Statistics, the Technometrics, and the Journal of Portfolio Management.
Ji-Ping Wang
Department Chair and Professor of Statistics and Data Science, Northwestern University
Contact Information: Email
HomepageMy research interest centers around statistical applications in bioinformatics and computational biology. I am actively engaged in developing advanced statistical and machine learning methods and tools specifically designed for the analysis of large-scale, high-dimensional genomic and genetic data. Some of recent working topics include species number estimation, nucleosome positioning mapping and prediction, next-generation sequencing analysis, RNA-seq normalization, Ribo-seq pattern differentiation, CRISPR-cas9 cleavage efficiency prediction, prediction of DNA bendability and its relationship to chromosome functions and etc. My lab has developed a few software tools that have been frequently used by researchers, including SPECIES (for species number estimation, CRAN), NuPoP (for nucleosome positioning prediction, bioconductor), DegNorm (for degradation normalization for RNA-seq, bioconductor), RiboDiPA (for differential pattern analysis for Ribo-seq data, GitHub, bioconductor), DNAcycP (for DNA cyclizability/bendability prediction, GitHub, Web server) and BoostMEC (for CRISPR-cas9 cleavage efficiency prediction, GitHub).
Lizhen Shi
Assistant Professor of Instruction, Northwestern University
Contact Information: Email
HomepageMy research bridges the areas of Computer Science, Bioinformatics, and Biology and centers around using state-of-the-art Big Data and Machine Learning technologies to address the challenges in genomics and metagenomics.
Satria Kautsar
Genomics Data Scientist, Lawrence Berkeley National Laboratory
Contact Information: Email
HomepageI build software and collaborate with experimental researchers to answer life science questions, focusing on the discovery of medicinally important natural products. Starting out in 2008 as a software engineer, now I set to apply my skills and experience at the interface of Computer Science, Biology, and Chemistry. I love learning, gaining a deep and thorough understanding of a new topic, then enjoys sharing that knowledge to others through direct mentoring, public speaking, or casual conversations. Moreover, I love to empower scientists in their quest to answer nature's fundamental and translational questions through powerful, easy to use software and databases.
Zhihan Zhou
Ph.D. Candidate in Computer Science, Northwestern University
Contact Information: Email
HomepageZhihan Zhou is a Ph.D. candidate in the Computer Science Department at Northwestern University, advised by Prof. Han Liu. He received his Bachelor's Degree in Mathematics at Zhejiang University. His research focuses on foundation models for health and human modeling. He is the main contributor of DNABERT and DNABERT-2.
Rob Egan
Software Engineer, Lawrence Berkeley National Laboratory
Contact Information: Email
HomepageRob Egan is a software developer at the DOE Joint Genome Institute in the research and development department. His interests include metagenome assembly, binning and analysis, along with high performance computing, high throughput computing, software optimization and algorithm development.
Fengchen Liu
Science IT Consultant, Lawrence Berkeley National Laboratory
Contact Information: Email
HomepageFengchen just joined the group as a Science IT Consultant. Prior to joining the Lab, he worked at a Fintech company as a senior AI Engineer, at RMS (Risk Management Solutions) as a Software Engineer, and at UC San Francisco for 7 years on computational epidemiology using HPC. His research background (researchgate.net/profile/fengchen_liu) includes predictive models of infectious diseases and control of epidemic disease through contact investigation.
Timothy Fong
Science IT Consultant, Lawrence Berkeley National Laboratory
Contact Information: Email
HomepageTimothy Fong is a ScienceIT consultant. Before joining the Lab, he worked in the private sector as a Data Scientist across a variety of industries, including computer vision, people analytics, and casino gaming. Timothy holds an M.S. in Statistics from Baruch College and a J.D. from University of San Francisco. When he’s not trying to develop the perfect Instant Pot recipe, he enjoys hiking and being outside.
Andrew Shen
Master Student in Artificial Intelligence, Northwestern University
Contact Information: Email
HomepageIncoming Masters in Artificial Intelligence student at Northwestern and recent grad from UCSD studying Bioinformatics and Computer Science. Interested in finding solutions to societal problems using computational methods and tools, particularly in the field of healthcare. Robust research background with Stanford Health Care, UCSD Bioinformatics, Harvard Medical School.