Yu-Hwa Lo came to the Jacobs School in July of 1999. He has established a new lab to investigate biologically inspired photonic systems. A member of the Materials and Device Layer for the California Institute of Technology and Telecommuncations, he is collaborating with Professors Andy Kummel and William Trogler (Chemistry and Biochemistry) on early-warning biosensors. He is responsible for designing infrared photon counters in a joint effort with IBM's Almaden Research Center to build a quantum-communications system. He was Associate Professor of electrical engineering at Cornell University, prior to coming to UCSD. He received his Ph.D. from UC Berkeley in electrical engineering in 1987.
Dr. Rao works at the intersection of genomics and image informatics, across biological scale (cells, tissue and organ). He is interested in developing multi-modal decision algorithms that link and integrate various measurements (imaging, genomics etc) to characterize disease. His algorithms for phenotypic measurements encompass data from 2D/3D microscopy, radiology and histopathology. He is also interested in methodological aspects of genomic analysis and image assessment. In the context of these investigations, Dr. Rao collaborates with clinicians, biologists, engineers and data scientists.
Alexandre Alloy obtained his PhD in computational biology at Columbia University where he used systems biology approaches to study the transcriptomics of paediatric acute leukaemia’s at the bulk and single-cell RNA sequencing levels. After graduation, he joined Bristol Myers Squibb to work as a computational biologist. His expertise revolves around immuno-oncology, biomarker identification, patient stratification and bioinformatics algorithm development.
Joshua Campbell received his Ph.D. in Bioinformatics from Boston University. He performed his postdoctoral research at Dana-Farber Cancer Institute and the Broad Institute of Harvard and MIT where he worked with The Cancer Genome Atlas (TCGA) to identify novel mutational drivers of lung cancer. He is currently an assistant professor in the Department of Medicine at Boston University School of Medicine where he develops novel Bayesian approaches to analyze data from single-cell genomic technologies to analyze cellular heterogeneity in lung and prostate cancer.
Edwin is enthusiastic and experienced Pathologist with extensive experience in pathology, experimental animal models of lung cancer and pulmonary fibrosis, immunohistochemistry (IHC), multiplex immunofluorescence (mIF), western blot (WB), DNA, RNA extraction (PCR) and digital pathology analysis. He has over 10 years of experience in research and teaching to technicians, graduate students, doctors and postdoctoral fellows. He also has extensive experience in performing standard laboratory techniques for molecular biology such as DNA and RNA extraction, cell culture, manual and automated IHC and mIF staining and experimental animal models. He is the author and co-author of more than 100 paper in lung cancer, interstitial lung diseases from human and animal models, and immunofrofiling using different image analysis-based assessment; several abstracts and presentations at national and international scientific meetings, three book chapters and many other reports on pulmonary pathology and medicine topics. He is highly training to develop and optimize immunoprofiling panels by immunohistochemistry and multiplex immunofluorescence, for immune markers to develop prognostic immune profiling for Non-Small Cell Lung Carcinoma and other types of cancer. Finally, he has experience and expertise in histomorphometry and digital analysis using different scanning system as Aperio AT2, Aperio IF, MultiOmixTM, Mantra and Vectra® and using different image analysis software’s as Image Pro-plus, Aperio Tool Box, GENIE, InForm, HALLO, Tissue Studio and Image Mainer.
Dr. Song (Stephen) Yi is an Assistant Professor of Oncology and Director of Bioinformatics, Developmental Therapeutics Lab, at Dell Medical School of the University of Texas at Austin. He is a joint faculty member at the MD Anderson Cancer Center. Dr. Yi is also an affiliated faculty with Department of Biomedical Engineering, and Institute of Cellular and Molecular Biology. Dr. Yi received his undergraduate’s degree from Peking University, and doctoral degree from University of Iowa. He was conferred with the NIH/NCI Transition Career Development Award and Dean’s Distinguished Dissertation Award for his work on signal transduction and evolution in human disease. Dr. Yi completed a postdoctoral fellowship in Cancer Systems Biology at Harvard Medical School and Dana-Farber Cancer Institute.
Jessica McDonough is a co-founder and VP at Attivare Tx, a new immunotherapy company developing technology from the Wyss Institute at Harvard. Jessica joined Attivare Tx in July of 2021 to develop innovative immunotherapies. Prior to joining Attivare, Jessica was a Business Development Lead at the Wyss Institute at Harvard from 2014-2021. Jessica was responsible for translating technologies in the areas of synthetic biology and molecular robotics. She also managed a venture capital alliance with Northpond Ventures. Prior to joining Wyss, Jessica worked at Decision Resources (now Clarivate) as a Principal in their custom consulting division. She worked with top pharmaceutical and biotech companies on over fifty engagements including topics such as therapeutic area landscapes, opportunity assessments, and valuations focusing on both the major and emerging markets. Jessica holds a Ph.D. from the Johns Hopkins University School of Medicine in Cellular and Molecular Medicine. While at Hopkins, her research focused on prevention of mother-to-child transmission of HIV and development of assays for sensitive detection of drug-resistant HIV variants. Jessica also holds a B.S. in Biochemistry from Worcester Polytechnic Institute.
Yu-Jui Chiu received his Ph.D. in Materials Science and Engineering at the University of California San Diego in 2017. After working in a start-up company in San Diego, he joined Cancer Early Detection Advanced Research Center (CEDAR) at OHSU, Oregon in 2018. His research focuses on developing single-cell platform and biomedical chip to achieve cancer detection from both tissue and liquid biopsy sample.
Miten is an Assistant Research Scientist at the University of California Santa Cruz. He did his PhD in Biomolecular Engineering and Bioinformatics at UC Santa Cruz in the nanopore group. His prior work and research interests include developing biological methods and software for: 1) analyzing genomics data; 2) long read sequencing of DNA and RNA; 3) resolving homopolymers and base modifications; 4) the nanopore MinION and PromethION sequencing platforms; and 5) sequencing and analysis of different classes of RNA (mRNA, rRNA, tRNA, non-coding RNA). His long term interests include combining sequence and structure information from DNA (genomics), RNA (coding and non-coding), and proteins, to better understand genome organization and function.
Eric received his PhD in molecular biology from Portland State University and has extensive experience in the fields of virology, microbiology, biochemistry, and biotechnology. Eric's research was primarily focused on virus-host interactions in terrestrial hot spring environments.
Namit Kumar is currently a Principal Scientist at the division of Informatics & Predictive Sciences in Bristol Myers Squibb (BMS). He received his PhD from Rutgers University, New jersey with dual major in Computational Biology and Molecular Biosciences conducting research on identifying drivers of intestinal development and disease. Prior to BMS, Dr. Kumar worked at Merck developing new single-cell sequencing methodologies like REAP-seq with applications including identifying and validating drug targets. His current research at BMS broadly focusses on using multi-omics approaches to identify clinically applicable biomarkers and indication selection strategies for drugs moving in early clinical trials.
Alexandre Alloy obtained his PhD in computational biology at Columbia University where he used systems biology approaches to study the transcriptomics of paediatric acute leukaemia’s at the bulk and single-cell RNA sequencing levels. After graduation, he joined Bristol Myers Squibb to work as a computational biologist. His expertise revolves around immuno-oncology, biomarker identification, patient stratification and bioinformatics algorithm development.
Yu-Hwa Lo came to the Jacobs School in July of 1999. He has established a new lab to investigate biologically inspired photonic systems. A member of the Materials and Device Layer for the California Institute of Technology and Telecommuncations, he is collaborating with Professors Andy Kummel and William Trogler (Chemistry and Biochemistry) on early-warning biosensors. He is responsible for designing infrared photon counters in a joint effort with IBM's Almaden Research Center to build a quantum-communications system. He was Associate Professor of electrical engineering at Cornell University, prior to coming to UCSD. He received his Ph.D. from UC Berkeley in electrical engineering in 1987.
Matt Davis PhD joined Gritstone Oncology (NASDAQ: GRTS) in 2015 and is currently the Director of Molecular Biology and Sequencing responsible for various neo-antigen discovery and translational genomics efforts. Prior to Gritstone, Dr. Davis conducted post-doctoral research at Warp Drive Bio in the discovery biology group. He holds a PhD in Genetics from Yale with thesis research under the supervision of Dr. Joseph Schlessinger and previous to his graduate work he conducted cancer genomics research at Dana Farber Cancer Institute and the Broad Institute.
Jun Wang is an Associate Professor in the Department of Biomedical Engineering at Stony Brook University. Prior to joining SBU, he was an assistant professor in the Chemistry Department of SUNY Albany. He received postdoctoral training in the Department of Chemistry and the NanoSystems Biology Cancer Center at the California Institute of Technology. He obtained his Ph.D. in Biological Engineering from Purdue University. He has received several top awards including Chorafas Foundation prize.
Dr. Ehrhardt is a biophysicist with a Ph.D. in human physiology. Throughout her career, she focused on driving biomedical research through efficient application of innovative technologies and strategies. She built and led successful teams in industry, including at Merck, where she headed a laboratory providing leading technologies for cell-based research from early discovery through manufacturing; and at BMS where Dr. Ehrhardt led and grew an international clinical assay team to robustly cover large scale registrational and translational clinical analysis generating clinical decision-driving data and mechanistic insights for immuno-oncology, cardiovascular, immunology, metabolic and rare disease studies. Before returning to Merck, Dr. Ehrhardt fulfilled one of her scientific aspirations at CHDI Foundation, designing and implementing successful clinical biomarker discovery and development strategies for Huntington’s disease. Currently, at Merck, Dr. Ehrhardt is providing strategic and technical leadership for the development and implementation of industry-leading and QC-friendly cell-based assays and models for potency determination that reflect the unique mechanisms of biologics products in clinical studies and beyond.
Ray’s lab studies include epigenetic regulation in retinal neurons. Eukaryotic genomes acquire heritable and reversible chemical modifications that play a large role in influencing expression patterns of genes. His lab uses the developing chicken eye and the human eye to study DNA methylation, an epigenetic modifier of the genome and how this modification effects transcription in retinal neurons. Additionally, he is actively involved with developing applied genomics and bioinformatics classroom materials for implementation into undergraduate courses.
Livnat Jerby is an Assistant Professor of Genetics at Stanford University. Her research focuses on multicellular dynamics, as a disease driver and therapeutic avenue, particularly in the context of cancer immunology. In her work, she aims to identify the drivers, molecular underpinnings, and causal structure of multifactorial immune evasion mechanisms, and use this information to identify new and more effective ways to augment and unleash targeted immunity via combinatorial interventions. To address this challenge at scale, she develops integrative approaches, fusing single-cell sequencing and imaging with machine learning, genetic and environmental perturbations.
Thus far, her research provided new perspectives to key facets of tumor biology, encompassing metabolism, genetics, and immunology. As a postdoctoral fellow in Aviv Regev's lab at the Broad Institute of MIT and Harvard, she identified regulators of T cell exclusion and dysfunction. She holds a B.Sc. in Computer Science and Biology and obtained her PhD in 2016 from Tel Aviv University, where she worked with Eytan Ruppin and developed new ways to interrogate cancer metabolism and genetics.
This fall Livnat joined Stanford Genetics to establish a multidisciplinary lab that will harness machine learning in combination with clinical data and extensive functional testing to dissect and target immune dysregulation in cancer, aiming to leverage the versatile, interconnected function of genes, cells, and tissues for disease detection, prevention, and treatment.
Ajay Nair’s research is focused on developing computational techniques to identify cellular regulatory interactions from high-throughput data. He completed his engineering master’s degree from IIT-Delhi holding first rank and Joint-PhD in Computational Biology from IIT-Bombay and Monash University, Australia. His postdoc training was with Prof. Andrea Califano and Prof. Robert Schwabe at Columbia University. Ajay and his team have identified regulatory interaction and identified drugs in Ovarian cancer and gastric cancer as well as identified and characterized disease causing fibroblasts in COVID-19 affected lungs, human ICC and liver metastases.
Dr. Rao works at the intersection of genomics and image informatics, across biological scale (cells, tissue and organ). He is interested in developing multi-modal decision algorithms that link and integrate various measurements (imaging, genomics etc) to characterize disease. His algorithms for phenotypic measurements encompass data from 2D/3D microscopy, radiology and histopathology. He is also interested in methodological aspects of genomic analysis and image assessment. In the context of these investigations, Dr. Rao collaborates with clinicians, biologists, engineers and data scientists.
