Radhika Khetani is the director of Data Science Learning in the Data Science and AI group at AstraZeneca in Gothenberg, Sweden. During her 9 years at the core, Radhika's focus was on developing bioinformatics workshops and training modules of various lengths for the Harvard community. Her passion is to make genomics data and its analysis accessible to everyone. She spent her last several years at the core training wet lab biologists to independently perform bioinformatics analyses. She joined the core from the High-Performance Biological Computing (HPCBio) group at University of Illinois (UIUC) where she was involved in several research projects, and was in charge of the training program. Her background is in molecular biology, but she switched to computational work as a postdoctoral fellow when she started studying the impact of stress factors on the health of honey bees. Her sequence-based analysis repertoire includes metagenomics, metatranscriptomics, RNA-Seq, genome and transcriptome assembly, in species across the spectrum of life. Radhika has a PhD in Molecular and Cellular Biology from Dartmouth College.

Victor Barrera graduated with a BSc in Biochemistry and began his thesis in Cancer Epigenetics. During his first PhD year he shifted to Bioinformatics, obtaining a MSc in Bioinformatics and Biostatistics, and designed custom pipeline and analysis for NGS epigenetic data. He is interested in the study of big volumes of data such as next generation sequencing or Big Data in order to find hidden relationships. He is experienced in custom analysis development and automation using Python, R and Bash as his main worktools. Victor was a Research Scientist at Harvard T.H. Chan Bioinformatics Core for eight years.

Sergey Naumenko graduated with BSc/MSc in Computer Science from Kharkiv National University of Radio and Electronics (Kharkiv, Ukraine), defended PhD thesis in Mathematical Biology and Bioinformatics in the joint laboratory of Evolutionary Genomics and Molecular Evolution (Moscow State University/Institute for Information Transmission Problems, Moscow, Russia), and went through a postdoctoral training at the Hospital for Sick Children (Toronto, Canada). While at the Core, Sergey focused on variant analysis (variant calling and annotation, variant prioritization, CNV calling, PureCN analysis), single cell RNA-seq analysis (indrop3 data processing, cell hashing), and on maintaining the bcbio ecosystem. Publications, GitHub, Twitter.

Amélie Julé is a computational biologist at the Oxford Kennedy Institute of Rheumatology and was a core team member for two years from 2021-2023. Amélie joined the core with a background in genetics and immunology, and a PhD in Global Health from the University of Oxford, UK. Her doctoral work focused on understanding the challenges that researchers based in low and middle income countries face when handling local clinical research data. She completed her postdoctoral training at Boston Children’s Hospital, where she leveraged single-cell RNA sequencing to characterize autoimmune responses in childhood arthritis and other diseases, and discovered a passion for bioinformatics. She’s particularly interested in the adaptive immune system and T cell/B cell receptor sequencing studies, and enjoys organizing complex datasets for visualization and communication with diverse audiences.

John Hutchinson is a Senior Scientific Consultant at Diamond Age Data Science. With a background in both molecular biology and bioinformatics, John joined the Core after completing influential work on non-coding RNAs (NEAT1 and MALAT1/NEAT2), allele-specific expression and methQTLs and served as the Associate Director of the Core from 2015-2022. Aside from helping develop and manage the Core and its staff, John drove the Core’s implementation of methods for DNA methylation, metabolic, proteomic and multi-omic data and played a pivotal role in the Core’s initiatives to implement reproducible research, manage data management and better visualize results.

Mary Piper is a research consultant at Pfizer. At the Core for seven years, she ultimately served dual roles as research scientist and assoicate director of the bioinformatics training core. As a bioinformatics trainer, her primary role of developing and instructing bioinformatics workshops focused on the analysis of next-generation sequencing data. Her background in scientific curriculum design and instruction began at the University of Michigan, where she taught undergraduates for over five years while completing her PhD in cellular and molecular biology and her MPH in epidemiology. 

Jihe Liu is a senior data scientist at Cohere Health. Jihe’s role at the core was to instruct bioinformatics workshops, develop training materials, and support selected data analysis projects. Jihe obtained his BS degree in Bioinformatics from Huazhong University of Science and Technology, and PhD degree in Chemistry (with focus on chemical biology and synthetic biology) from University of Pittsburgh. He received postdoctoral training at The Jackson Laboratory, where he worked on genomic analysis of Glioblastoma using short-read and long-read sequencing technologies. 

Preetida Bhetariya is a Senior Scientist with AstraZeneca in early oncology. She received her PhD in Biotechnology from Institute of Genomics and Integrative Biology, India where she studied Aspergillus genomics for secondary metabolites. Along with molecular and functional genomics approaches, she developed a diagnostic test for fungal (Aspergillus) detection from clinical samples. She continued pursuing her computational genomics interests during her post-doctoral training at University of Utah where she used RNA-seq to study microbial interactions in Multiple Sclerosis and characterized human gene expression patterns in MS and other autoimmune diseases. Following her passion for diagnostic research, she moved to Dr. Gabor Marth’s lab where she studied cancer genomics; developing a bioinformatics pipeline for low-frequency variant calling for circulating tumor DNA from liquid biopsies. She is an expert in designing custom custom analysis workflows in Python and R. While at the core, she supported the data analytics of projects involving single cell genomics and cancer genomics. Github, Google Scholar

Brad Chapman is a Principal Data Science Architect at Ginkgo Bioworks Inc. He has spent more than 15 years answering biological questions with computational approaches after switching over from a background in wet-lab research. He combines automated high-throughput analysis pipelines with custom visualization and processing tools. By utilizing a wide variety of languages, he strives to maximize code re-use while maintaining the flexibility to answer highly-specific collaborative questions. He has a PhD in plant biology from the University of Georgia and can be found on Twitter as chapmanb.

Rory Kirchner is a Senior Test Engineer III at Ginkgo Bioworks Inc. His background is in neuroscience and engineering from the Harvard-MIT Health Science and Technology department. As a research scientist at the core, he worked on creating software to implement best-practice approaches for common informatics analyses and methods development for tackling novel informatics problems. His code can be found on github.

Lorena Pantano is the Director, Head of Computational Biology at NextRNA Therapeutics. Lorena graduated with a BSc in Biochemistry, and extended her career in Bioinformatics during her MSc and PhD thesis. Her interests are the application of statistical and mathematical models to large-scale data, mainly (small) RNA-seq data. She likes to think of new visualization concepts to improve the interpretation of complex data providing a dynamic user-data interaction. She is involved on the development/maintenance of SeqBuster, a framework for the analysis of small RNA seq data that integrates Java, Python and R modules. You can find her on Twitter.

Joon Yoon was a Research Associate while at the Harvard Chan Bioinformatics Core. Currently a senior scientist at Samsung Biologics, Joon obtained his MSc and PhD degrees in Bioinformatics from the Seoul National University where he defended his thesis on custom workflows and visualizations for transcriptomic analyses (using R and python scripting). During his Ph.D. Joon joined the bioinformatics solution company C&K Genomics’ RNA-seq team as a research consultant where he helped set update their bulk RNA-seq analysis workflows by switching out outdated protocols and expanding on types of analyses. While there he also participated in the T2D international consortium and several other RNA-seq projects.

Oliver Hofmann is the head of bioinformatics at the University of Melbourne Center for Cancer Research. Previously the Director of the Core, Oliver continues to consult for the Core as an Affiliated Faculty member of HSPH and the HSCI. Oliver worked in a molecular biology wetlab environment before switching to natural language processing, database development and curation as part of his PhD thesis, eventually branching out to sequence clustering and pattern recognition as a visiting researcher at deCODE Genetics. Oliver has a PhD in Biochemistry from the University of Cologne, Germany and can be found on Twitter and blogs about workshops and conferences.

Winston Hide created the Core in his role as an Associate Professor of Bioinformatics and Computational Biology in the Department of Biostatistics at Harvard T.H. Chan School of Public Health. Dr Hide is currently an Associate Professor of Pathology at the Beth Israel Deaconess Medical Center where he also co-directs the Precision RNA Medicine Core. He founded and directed the South African National Bioinformatics Institute (SANBI) near Cape Town. With over 20 years of experience in computational biology, his expertise addresses integration of ‘omics data to deliver clinical translation. He uses standardized approaches to disease gene discovery in stem cells and cancer stem cells, host response to pathogens, and complex diseases.

Ilya Sytchev is a Senior Bioinformatics Software Developer in the Department of Biostatistics. He was one of the founders of OpenWetWare - an online community for biologists and is currently helping build and maintain the HSCI Stem Cell Commons. He has a BS in Computer Science from University of Massachusetts Boston and a MS in Bioinformatics from Northeastern University.

Kayleigh Rutherford works at Icahn School of Medicine at Mount Sinai as a Bioinformatician II. She graduated with a BSc in Genetics and Computer Science from the University of Cape Town, and went on to complete a Medical Science Honours in Bioinformatics, with a thesis that focused on computational methods for drug repositioning. She came to Boston to pursue a Masters in Bioinformatics and since graduating, joined the core where she focuses on statistical analysis and visualisations of large-scale data from siRNA and compound screens. She has since moved on to a Computational Biology position at Memorial Sloan Kettering.

Rachel Boschetto served as dedicated administrative support for the core for many years. She was an all-around financial guru and grants manager. Rachel is now a Senior Grants Manager at Harvard Medical School

Michael Steinbaugh is the Director of Translational Science at Redona Therapeutics. He graduated with a BSc in Microbiology, Immunology and Molecular Genetics from UCLA and did his Ph.D. at the University of Michigan Medical School where he studied stress resistance and xenobiotic metabolism in slow-aging mice. Mike did his postdoc at the Joslin where he worked in Keith Blackwell’s group on lipid homeostasis and lifespan extension in C. elegans. Mike has a keen interest in R and Bioconductor development.

Yufei Lin was an Intern in the core and came to us from the Boston University where she was pursuing a Masters in Statistical Practice, which fostered her interest in the application of statistics to biology. Yufei has an extensive and varied background in data science and analysis and a Bachelor of Management in Electronic Commerce. Her working experience in a neuroscience lab and a biomedical genetics lab makes her determined to pursue bioinformatics as a career, specifically in genomics studies, where she is most interested in studying next generation sequencing data to find relationships between the genome and disease. She is experienced in statistical analysis and visualization of large-scale data using R.

Andreas Sjödin was a Research Associate in the Department of Biostatistics and is currently the Deputy Research Director at the FOI in Umea, Sweden. He has been in the field of genomics for more than ten years and closely followed the development of emerging sequencing technologies. The focus of his research has changed from plant transcriptomics through pathogen genome sequencing to human WGS and metagenomics. He is also an expert on forensics of select agents (BSATs) using sequencing technologies. Andreas has a PhD in Cell and Molecular Biology of Plants from Umeå University. Follow him on twitter.
 

John Morrissey was part of the FAS Research Computing team and provided research computing support for the Harvard Chan School of Public Health. Prior to joining Research Computing, John was a Senior Software Engineer at Frontier Communications where he was the lead on writing new code and modifying existing code, designing/implementing systems and network infrastructure, performance planning and tuning, and final escalation for production troubleshooting and failure analysis. He works in close collaboration with core staff and external partners to identify and resolve bottlenecks in our workflows. You can follow his latest work on Twitter. John has a BS in Information Technology from Rochester Institute of Technology.