Charles Danko
Associate Professor
Charles is an assistant professor at the Baker Institute and the College of Veterinary Medicine, Cornell University. His research is focused on understanding gene regulation using methods from molecular biology and genetics, computer science, statistics, and machine learning. Learn about active research projects in the Research page.
@charlesdanko.bsky.social
Ed Rice
Laboratory Manager
Ed is a professional laboratory manager, with over 20 years of molecular biology experience. As the lead bench scientist, Ed has his hands in virtually every project in the Danko lab. He has a particular scientific interest in understanding the molecular pathways underlying autoimmune disorders.
Adam He
Computational Biology Graduate Student
Adam is a graduate student in the Computational Biology program at Cornell. He is interested in both the application of machine learning methods to understanding transcriptional regulation and, more broadly, the role that transcriptional regulators play in development and evolution.
Brent Basso
Computational Biology Graduate Student
Brent received his bachelor's degree from the University of Rhode Island and then spent two years teaching middle school science at the Bay View Academy in Riverside, RI. After my time as a teacher, I received a master's degree from the University of Connecticut where I worked in the labs of Dr. Sarah Hird and Dr. Charlie Giardina before moving to the Boston area for a job. There I developed sequencing based quality control methods for Sarepta, a gene therapy company.
My project in the Lis and Danko labs combines new sequencing methods and novel analytical techniques to examine the evolution of divergent noncoding transcription and the behavior of RNA Polymerase II at divergent promoters.
Outside of the lab, I am active in the local rowing community and love spending time on the water or hiking with my partner Ally and our dogs Marty and Lucy
Banseok Lee
GG&D Graduate Student
Banseok is a graduate student in the Genetics, Genomics, and Development program at Cornell. His research interest lies in the dynamics of transcriptional regulation during spermatogenesis and how it is associated with the phenotypic differences between species. He is trying to tackle these intriguing questions using wet lab techniques and computational tools.
Nating Wang
Computational Biology Graduate Student
Nating Wang received an M.S. in Statistics from Yale University. She is developing BayesPrism as a deconvolution tool for spatial and multiomic data, with extensions that enable integration of bulk and single-cell datasets across different modalities.
Anita Rogic
GG&D Graduate Student
Anita is a graduate student in the Genetics, Genomics, and Development program. She worked at the Ichan School of Medicine at Mount Sinai (NYC) studying the mechanisms of inflammatory breast cancer and its treatment in mouse xenograft models. She is currently interested in applying machine learning methods to uncover the regulatory syntax that governs gene expression and identifying causal SNPs associated with autoimmunity.
Saloni Dhopte
GG&D Graduate Student
Saloni is a graduate student in Genetics, Genomics and Development. She completed her undergraduate education at the University of California, Davis where she studied R-loops and their role in causing genome instability. Now at Cornell, she is co-advised by Dr. Paula Cohen, and is interested in the mechanisms of transcriptional regulation throughout spermatogenesis.
Ameen Haj Yahia
GG&D Graduate Student
Ameen is a new graduate student working jointly in the Danko and Lammerding labs to study how cell compression alters gene expression through changes in chromatin and nuclear packaging.
Gilad Barshad
Postdoctroal Associate, 2019-2024
Gilad received his PhD from Ben Gurion University, Beer-Sheva, Israel in 2019. During his PhD Gilad studied the mitochondrial-nuclear co-regulation of gene expression. Looking through an evolutionary lens, Gilad now hopes to shed new light on the relationship between genomic architecture and transcriptional regulation.
Current position: Assistant Professor, Technion
Danko lab publications.
Blaine Harlan
Postdoctroal Associate, 2021-2023
Blaine earned her PhD from Cornell University performing scATAC-seq data collection, analysis, and technology development. Blaine's interest is currently in tech development of single cell genomic assays and applications in cancer and germ cell development.
Current position: Postdoctoral Associate, Yale University
Jyoti Lama
Postdoctroal Associate, 2021-2023
Jyoti completed her PhD from University of Houston studying host tolerance to transposable elements. Jyoti's focus in the Danko and Cohen labs is to understand how changes in transcription and chromatin influence germ cell development.
Current position: Bioinformatics Scientist at Mass. Eye and Ear, Harvard medical school
Alexandra Chivu
GG&D Graduate Student, 2019-2023
Alex worked at the Genome Institute of Singapore (GIS) & Medical Research Council (MRC), London studying transcription bursts and epigenetic regulation in cancer and immunity. Currently Alex is interested in understanding the impact of chromatin architecture on transcriptional regulation, as well as developing new RNA-based technologies.
Current position: Associate, Flagship Pioneering
Danko lab publications.
Jon Villanueva
Biomedical and Biological Sciences Graduate Student, 2018-2023
Jonathan Villanueva is a graduate student in the Biomedical and Biological Sciences program at Cornell. He is interested in utilizing dry and wet lab techniques to identify how specific mutational combinations alter the gene regulatory mechanisms (enhancers and miRNAs) that drive colon cancer development.
Current position: Postdoctoral Scholar, Spence lab, University of Michigan
Danko lab publications.
James Lewis
Postdoctroal Associate, 2016-2021
James received his postdoc from Bob Reed at Cornell. James is interested in understanding the molecular basis of evolutionary adaptation, especially for traits driven by cis-regulatory changes.
Current position: Assistant Professor, Clemson UniversityDanko lab publications.
Shao-Pei Chou
GG&D Graduate Student, 2016-2021
Shao-Pei is a graduate student in the Genetics, Genomics, and Development program at Cornell. She likes to develop new computational methods that can better tackle the problems and provide a different perspectives to examine the biological data. Here is a method she developed recently: AlleleHMM. Her current project is to identify genomic factors that play a role in transcription regulation using allele-specific analysis.
Current position: Computational Biologist, Ginkgo BioworksDanko lab publications.
Adriana Alexander
Biomedical and Biological Sciences Graduate Student, 2017-2021
Adriana is a graduate student in the Biological and Biomedical Sciences Program at Cornell. She is interested in understanding the mechanisms controlling transcriptional inactivation during spermatogenesis using a combination of wet lab and computational tools.
Current position: Consumer Safety Officer, FDADanko lab publications.
Mridusmita Saikia
Postdoctroal Associate, 2016-2020
A biochemist by training, Mridu received her PhD from University of Chicago in 2009, where she studied the role of posttranscriptional modifications present in cellular RNA. During her postdoctoral training she continued to study the non-coding RNAs, and their function in gene expression control, especially in the context of human diseases. Mridu is now making her debut into single cell genomics, her goal is to establish a single cell RNA sequencing technology, and adapt that technology to study canine immune cells.
Current position: Lecturer, Biomedical Engineering, Cornell UniversityDanko lab publications.
Lauren Choate
GG&D Graduate Student, 2015-2020
Lauren is a graduate student in the Genetics, Genomics, and Development program at Cornell. She is interested in understanding the role of disease risk alleles on transcriptional regulation in autoimmunity using computational and wet lab techniques.
Current position: Cytogeneticist, Brigham and Women's HospitalDanko lab publications.
Paul Munn
Computational Biology Graduate Student, 2016-2020
Paul is a graduate student in the Computational Biology program at Cornell. He is interested in both developing machine learning techniques to aid in the identification of transcription unit boundaries, and in improving our understanding of chromatin structure and how it affects gene regulation.
Current position: Computational Biologist, TREx core, Cornell UniversityDanko lab publications.
Zhong Wang
Programer, Research Associate, 2015-2019
Zhong Wang arrived at Cornell University with 6 years of experience in Statistical Genetics and Biostatistics. He conducted postdoctoral training at Penn State College of Medicine and Yale School of Public Health, where he worked in the areas of statistical modeling and software development.
Current position: Professor, Dalian University of Technology, China
Danko lab publications.
Tinyi Chu
Croucher Foundation Graduate Fellow, 2014-2019
Tinyi is a graduate student in the Computational Biology program at Cornell and a scholar of the Croucher Foundation. He is actively working on developing bioinformatic tools for analyzing PRO-seq data, and is broadly interested in understanding how the rewiring of transcriptional regulatory networks plays a role in oncogenesis.
Current position: Postdoc (Dana Pe'er), Memorial Sloan Kettering Cancer Center, New York
Danko lab publications.
