Justin L. Cotney, Ph.D.Associate Professor
Director, Graduate Program in Genetics and Developmental Biology
- Education & Training
- Committees & Organizations
- Research Opportunities
- Lab Rotations
|B.S.||Birmingham Southern College||Biology|
|Ph.D.||Emory University||Genetics & Molecular Biology|
|Postdoctoral||Yale University||Postdoctoral Fellow - Snyder Laboratory|
|Postdoctoral||Yale University School of Medicine||Postdoctoral Fellow - Noonan Laboratory|
|Name of Award/Honor||Awarding Organization|
|Rudolph J. Anderson Fellow||Yale University|
|Name & Description||Category||Role||Type||Scope||Start Year||End Year|
|Research Advisory Board of Shriners Hospitals for Children||Advisory Committee||Member||External||National||2018|
|Genetics and Developmental Biology Area of Concentration||Assistant Director||UConn Health||University||2018|
|Graduate Student Admission Committee||Community Service||Member||UConn Health||University||2018||2020|
|American Society for Human Genetics||Professional/Scientific Organization||External||National||2014|
|Society of Craniofacial Genetics and Developmental Biology||Professional/Scientific Organization||External||National||2013|
|American Association for the Advancement of Science||Professional/Scientific Organization||External||National||2002|
|NIH Genetics of Health and Disease Study Section||Study Section||Reviewer||External||National|
The Cotney Lab is interested in determining how gene regulatory elements, namely enhancers, control gene expression during mammalian development. We aim to understand how new gene regulatory functions evolve, to identify mechanisms of enhancer function over large genomic distances, and globally identify variants of enhancer sequences that are associated with human disease.
Postdoctoral positions in comparative functional genomics for both experienced molecular biologists and computational biologists are available in the Cotney Lab within the Department of Genetics and Genome Sciences and the Institute for Systems Genomics at UConn Health . Our laboratory is applying functional genomics techniques (ChIP-Seq, RNA-Seq, ChIA-PET, Hi-C, etc) to identify novel gene regulatory elements in early mammalian embryonic development. We seek to understand the genetic basis of the evolution of the human form and developmental disorders by integrating multiple types of functional genomics data from a variety of tissues and species.
We seek molecular biologists with a variety of experimental experience including:
- General tissue culture techniques, including culturing of human and mouse cell lines, primary cells, embryonic stem cells and iPS.
- Transient and stable cell transfection, virus-based infection.
- RNAi-based knockdown and vector mediated ectopic expression, markerbased positive clone selection.
- Cell-based assays to evaluate viability.
- Protein analysis by western blotting, enzymatic assays.
- DNA/RNA sequencing
- Chromatin immunoprecipitation
- Genome editing (CRISPR)
- Enhancer screens and activity measurement
We seek computational biologists with experience related to functional genomics:
- Scripting languages such as Python, Perl, or Awk
- Statistical packages such as R or Matlab
- Next generation sequencing data such as ChIP-Seq, RNA-Seq, etc.
- Statistical genetics including GWAS and 1000 Genomes data sets.
- Comparative genomics such as multi-species alignments and conservation analysis.
- Visualization of genomic data including Circos, IGV, UCSC Genome browser.
- 3D Modeling or experience with game development
The ideal candidate would have a mixture of both experimental and computational skills.
Accepting Lab Rotation Students: Summer 2022, Fall 2022, and Spring 2023
We will be accepting graduate students from the Genetics and Developmental Biology Graduate program and professional students from the Schools of Medicine and Dentistry for rotations. Please inquire for possible projects.
|Title or Abstract||Type||Sponsor/Event||Date/Year||Location|
|Leveraging functional genomics to understand developmental abnormalities and human disease||Talk||University of Kansas Medical Center Dept. of Anatomy||2021||Virtual|
|Leveraging functional genomics to understand human developmental abnormalities||Talk||Emory University School of Medicine Dept. of Human Genetics||2021||Virtual|
|Leveraging functional genomics to understand human craniofacial development and abnormalities||Talk||University of Missouri Kansas City Dept. of Oral and Craniofacial Sciences||2021||Virtual|
|A distant locus control region of the HoxA gene cluster has unique superenhancer properties and is essential for normal craniofacial development and viability.||Plenary Lecture||EMBO Enhanceropathies||2021||Santander, Spain|
|Single cell epigenomics of craniofacial development reveal cell type specific cis-regulatory sequences||Poster||Gordon Research Conference on Craniofacial Morphogenesis||2020||Barga, Italy|
|Functional genomics approaches for uncovering the role of regulatory sequences in developmental abnormalities and disease||Plenary Lecture||European Society of Human Genetics||2019||Gothenberg, Sweden|
|Functional Genomics approaches for Systems Neuroscience||Lecture||Kavli Institute for Neuroscience||2019||Tromso, Norway|
|High Throughput Methods for Dissection of Human Craniofacial Cis-Regulome||Talk||ISG Networking Workshop||2018||Storrs|
|High Resolution Epigenomic Atlas of Early Human Craniofacial Development||Talk||Gordon Conference: Craniofacial Morphogenesis||2018||Luca, Italy|
|High Resolution Epigenomic Atlas of Early Human Craniofacial Development||Talk||American Society for Human Genetics||2018||San Diego, CA|
|Epigenomic Annotation of Early Human Craniofacial Development||Talk||ISG Computational Biology Core Open House||2018||Storrs|
|Roundtable on Open Science at UConn Library||Panel Discussion||UConn Library||2018||Storrs|
|Functional Genomics Approaches for Understanding Human Developmental Disorders||Talk||Connecticut Childrens' Medical Center||2018||Farmington, CT|
|High Resolution Epigenomic Atlas of Early Human Craniofacial Development||Poster||Cold Spring Harbor Laboratory Biology of Genomes||2017||Cold Spring Harbor, NY|
|High Resolution Epigenomic Atlas of Early Human Craniofacial Development||Poster||Gordon Conference: Epigenomics||2017||Holderness, NH|
|High Resolution Epigenomics in Early Human Craniofacial Development||Talk||UCHC MD/PHD Research Club||2017||Farmington, CT|
|Current Technologies for Studying Chromatin||Lecture||JAXGM ChIA-PET Workshop||2017||Farmington, CT|
|Regulation of autism risk networks by the chromatin remodeler CHD8 during human neurodevelopment||Talk||UConn Autism Workshop||2016||UConn Health|
|Roadmap to Identifying Craniofacial Enhanceropathies||Poster||ASHG 2016||2016||Vancouver, BC, Canada|
|Unlocking the regulome to understand craniofacial disorders and skeletal development||Talk||UConn Musculoskeletal Institute Research Day||2016||Avon, CT|
|Roadmap to identifying craniofacial enhanceropathies||Talk||Institute for Systems Genomics Networking Workshop||2016||JAXGM|
|Roadmap to identifying craniofacial enhanceropathies||Talk||Epigenomics Workshop||2016||UCHC|
|Functional Genomics Approaches to Understand Human Development, Evolution, and Disease||Talk||Skeletal Biology and Regeneration Graduate Program and Dept. of Cell Bio.||2016||UCHC|
|Developmental Enhancers: Roles in Human Evolution and Disease||Talk||Regenerative Biology Research in Progress||2015||UCHC|
|Developmental Enhancers: Roles in Human Evolution and Disease||Talk||UCSF Institute for Human Genetics||2014||San Francisco, CA|
|Developmental Enhancers: Roles in Human Evolution and Disease||Talk||UCHC Dept. of Genetics and Genome Sciences||2014||Farmington, CT|
|Developmental Enhancers: Roles in Human Evolution and Disease||Talk||JAX GM||2013||Farmington, CT|
|36th Annual Meeting of the Society of Craniofacial Genetics and Developmental Biology||Talk||Society of Craniofacial Genetics and Developmental Biology||2013||Boston, MA|
|3rd Kavli Community Symposium||Talk||Kavli Community Symposium||2013||Trondheim, NORWAY|
|Gordon Research Seminar: Human Genetics and Genomics||Talk||Gordon Research Seminar||2013||Smithfield, RI|
|Yale Center for Genome Analysis||Talk||Yale School of Medicine||2013||New Haven, CT|
|The evolution of lineage-specific regulatory activities in the human embryonic limb||Poster||Gordon Research Conference: Human Genetics and Genomics||2013||Smithfield, RI|
|The evolution of lineage-specific regulatory activities in the human embryonic limb||Poster||Biology of Genomes, Cold Spring Harbor Laboratory||2013||Cold Spring Harbor, NY|
|Illumina Northeast User Meeting||Talk||Illumina Northeast User Meeting||2012||New Haven, CT|
|Enhancers maintain a constitutive open chromatin state independent of tissue-specific activity during embryonic development||Poster||Systems Biology, Cold Spring Harbor Laboratory||2012||Cold Spring Harbor, NY|
|Chromatin state transitions identify tissue-specific regulatory elements and predict gene expression gradients during mammalian embryonic development||Poster||Biology of Genomes, Cold Spring Harbor Laboratory||2011||Cold Spring Harbor, NY|
|Control of embryonic limb development through changes in global chromatin organization and gene expression||Poster||Systems Biology, Cold Spring Harbor Laboratory||2010||Cold Spring Harbor, NY|
|Mitochondria contain two members of a dual-function class of proteins that dynamically regulate mitochondrial gene expression||Poster||Nucleic Acids Enzymes, Keystone Symposium||2006||Taos, NM|
|Probing the molecular basis of the substrate and inhibitor specificities of cholinesterase 1 and cholinesterase 2 from amphioxus||Poster||Experimental Biology||2002||New Orleans, LA|