Photo of Justin L. Cotney, Ph.D.

Justin L. Cotney, Ph.D.

Associate Professor, Genetics and Genome Sciences
Academic Office Location:
Genetics & Genome Sciences
UConn Health
400 Farmington Avenue
Farmington, CT 06030-6403
Phone: 860-679-8579

Cotney Lab Website

Department of Genetics and Genome Sciences

Genetics and Developmental Biology Graduate Program

Skeletal Biology and Regeneration Graduate Program

B.S.Birmingham Southern CollegeBiology
Ph.D.Emory UniversityGenetics & Molecular Biology

Post-Graduate Training
PostdoctoralYale UniversityPostdoctoral Fellow - Snyder Laboratory
PostdoctoralYale University School of MedicinePostdoctoral Fellow - Noonan Laboratory

Name of Award/HonorAwarding Organization
Marylou Buyse Distinguished Scientist in Craniofacial Research AwardSociety for Craniofacial Genetics & Developmental Biology
Rudolph J. Anderson FellowYale University
Name & DescriptionCategoryRoleTypeScopeStart YearEnd Year
Research Advisory Board of Shriners Hospitals for ChildrenAdvisory CommitteeMemberExternalNational20182023
Genetics and Developmental Biology Area of ConcentrationAssistant DirectorUConn HealthUniversity2018
Graduate Student Admission CommitteeCommunity ServiceMemberUConn HealthUniversity20182020
American Society for Human GeneticsProfessional/Scientific OrganizationExternalNational2014
Society of Craniofacial Genetics and Developmental BiologyProfessional/Scientific OrganizationExternalNational2013
American Association for the Advancement of ScienceProfessional/Scientific OrganizationExternalNational2002
NIH Genetics of Health and Disease Study SectionStudy SectionReviewerExternalNational

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

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.

Journal Articles

Title or AbstractTypeSponsor/EventDate/YearLocation
Lecture for 2023 Marylou Buyse Distinguished Scientist in Craniofacial Research AwardPlenary LectureSociety for Craniofacial Genetics and Developmental Biology2023Cincinnati, OH
Multiomics approaches to understand human developmental abnormalitiesLectureCincinnati Children's Hospital Medical Center2022Cincinnati, OH
Multiomics approaches to understand ?human developmental abnormalitiesLectureBaylor College of Medicine2022Virtual
Developmental enhancers: Substrates for evolution and contributors to disease riskLectureEmory University Genetics and Molecular Biology Graduate Program2022Atlanta, GA
Leveraging functional genomics to understand human craniofacial development and abnormalitiesTalkEmory University Department of Orthopaedics2022Atlanta, GA
Leveraging functional genomics to understand human craniofacial development and abnormalitiesLectureGordon Research Craniofacial Morphogenesis and Tissue Regeneration2022Ventura, CA
Leveraging functional genomics to understand developmental abnormalities and human diseaseTalkUniversity of Kansas Medical Center Dept. of Anatomy2021Virtual
Leveraging functional genomics to understand human developmental abnormalitiesTalkEmory University School of Medicine Dept. of Human Genetics2021Virtual
Leveraging functional genomics to understand human craniofacial development and abnormalitiesTalkUniversity of Missouri Kansas City Dept. of Oral and Craniofacial Sciences2021Virtual
A distant locus control region of the HoxA gene cluster has unique superenhancer properties and is essential for normal craniofacial development and viability.Plenary LectureEMBO Enhanceropathies2021Santander, Spain
Single cell epigenomics of craniofacial development reveal cell type specific cis-regulatory sequencesPosterGordon Research Conference on Craniofacial Morphogenesis2020Barga, Italy
Functional genomics approaches for uncovering the role of regulatory sequences in developmental abnormalities and diseasePlenary LectureEuropean Society of Human Genetics2019Gothenberg, Sweden
Functional Genomics approaches for Systems NeuroscienceLectureKavli Institute for Neuroscience2019Tromso, Norway
High Throughput Methods for Dissection of Human Craniofacial Cis-RegulomeTalkISG Networking Workshop2018Storrs
High Resolution Epigenomic Atlas of Early Human Craniofacial DevelopmentTalkGordon Conference: Craniofacial Morphogenesis2018Luca, Italy
High Resolution Epigenomic Atlas of Early Human Craniofacial DevelopmentTalkAmerican Society for Human Genetics2018San Diego, CA
Epigenomic Annotation of Early Human Craniofacial DevelopmentTalkISG Computational Biology Core Open House2018Storrs
Roundtable on Open Science at UConn LibraryPanel DiscussionUConn Library2018Storrs
Functional Genomics Approaches for Understanding Human Developmental DisordersTalkConnecticut Childrens' Medical Center2018Farmington, CT
High Resolution Epigenomic Atlas of Early Human Craniofacial DevelopmentPosterCold Spring Harbor Laboratory Biology of Genomes2017Cold Spring Harbor, NY
High Resolution Epigenomic Atlas of Early Human Craniofacial DevelopmentPosterGordon Conference: Epigenomics2017Holderness, NH
High Resolution Epigenomics in Early Human Craniofacial DevelopmentTalkUCHC MD/PHD Research Club2017Farmington, CT
Current Technologies for Studying ChromatinLectureJAXGM ChIA-PET Workshop2017Farmington, CT
Regulation of autism risk networks by the chromatin remodeler CHD8 during human neurodevelopmentTalkUConn Autism Workshop2016UConn Health
Roadmap to Identifying Craniofacial EnhanceropathiesPosterASHG 20162016Vancouver, BC, Canada
Unlocking the regulome to understand craniofacial disorders and skeletal developmentTalkUConn Musculoskeletal Institute Research Day2016Avon, CT
Roadmap to identifying craniofacial enhanceropathiesTalkInstitute for Systems Genomics Networking Workshop2016JAXGM
Roadmap to identifying craniofacial enhanceropathiesTalkEpigenomics Workshop2016UCHC
Functional Genomics Approaches to Understand Human Development, Evolution, and DiseaseTalkSkeletal Biology and Regeneration Graduate Program and Dept. of Cell Bio.2016UCHC
Developmental Enhancers: Roles in Human Evolution and DiseaseTalkRegenerative Biology Research in Progress2015UCHC
Developmental Enhancers: Roles in Human Evolution and DiseaseTalkUCSF Institute for Human Genetics2014San Francisco, CA
Developmental Enhancers: Roles in Human Evolution and DiseaseTalkUCHC Dept. of Genetics and Genome Sciences2014Farmington, CT
Developmental Enhancers: Roles in Human Evolution and DiseaseTalkJAX GM2013Farmington, CT
36th Annual Meeting of the Society of Craniofacial Genetics and Developmental BiologyTalkSociety of Craniofacial Genetics and Developmental Biology2013Boston, MA
3rd Kavli Community SymposiumTalkKavli Community Symposium2013Trondheim, NORWAY
Gordon Research Seminar: Human Genetics and GenomicsTalkGordon Research Seminar2013Smithfield, RI
Yale Center for Genome AnalysisTalkYale School of Medicine2013New Haven, CT
The evolution of lineage-specific regulatory activities in the human embryonic limbPosterGordon Research Conference: Human Genetics and Genomics2013Smithfield, RI
The evolution of lineage-specific regulatory activities in the human embryonic limbPosterBiology of Genomes, Cold Spring Harbor Laboratory2013Cold Spring Harbor, NY
Illumina Northeast User MeetingTalkIllumina Northeast User Meeting2012New Haven, CT
Enhancers maintain a constitutive open chromatin state independent of tissue-specific activity during embryonic developmentPosterSystems Biology, Cold Spring Harbor Laboratory2012Cold Spring Harbor, NY
Chromatin state transitions identify tissue-specific regulatory elements and predict gene expression gradients during mammalian embryonic developmentPosterBiology of Genomes, Cold Spring Harbor Laboratory2011Cold Spring Harbor, NY
Control of embryonic limb development through changes in global chromatin organization and gene expressionPosterSystems Biology, Cold Spring Harbor Laboratory2010Cold Spring Harbor, NY
Mitochondria contain two members of a dual-function class of proteins that dynamically regulate mitochondrial gene expressionPosterNucleic Acids Enzymes, Keystone Symposium2006Taos, NM
Probing the molecular basis of the substrate and inhibitor specificities of cholinesterase 1 and cholinesterase 2 from amphioxusPosterExperimental Biology2002New Orleans, LA