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Justin L Cotney, PhD
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Associate Professor of Genomic Science in Surgery
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Member, UPenn Cardiovascular Institute
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Department: Surgery
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Graduate Group Affiliations
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Contact information
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Division of Plastic Surgery
2d Children’s Hospital of Philadelphia
30 Hub for Clinical Collaboration, 11th Fl.
3a 3500 Civic Center Blvd.
Philadelphia, PA 19104
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2d Children’s Hospital of Philadelphia
30 Hub for Clinical Collaboration, 11th Fl.
3a 3500 Civic Center Blvd.
Philadelphia, PA 19104
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Fax: 215-590-5490
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Email:
cotneyj@chop.edu
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cotneyj@chop.edu
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Publications
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Links
b7 Search PubMed for articles
6f Cardiac resources
57 Github resources
7a Craniofacial resources
92 Craniofacial Bulk Gene Expression
9b Craniofacial Single Cell Gene Expression
8d Cotney Lab Website at the Center for Craniofacial Innovation
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b7 Search PubMed for articles
6f Cardiac resources
57 Github resources
7a Craniofacial resources
92 Craniofacial Bulk Gene Expression
9b Craniofacial Single Cell Gene Expression
8d Cotney Lab Website at the Center for Craniofacial Innovation
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Education:
21 7 BS 14 (Biology) c
44 Birmingham-Southern College, Birmingham, AL, 2002.
21 8 PhD 2b (Genetics and Molecular Biology) c
36 Emory University, Atlanta, GA, 2008.
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Permanent link21 7 BS 14 (Biology) c
44 Birmingham-Southern College, Birmingham, AL, 2002.
21 8 PhD 2b (Genetics and Molecular Biology) c
36 Emory University, Atlanta, GA, 2008.
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190 We use a variety of functional genomics techniques including ChIP-Seq, RNA-Seq, ATAC-Seq, and HiC at both bulk and single cell levels to identify gene regulatory networks active during human organogenesis. We integrate this data with a variety of public datasets including transcriptomic (GTEx), epigenomic (Roadmap Epigenome, ENCODE), and genetic resources (UKBB, All Of Us, DECIPHER, GMKF).
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b9 We model our findings in culture models of human development including Neural Crest and cardiac organoids as well as mice and zebrafish (collaboration with Dr. Eric Liao's lab).
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b5 We aim to provide a better understanding of rare variation in noncoding regions and identify additional disease causing genes related to craniofacial and cardiac development.
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Description of Research Expertise
190 The Cotney Lab is interested in determining how gene regulatory elements, also known as enahancers, 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.8
190 We use a variety of functional genomics techniques including ChIP-Seq, RNA-Seq, ATAC-Seq, and HiC at both bulk and single cell levels to identify gene regulatory networks active during human organogenesis. We integrate this data with a variety of public datasets including transcriptomic (GTEx), epigenomic (Roadmap Epigenome, ENCODE), and genetic resources (UKBB, All Of Us, DECIPHER, GMKF).
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b9 We model our findings in culture models of human development including Neural Crest and cardiac organoids as well as mice and zebrafish (collaboration with Dr. Eric Liao's lab).
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b5 We aim to provide a better understanding of rare variation in noncoding regions and identify additional disease causing genes related to craniofacial and cardiac development.
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162 Khouri-Farah N, Winchester EW, Schilder BM, Robinson K, Curtis SW, Skene NG, Leslie-Clarkson EJ, Cotney J.: Gene expression patterns of the developing human face at single cell resolution reveal cell type contributions to normal facial variation and disease risk. bioRxiv Feb 2025.
24e Li Q, Faux P, Wentworth Winchester E, Yang G, Chen Y, Ramírez LM, Fuentes-Guajardo M, Poloni L, Steimetz E, Gonzalez-José R, Acuña V, Bortolini MC, Poletti G, Gallo C, Rothhammer F, Rojas W, Zheng Y, Cox JC, Patel V, Hoffman MP, Ding L, Peng C, Cotney J, Navarro N, Cox TC, Delgado M, Adhikari K, Ruiz-Linares A: PITX2 expression and Neanderthal introgression in HS3ST3A1 contribute to variation in tooth dimensions in modern humans. Current Biology 35: 131-144, Jan. 12 2025 Notes: doi: 10.1016/j.cub.2024.11.027.
14d Curtis SW, Cook LE, Paraiso K, Visel A, Cotney JL, Murray JC, Beaty TH, Marazita ML, Carlson JC, Leslie-Clarkson EJ.: Functional Annotation of De Novo Variants Found Near GWAS Loci Associated With Cleft Lip With or Without Cleft Palate. Birth Defects Res 2025.
16a Gilmore RB, Liu Y, Stoddard CE, Chung MS, Carmichael GG, Cotney J: Identifying key underlying regulatory networks and predicting targets of orphan C/D box SNORD116 snoRNAs in Prader-Willi syndrome. Nucleic Acids Research Nov. 22 2024 (Epub) Notes: Preprint article in bioRxiv Oct. 5, 2023.
15a Piña JO, Raju R, Roth DM, Winchester EW, Padilla C, Iben J, Faucz FR, Cotney JL, D'Souza RN: Spatial Multi-omics Reveals the Role of the Wnt Modulator, Dkk2, in Palatogenesis' Journal of Dental Research June 23 2024 (Epub) Notes: Preprint article in bioRxiv Feb. 28, 2024.
142 Khan NM, Wilderman A, Kaiser JM, Kamalakar A, Goudy SL, Cotney J, Drissi H: Enhanced osteogenic potential of iPSC-derived mesenchymal progenitor cells following genome editing of GWAS variants in the RUNX1 gene. Bone Research 12(1): 70, Dec. 6 2024.
161 Gilmore RB, Gorka D, Stoddard CE, Cotney JL, Chamberlain SJ: Generation of isogenic models of Angelman syndrome and Prader-Willi syndrome in CRISPR/Cas9-engineered human embryonic stem cells. PLoS One 19(11): e0311565, Nov. 1 2024 Notes: Preprint article in bioRxiv Aug. 30, 2023.
154 Vihma H, Li K, Welton-Arndt A, Smith AL, Bettadapur KR, Gilmore RB, Gao E, Cotney JL, Huang HC, Collins JL, Chamberlain SJ, Lee HM, Aubé J, Philpot BD: Ube3a unsilencer for the potential treatment of Angelman syndrome. Nature Communications 15(1): 5558, July 8 2024.
1f2 Alade A, Mossey P, Awotoye W, Busch T, Oladayo A, Aladenika E, Olujitan M, Gowans JJL, Eshete MA, Adeyemo WL, Zeng E, Otterloo E, O'Rorke M, Adeyemo A, Murray JC, Cotney J, Lachke SA, Romitti P, Butali A, Wentworth E, Anand D, Naicker T: Rare variants analyses suggest novel cleft genes in the African population. Science Reports 14(1): 14279, June 20 2024 Notes: Preprint article published via Research Square Feb. 27, 2024.
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Selected Publications
172 Lavický J, Lopez MG, Chochola V, Kompaníková P, Rakultsev V, Raška J, Winchester EW, Tuaima H, Englmaier L, Verner J, Švandová E, Buchtová M, Cotney J, Bryja V, Bohačiaková D, Bárta T, Krivanek J.: Unraveling the Transcription Factor Code of Odontoblast Differentiation. J Dent Res 2026.162 Khouri-Farah N, Winchester EW, Schilder BM, Robinson K, Curtis SW, Skene NG, Leslie-Clarkson EJ, Cotney J.: Gene expression patterns of the developing human face at single cell resolution reveal cell type contributions to normal facial variation and disease risk. bioRxiv Feb 2025.
24e Li Q, Faux P, Wentworth Winchester E, Yang G, Chen Y, Ramírez LM, Fuentes-Guajardo M, Poloni L, Steimetz E, Gonzalez-José R, Acuña V, Bortolini MC, Poletti G, Gallo C, Rothhammer F, Rojas W, Zheng Y, Cox JC, Patel V, Hoffman MP, Ding L, Peng C, Cotney J, Navarro N, Cox TC, Delgado M, Adhikari K, Ruiz-Linares A: PITX2 expression and Neanderthal introgression in HS3ST3A1 contribute to variation in tooth dimensions in modern humans. Current Biology 35: 131-144, Jan. 12 2025 Notes: doi: 10.1016/j.cub.2024.11.027.
14d Curtis SW, Cook LE, Paraiso K, Visel A, Cotney JL, Murray JC, Beaty TH, Marazita ML, Carlson JC, Leslie-Clarkson EJ.: Functional Annotation of De Novo Variants Found Near GWAS Loci Associated With Cleft Lip With or Without Cleft Palate. Birth Defects Res 2025.
16a Gilmore RB, Liu Y, Stoddard CE, Chung MS, Carmichael GG, Cotney J: Identifying key underlying regulatory networks and predicting targets of orphan C/D box SNORD116 snoRNAs in Prader-Willi syndrome. Nucleic Acids Research Nov. 22 2024 (Epub) Notes: Preprint article in bioRxiv Oct. 5, 2023.
15a Piña JO, Raju R, Roth DM, Winchester EW, Padilla C, Iben J, Faucz FR, Cotney JL, D'Souza RN: Spatial Multi-omics Reveals the Role of the Wnt Modulator, Dkk2, in Palatogenesis' Journal of Dental Research June 23 2024 (Epub) Notes: Preprint article in bioRxiv Feb. 28, 2024.
142 Khan NM, Wilderman A, Kaiser JM, Kamalakar A, Goudy SL, Cotney J, Drissi H: Enhanced osteogenic potential of iPSC-derived mesenchymal progenitor cells following genome editing of GWAS variants in the RUNX1 gene. Bone Research 12(1): 70, Dec. 6 2024.
161 Gilmore RB, Gorka D, Stoddard CE, Cotney JL, Chamberlain SJ: Generation of isogenic models of Angelman syndrome and Prader-Willi syndrome in CRISPR/Cas9-engineered human embryonic stem cells. PLoS One 19(11): e0311565, Nov. 1 2024 Notes: Preprint article in bioRxiv Aug. 30, 2023.
154 Vihma H, Li K, Welton-Arndt A, Smith AL, Bettadapur KR, Gilmore RB, Gao E, Cotney JL, Huang HC, Collins JL, Chamberlain SJ, Lee HM, Aubé J, Philpot BD: Ube3a unsilencer for the potential treatment of Angelman syndrome. Nature Communications 15(1): 5558, July 8 2024.
1f2 Alade A, Mossey P, Awotoye W, Busch T, Oladayo A, Aladenika E, Olujitan M, Gowans JJL, Eshete MA, Adeyemo WL, Zeng E, Otterloo E, O'Rorke M, Adeyemo A, Murray JC, Cotney J, Lachke SA, Romitti P, Butali A, Wentworth E, Anand D, Naicker T: Rare variants analyses suggest novel cleft genes in the African population. Science Reports 14(1): 14279, June 20 2024 Notes: Preprint article published via Research Square Feb. 27, 2024.
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