Current Preprints and Manuscripts:

  1. Curtis SW, Carlson JC, Beaty TH, Murray JC, Weinberg SM, Marazita ML, Cotney JL, Cutler DJ, Epstein MP, Leslie EJ. Rare genetic variants in SEC24D modify orofacial cleft phenotypes. medRxiv [Preprint]. 2023 Mar 27:2023.03.24.23287714. doi: 10.1101/2023.03.24.23287714. PMID: 37034635; PMCID: PMC10081436.
  2. Oliver Piña J, Roth DM, Raju R, Winchester EW, Chattaraj P, Kidwai F, Faucz FR, Iben J, Padilla C, Cotney JL, D'Souza RN. Dkk2 interacts with Pax9 in palate mesenchyme to pattern and tune osteogenesis. bioRxiv [Preprint]. 2023 May 17:2023.05.16.541037. doi: 10.1101/2023.05.16.541037. PMID: 37292772; PMCID: PMC10245699.
  3. Andrea WildermanEva D'haeneMachteld Baetens, Tara N. Yankee, Emma Wentworth Winchester, Nicole GliddenEllen RoetsJo Van DorpeSarah VergultTimothy C. CoxJustin Cotney. A distant global control region is essential for normal expression of anterior HOXA genes during mouse and human craniofacial development.
  4. Geller E, Gockley J, Emera D, Uebbing S, Cotney J, Noonan JP. Massively parallel disruption of enhancers active during human corticogenesis. In Revision. bioRxiv 2019:852673.
  5. Rachel B. Gilmore, Dea Gorka, Christopher E. Stoddard, Justin L. Cotney, Stormy J. Chamberlain. Generation of isogenic models of Angelman syndrome and Prader-Willi syndrome in CRISPR/Cas9-engineered human embryonic stem cells. bioRxiv 2023.08.30.555563; doi:

Peer Reviewed Articles:

  1. Curtis SW, Carlson JC, Beaty TH, Murray JC, Weinberg SM, Marazita ML, Cotney JL, Cutler DJ, Epstein MP, Leslie EJ. Rare variant modifier analysis identifies variants in SEC24D associated with orofacial cleft subtypes. Hum Genet. 2023 Oct;142(10):1531-1541. doi: 10.1007/s00439-023-02596-4. Epub 2023 Sep 7. PMID: 37676273.
  2. Piña JO, Raju R, Roth DM, Winchester EW, Chattaraj P, Kidwai F, Faucz FR, Iben J, Mitra A, Campbell K, Fridell G, Esnault C, Cotney JL, Dale RK, D'Souza RN. Multimodal spatiotemporal transcriptomic resolution of embryonic palate osteogenesis. Nat Commun. 2023 Sep 14;14(1):5687. doi: 10.1038/s41467-023-41349-9. PMID: 37709732; PMCID: PMC10502152.
  3. Yankee TN, Oh S, Winchester EW, Wilderman A, Robinson K, Gordon T, Rosenfeld JA, VanOudenhove J, Scott DA, Leslie EJ, Cotney J. Integrative analysis of transcriptome dynamics during human craniofacial development identifies candidate disease genes. Nat Commun. 2023 Aug 2;14(1):4623. doi: 10.1038/s41467-023-40363-1. PMID: 37532691; PMCID: PMC10397224.
  4. Winchester EW, Hardy A, Cotney J. Integration of multimodal data in the developing tooth reveals candidate regulatory loci driving human odontogenic phenotypes. Front Dent Med. 2022;3:1009264. doi: 10.3389/fdmed.2022.1009264. Epub 2022 Nov 30. PMID: 37034481; PMCID: PMC10078798.
  5. Yoon B, Yeung P, Santistevan N, Bluhm L, Kawasaki K, Kueper J, Dubielzig R, Vanoudenhove J, Cotney J, Liao EC, Grinblat Y. Zebrafish models of Alx-linked frontonasal dysplasia reveal a role for Alx1 and Alx3 in the anterior segment and vasculature of the developing eye. Biol Open2022 Feb 10;doi: 10.1242/bio.059189. [Epub ahead of print] PubMed PMID: 35142342.
  6. Welzenbach J, Hammond NL, Nikolić M, Thieme F, Ishorst N, Leslie EJ, Weinberg SM, Beaty TH, Marazita ML, Mangold E, Knapp M, Cotney J, Rada-Iglesias A, Dixon MJ, Ludwig KU. Integrative approaches generate insights into the architecture of non-syndromic cleft lip with or without cleft palate. HGG Adv2021 Jul 8;2(3):100038doi: 10.1016/j.xhgg.2021.100038. eCollection 2021 Jul 8. PubMed PMID: 35047836; PubMed Central PMCID: PMC8756534.
  7. Pettinato AM, Yoo D, VanOudenhove J, Chen YS, Cohn R, Ladha FA, Yang X, Thakar K, Romano R, Legere N, Meredith E, Robson P, Regnier M, Cotney JL, Murry CE, Hinson JT. Sarcomere function activates a p53-dependent DNA damage response that promotes polyploidization and limits in vivo cell engraftment. Cell Rep2021 May 4;35(5):109088doi: 10.1016/j.celrep.2021.109088. PubMed PMID: 33951429; PubMed Central PMCID: PMC8161465.
  8. Betty Bonfante, Pierre Faux, Nicolas Navarro, Javier Mendoza-Revilla, Morgane Dubied, Charlotte Montillot, E Wentworth, Lauriane Poloni, Ceferino Váron González, Phil Jones, Macarena Fuentes-Guajardo, Juan Camilo Chacón-Duque,Malena Hurtado, Valeria Villegas, Vanessa Granja, Victor Acuña-Alonzo, ClaudiaJaramillo, William Arias, Rodrigo Barquera Lozano, Paola Everardo, Jorge Gómez-Valdés, Hugo Villamil-Ramírez, Caio C. Silva de Cerqueira, Tábita Hunemeier, Virginia Ramallo, Lavinia Schuler-Faccini, Francisco M. Salzano, Rolando Gonzalez-José, Maria-Cátira Bortolini, Samuel Canizales-Quinteros, Carla Gallo, GiovanniPoletti, Gabriel Bedoya, Francisco Rothhammer, Christel Thauvin, Laurence Faivre, Caroline Costedoat, David Balding, Timothy Cox, Manfred Kayser, Laurence Duplomb, Binnaz Yalcin, J Cotney, Kaustubh Adhikariand Andrés Ruiz-Linares. A GWAS in Latin Americans implicates a region of Denisovan introgression and VPS13B in facial variation. SCIENCE ADVANCES.  : EABC6160.
  9. Severin Uebbing, Jake Gockley, Steven K. Reilly, Acadia A. Kocher, Evan Geller, Neeru Gandotra, Curt Scharfe, Justin Cotney, James P. Noonan. Massively parallel discovery of human-specific substitutions that alter neurodevelopmental enhancer activity.
  10. Shannon H. Carroll, Claudio Macias Trevino, Edward B. Li, Kenta Kawasaki, Nikita Myers, Shawn A. Hallett, Nora Alhazmi, Justin Cotney, Russ P. Carstens, Eric C. Liao. An Irf6-Esrp1/2 regulatory axis controls midface morphogenesis in vertebrates.
  11. Langouët M, Gorka D, Orniacki C, Dupont-Thibert CM, Chung MS, Glatt-Deeley HR, et al. Specific ZNF274 binding interference at SNORD116 activates the maternal transcripts in Prader-Willi syndrome neurons. Human Molecular Genetics. Volume 29, Issue 19, 1 October 2020, Pages 3285–3295.
  12. Pini J, Kueper J, Hu YD, Kawasaki K, Yeung P, Tsimbal C, et al. ALX1-related Frontonasal Dysplasia Results From Defective Neural Crest Cell Development and Migration. EMBO Molecular Medicine. 2020 Sept. 11.
  13. VanOudenhove J, Yankee T, Wilderman A, Cotney J. Epigenomic and transcriptomic dynamics identify coordinated networks of genes and cardiac disease relevant loci during human heart organogenesis. Circulation Research. 2020;127:e184–e209 doi: 10.1161/CIRCRESAHA.120.316704.
    1. Editorial in Circulation Research:
    2. Coverage by UConn Today:
    3. Coverage in Science Daily:
  14. Sharma T, Cotney J, Singh V, Sanjay A, Reichenberger EJ, Ueki Y, et al. Investigating global gene expression changes in a murine model of cherubism. Bone 2020;135::115315.
  15. TA Stewart, C Liang, JL Cotney, JP Noonan, TJ Sanger, GP Wagner.Evidence against tetrapod-wide digit identities and for a limited frame shift in bird wings.Nature communications 10 (1), 3244
  16. JS. HsiaoND GermainA WildermanC Stoddard, LA WojenskiGJ VillafanoL CoreJ CotneySJ Chamberlain. A bipartite boundary element restricts UBE3A imprinting to mature neurons. Proceedings of the National Academy of Sciences 116 (6), 2181-2186.
  17. Blankvoort S, Witter MP, Noonan JP, Cotney J*, Kentros C*. Marked Diversity of Unique Cortical Enhancers Enables Neuron-Specific Tools by Enhancer-Driven Gene Expression. Current Biology  * Corresponding authors.
  18. Wilderman A, VanOudenhove J, Kron J, Noonan JP, Cotney J. High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development. Cell Reports. Vol 23:5, p1581-1597, May 1, 2018.
    1. Coverage by UConn Today: Blueprint for the skull
    2. Coverage in Science Daily: A search for cleft palate's cause reveals a map of the facial genome.
  19. Kalsner L, Twachtman-Bassett J, Tokarski K, Stanley C, Dumont-Mathieu T, Cotney J, Chamberlain S. Genetic testing including targeted gene panel in a diverse clinical population of children with autism spectrum disorder: Findings and implications. Mol Genet Genomic Med. 5 ed. 2017 Dec 21;82(1):150.
  20. Oran AR, Adams CM, Zhang X-Y, Gennaro VJ, Pfeiffer HK, Mellert HS, Seidel H, Masicoli K, Kaplan J, Gaballa M, Shen C, Rigoutsos I, King M, Cotney J, et al. Multi-focal control of mitochondrial gene expression by oncogenic MYC provides potential therapeutic targets in cancer. Oncotarget. Impact Journals; 2016 Aug 31;7(45):72395–414.
  21. Cotney J, Muhle RA, Sanders SJ, Liu L, Willsey AJ, Niu W, et al. The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment. Nature Communications. 2015;6:6404.
  22. Reilly SK, Yin J, Ayoub AE, Emera D, Leng J, Cotney J, et al. Evolutionary genomics. Evolutionary changes in promoter and enhancer activity during human corticogenesis. Science. 2015 Mar 6;347(6226):1155–9.
  23. Cotney JL, Noonan JP. Chromatin immunoprecipitation with fixed animal tissues and preparation for high-throughput sequencing. Cold Spring Harb Protoc. Cold Spring Harbor Laboratory Press; 2015;2015(2):pdb.prot084848.
  24. Willsey AJ, Sanders SJ, Li M, Dong S, Tebbenkamp AT, Muhle RA, Reilly SK, Lin L, Fertuzinhos S, Miller JA, Murtha MT, Bichsel C, Niu W, Cotney J, (16 additional authors), Noonan JP, Roeder K, Devlin B, Sestan N, State MW. (2013). Co-expression networks implicate human mid-fetal deep cortical projection neurons in the pathogenesis of autism. Cell 155, 1008-1021.
  25. Cotney, J.*, Leng, J.*, Yin, J., Reilly, S.K., Demare, L.E., Emera, D., Ayoub, A.E., Rakic, P., and Noonan, J.P. (2013). The evolution of lineage-specific regulatory activities in the human embryonic limb. Cell 154, 185–196.
    1. Commentary in Nature News & Views: Flicek, P. (2013) Evolutionary biology: The handiwork of tinkering. Nature 500: 158-159.
  26. Demare, L.E., Leng, J., Cotney, J., Reilly, S.K., Yin, J., Sarro, R., and Noonan, J.P. (2013). The genomic landscape of cohesin-associated chromatin interactions. Genome Res 23, 1224–1234.
  27. Clark VE, Erson-Omay EZ, Serin A, Yin J, Cotney J, Ozduman K, Avşar T, Li J, Murray PB, Henegariu O, et al. 2013. Genomic analysis of non-NF2 meningiomas reveals mutations in TRAF7, KLF4, AKT1, and SMO. Science 339: 1077–1080.
  28. Bandyopadhyay U*, Cotney J*, Nagy M, Oh S, Leng J, Mahajan M, Mane S, Fenton WA, Noonan JP, Horwich AL. 2013. RNA-Seq Profiling of Spinal Cord Motor Neurons from a Presymptomatic SOD1 ALS Mouse. PLoS ONE 8: e53575.
  29. Cotney J, Leng J, Oh S, Demare LE, Reilly SK, Gerstein MB, and Noonan JP. 2012. Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb. Genome Res 22: 1069–1080.
  30. Raimundo N, Song L, Shutt TE, McKay SE, Cotney J, Guan M-X, Gilliland TC, Hohuan D, Santos-Sacchi J, and Shadel GS. 2012. Mitochondrial stress engages E2F1 apoptotic signaling to cause deafness. Cell 148: 716–726.
  31. Surovtseva YV, Shutt TE, Cotney J, Cimen H, Chen SY, Koc EC, and Shadel GS. 2011. Mitochondrial ribosomal protein L12 selectively associates with human mitochondrial RNA polymerase to activate transcription. Proc Natl Acad Sci USA 108: 17921–17926.
  32. Ayoub AE, Oh S, Xie Y, Leng J, Cotney J, Dominguez MH, Noonan JP, and Rakic P. 2011. Transcriptional programs in transient embryonic zones of the cerebral cortex defined by high-resolution mRNA sequencing. Proc Natl Acad Sci USA 108: 14950–14955.
  33. Shutt TE, Lodeiro MF, Cotney J, Cameron CE, and Shadel GS. 2010. Core human mitochondrial transcription apparatus is a regulated two-component system in vitro. Proc Natl Acad Sci USA 107: 12133–12138.
  34. Cotney J, McKay SE, and Shadel GS. 2009. Elucidation of separate, but collaborative functions of the rRNA methyltransferase-related human mitochondrial transcription factors B1 and B2 in mitochondrial biogenesis reveals new insight into maternally inherited deafness. Hum Mol Genet 18: 2670–2682.
  35. Cotney J, Wang Z, and Shadel GS. 2007. Relative abundance of the human mitochondrial transcription system and distinct roles for h-mtTFB1 and h-mtTFB2 in mitochondrial biogenesis and gene expression. Nucleic Acids Res 35: 4042–4054.
  36. Wang Z, Cotney J, and Shadel GS. 2007. Human mitochondrial ribosomal protein MRPL12 interacts directly with mitochondrial RNA polymerase to modulate mitochondrial gene expression. J Biol Chem 282: 12610–12618.
  37. Cotney J, and Shadel GS. 2006. Evidence for an early gene duplication event in the evolution of the mitochondrial transcription factor B family and maintenance of rRNA methyltransferase activity in human mtTFB1 and mtTFB2. J Mol Evol 63: 707–717.
  38. Pezzementi L, Johnson K, Cotney J, Barker A, and Manning E. Amino acids involved in substrate and inhibitor specificity in cholinesterase 2 from amphioxus. Cholinesterases in the Second Millennium: Biomolecular and Pathological Aspects, (N.C. Inestrosa and E.O. Campos, eds.), 2004. MIFAB: Santiago, Chile, pp. 223-224.
  39. Pezzementi L, Johnson K, Tsigelny I, Cotney J, Manning E, Barker A, and Merritt S. 2003. Amino acids defining the acyl pocket of an invertebrate cholinesterase. Comp. Biochem. Physiol. B, Biochem. Mol. Biol. 136: 813–832.

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