Publications

Author(s)Link to PublicationYearJournal
Moquin, SA, Thomas, S,* Whalen, S, Warburton, A, Fernandez SG,* McBride AA, Pollard, KS, Miranda, JJL.The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation2018J Virol. 2018 Feb 1; 92(3): e01413- PMID: 29142137 PMCID: PMC5774889.
Barbosa M, Joshi RS, Garg P, Martin-Trujillo A, Patel N, et al.Identification of rare de novo epigenetic variations in congenital disorders.2018bioRxiv Jan.19, 2018
Manheimer KB, Richter F, Edelmann LJ, D'Souza SL, Shi L, Shen Y, Homsy J, Boskovski MT, Tai AC, Gorham J, Yasso C, Goldmuntz E, Brueckner M, Lifton RP, Chung WK, Seidman CE, Seidman JG, Gelb BD.Robust identification of mosaic variants in congenital heart disease2018Hum Genet. 2018 Feb;137(2):183-193. PMID: 29417219.
Hoang TT, Goldmuntz E, Roberts AE, Chung WK, Kline JK, et al. The Congenital Heart Disease Genetic Network Study: Cohort description. 2018PLoS One. 2018 Jan 19;13(1):e0191319. PMID:29351346 PMC5774789.
Manheimer, KB; Patel, N; Richter, F; Gorham, J; Tai, AC; Homsy, J; Boskovski, MT; Parfenov, M; Goldmuntz, E; Chung, WK; Brueckner, M; Tristani-Firouzi, M; Srivastava, D; Seidman, JG; Seidman CE; Gelb BD; Sharp AJ. Robust identification of deletions in exome and genome sequence data based on clustering of Mendelian errors.2018Hum Mutat. 2018 Jun;39(6):870-881. PMID: 29527824.
Dickel DE, Ypsilanti AR, Pla R, Zhu Y, Barozzi I, Mannion BJ, Khin YS, Fukuda-Yuzawa Y, Plajzer-Frick I, Pickle CS, Lee EA, Harrington AN, Pham QT, Garvin TH, Kato M, Osterwalder M, Akiyama JA, Afzal V, Rubenstein JLR, Pennacchio LA, Visel A. Ultraconserved Enhancers Are Required for Normal Development. 2018Cell. 2018 Jan 25;172(3):491-499. PMID:29358049 PMC5786478.
Matsunami N, Shanmugam H, Baird L, Stevens J, Byrne JL, Barnhart DC, Rau C, Feldkamp ML, Yoder BA, Leppert MF, Yost HJ, Brunelli L. Germline but not somatic de novo mutations are common in human congenital diaphragmatic hernia. 2018Birth Defects Res. 2018 Apr 17;110(7):610-617. PMID:29570242 PMC5903934.
Sun X, Hota SK, Zhou YQ, Novak S, Miguel-Perez D, Christodoulou D, Seidman CE, Seidman JG, Gregorio CC, Henkelman RM, Rossant J, Bruneau BG. Cardiac enriched BAF chromatin remodeling complex subunit Baf60c regulates gene expression programs essential for heart development and function.2018Biol Open. 2018 Jan 5;7(1). PMID:29183906 PMC5829499.
Martinelli S, Krumbach OHF, Pantaleoni F, Coppola S, Amin E, Pannone L, Nouri K, Farina L, Dvorsky R, Lepri F, Buchholzer M, Konopatzki R, Walsh L, Payne K, Pierpont ME, Vergano SS, Langley KG, Larsen D, Farwell KD, Tang S, Mroske C, Gallotta I, Di Schiavi E, Della Monica M, Lugli L, Rossi C, Seri M, Cocchi G, Henderson L, Baskin B, Alders M, Mendoza-Londono R, Dupuis L, Nickerson DA, Chong JX; University of Washington Center for Mendelian Genomics, Meeks N, Brown K, Causey T, Cho MT, Demuth S, Digilio MC, Gelb BD, Bamshad MJ, Zenker M, Ahmadian MR, Hennekam RC, Tartaglia M, Mirzaa GM.Functional Dysregulation of CDC42 Causes Diverse Developmental Phenotypes2018Am J Hum Genet. 2018 Jan 17. PMID: 29394990 PMCID: 5985417.
Gorsi B, Mosbruger T, Smith M, Hill JT, Yost HJ. Nkx2.5-dependent alterations of the embryonic heart DNA methylome identify novel cis-regulatory elements in cardiac development2017bioRxiv. 2017 doi:10.1101/186395.
Agopian AJ, Goldmuntz E, Hakonarson H, Sewda A, Taylor D, Mitchell LE Genome-Wide Association Studies and Meta-Analyses for Congenital Heart Defects2017Circ Cardiovasc Genet. 2017;10:e001449
Lyozin GT, Kosaka Y, Bhattacharje G, Yost HJ, Brunelli L. Direct Isolation of Seamless Mutant Bacterial Artificial Chromosomes2017Curr Protoc Mol Biol. 2017 Apr 3;118:8.6.1-8.6.29. doi: 10.1002/cpmb.34. PMID: 28369677
Nora EP, Goloborodko A, Volton AL, Gibcus J, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG  Targeted degradation of CTCF decouples local insulation of chromosome domains from higher-order genomic compartmentalization2017Cell Volume 169, Issue 5, p930–944.e22, 18 May 2017
Shankaran SS, Dahlem TJ, Bisgrove BW, Yost HJ, Tristani-Firouzi M CRISPR/Cas9-Directed Gene Editing for the Generation of Loss-of-Function Mutants in High-Throughput Zebrafish F0 Screens2017Curr Protoc Mol Biol. 2017 Jul 5;119:31.9.1-31.9.22. doi: 10.1002/cpmb.42. PMID: 28678442
Chen J, Fu Y, Day DS, Sun Y, Wang S, Liang, X, et al VEGF amplifies transcription through ETS1 acetylation to enable angiogenesis2017Nat Commun. 2017 Aug 29;8(1):383
Hill JT, Demarest B, Gorsi B, Smith M, Yost HJ. Heart morphogenesis gene regulatory networks revealed by temporal expression analysis.2017Development. 2017 Aug 14. pii: dev.154146. doi: 10.1242/dev.154146. PMID: 28807900
Dickel DE, Barozzi I, Zhu Y, Fukuda-Yuzawa Y, Osterwalder M, Mannion BJ, May D, Spurrell CH, Plajzer-Frick I, Pickle CS, Lee E, Garvin TH, Kato M, Akiyama JA, Afzal V, Lee AY, Gorkin DU, Ren B, Rubin EM, Visel A, Pennacchio LA  Genome-wide compendium and functional assessment of in vivo heart enhancers.2016Nature Communications 2016; 7: 12923. PMID: In Process PMCID: 5059478
Zhou, Pingzhu; Pu, William T. Recounting Cardiac Cellular Composition2016Circ Res 2016 Feb 5; 118(3):368-70 PMID: 26846633 PMC ID: 4755297
Whalen, Sean; Truty, Rebecca M; Pollard, Katherine S. Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin.2016Nat Genet 2016 May; 48(5):488-96 PMID: 27064255 PMC ID: 4910881
Karanth, Santhosh; Zinkhan, Erin K; Hill, Jonathon T; Yost, H Joseph; Schlegel, Amnon. FOXN3 Regulates Hepatic Glucose Utilization.2016Cell Rep 2016 Jun 21; 15(12):2745-55 PMID: 27292639 PMC ID: 4917433
Thomas R, Thomas S, Holloway A, Pollard K. Features that define the best ChIP-seq peak calling algorithms2016Briefings In Bioinformatics, 2016, 10. PMID: 27169896; PMCID: In process.
Ang Y, Rivas R, Ribeiro A, Srivas R, Rivera J, Stone N, Pratt K, Mohamed T, Fu J, Spencer C,  Tippens N, Li M, Narasimha A, Radzinsky E, Moon-Grady A, Yu H, Pruitt B, Snyder M, Srivastava D. Disease Model of GATA4 Mutation Reveals Transcription Factor Cooperativity in Human Cardiogenesis 2016Cell Dec 2016, Vol 167, Issue 7, 1734–1749.e22
Refaat, Marwan M; Fahed, Akl C; Hassanieh, Sylvana; Hotait, Mostafa; Arabi, Mariam; Skouri, Hadi; Seidman, Jonathan G; Seidman, Christine E; Bitar, Fadi F; Nemer, Georges. The Muscle-Bound Heart2016Card Electrophysiol Clin 2016 Mar; 8(1):223-31 PMID: 26920199 PMC ID: In Process
Edwards, Jonathan J; Gelb, Bruce D. Genetics of Congential Heart Disease2016Curr Opin Cardiol 2016 May; 31(3):235-41 PMID: 26872209 PMC ID: 4868504
Luna-Zurita, Luis; Stirnimann, Christian U; Glatt, Sebastian; Kaynak, Bogac L; Thomas, Sean; Baudin, Florence; Samee, Md Abul Hassan; He, Daniel; Small, Eric M; Mileikovsky, Maria; Nagy, Andras; Holloway, Alisha K; Pollard, Katherine S; Müller, Christoph W; Bruneau, Benoit G. Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis2016Cell 2016 Feb 25; 164(5):999-1014 PMID: 26875865 PMC ID: 4769693
Haliburton, Genevieve D E; McKinsey, Gabriel L; Pollard, Katherine S. Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development.2016Neurogenetics 2016 Jan; 17(1):1-9 PMID: 26382291 PMC ID: 4701781
Priest, James R; Osoegawa, Kazutoyo; Mohammed, Nebil; Nanda, Vivek; Kundu, Ramendra; Schultz, Kathleen; Lammer, Edward J; Girirajan, Santhosh; Scheetz, Todd; Waggott, Daryl; Haddad, Francois; Reddy, Sushma; Bernstein, Daniel; Burns, Trudy; Steimle, Jeffrey D; Yang, Xinan H; Moskowitz, Ivan P; Hurles, Matthew; Lifton, Richard P; Nickerson, Debbie; Bamshad, Michael; Eichler, Evan E; Mital, Seema; Sheffield, Val; Quertermous, Thomas; Gelb, Bruce D; Portman, Michael; Ashley, Euan A. De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects.2016PLoS Genet 2016 Apr 8; 12(4) PMID: 27058611 PMC ID: 4825975
Barozzi, Iros; Visel, Axel; Dickel, Diane E. Fishing for Function in the Human Gene Pool2016Trends Genet 2016 Jul; 32(7):392-4 PMID: 27220646 PMC ID: 4912909
Day DS, Zhang B, Stevens SM, Ferrari F, Larschan EN, Park PJ, Pu WT  Comprehensive analysis of promoter-proximal RNA polymerase II pausing across mammalian cell types.2016 Genome Biol. 2016 Jun 3;17(1):120.  PMID: 27259512
Stevens, Sean M; Gise, Alexander von; VanDusen, Nathan; Zhou, Bin; Pu, William T. Epicardium is required for cardiac seeding by yolk sac macrophages, precursors of resident macrophages of the adult heart2016Dev Biol 2016 May 15; 413(2):153-9 PMID: 26988120 PMC ID: In Process
Ang, Siang-Yun; Uebersohn, Alec; Spencer, C Ian; Huang, Yu; Lee, Ji-Eun; Ge, Kai; Bruneau, Benoit G. KMT2D regulates specific programs in heart development via histone H3 lysine 4 di-methylation.2016Development 2016 Mar 1; 143(5):810-21 PMID: 26932671 PMC ID: 4813342
Alexander JM, Hota SK, He D, Thomas S, Ho L, Pennacchio LA, Bruneau BG. Brg1 modulates enhancer activation in mesoderm lineage commitment.2015Development. 2015 Apr 15;142(8):1418-30. doi: 10.1242/dev.109496. Epub 2015 Mar 26. PMID: 25813539; PMCID: PMC4392595.
Damerla RR, Cui C, Gabriel GC, Craige B, Gibbs BC, Francis R, Li Y, Chatterjee B, San Agustin JT, Equether T, Subramanian R, Witman GB, Michaud JL, Pazour GJ, Lo CW. Novel Jbts17 mutant mouse model of Joubert syndrome with cilia transition zone defects and cerebellar and other ciliopathy related anomalies2015Hum Mol Genet. 2015 Jul 15;24(14):3994-4005. doi: 10.1093/hmg/ddv137. Epub 2015 Apr 15. PMID: 25877302; PMCID: PMC4476446.
Jiang, Jianming; Burgon, Patrick G; Wakimoto, Hiroko; Onoue, Kenji; Gorham, Joshua M; O'Meara, Caitlin C; Fomovsky, Gregory; McConnell, Bradley K; Lee, Richard T; Seidman, J G; Seidman, Christine E. Cardiac myosin binding protein C regulates postnatal myocyte cytokinesis.2015Proc Natl Acad Sci U S A 2015 Jul 21; 112(29):9046-51 PMID: 26153423 PMC ID: 4517252
Gelb, Bruce D. Complex genetics and the etiology of human congenital heart disease2015Circ Cardiovasc Genet 2015 Jun; 8(3):529-36 PMID: 26082554 PMC ID: 4870049
Homsy J, Zaidi S, Shen Y, Ware JS, Samocha KE, Karczewski KJ, DePalma SR, McKean D, Wakimoto H, Gorham J, Jin SC, Deanfield J, Giardini A, Porter Jr. GA, Kim R, Bilguvar K, López-Giráldez F, Tikhonova I, Mane S, Romano-Adesman A, Qi H, Vardarajan B, Ma L, Daly M, Roberts AE, Russell MW, Mital S, Newburger JW, Gaynor JW, Breitbart RE, Iossifov I, Ronemus M, Sanders SJ, Kaltman JR, Seidman JG, Brueckner M, Gelb BD, Goldmuntz E, Lifton RP, Seidman CE, Chung WK. De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies.2015Science, 2015; 350(6265):1262-1266. PMID: 26785492; PMCID: 4890146.
Gittelman, Rachel M; Hun, Enna; Ay, Ferhat; Madeoy, Jennifer; Pennacchio, Len; Noble, William S; Hawkins, R David; Akey, Joshua M. Comprehensive identification and analysis of human accelerated regulatory DNA.2015Genome Res 2015 Sep; 25(9):1245-55 PMID: 26104583 PMC ID: 4561485
Akawi N, McRae J, Ansari M, Balasubramanian M, Blyth M, Brady AF, Clayton S, Cole T, Deshpande C, Fitzgerald TW, Foulds N, Francis R, Gabriel G, Gerety SS, Goodship J, Hobson E, Jones WD, Joss S, King D, Klena N, Kumar A, Lees M, Lelliott C, Lord J, McMullan D, O’Regan M, Osio D, Piombo V, Prigmore E, Rajan D, Rosser E, Sifrim A, Smith A, Swaminathan GJ, Turnpenny P, Whitworth J, Wright CF, Firth HV, Barrett JC, Lo CW, FitzPatrick DR & Hurles ME for the DDD study. Discovery of four recessive developmental disorders using probabilistic genotype and phenotype matching among 4,125 families2015Nat Genet. 2015 Nov;47(11):1363-9. doi: 10.1038/ng.3410. Epub 2015 Oct 5. PMID: 26437029; PMCID: in process.
Nobuta, Hiroko; Cilio, Maria Roberta; Danhaive, Olivier; Tsai, Hui-Hsin; Tupal, Srinivasan; Chang, Sandra M; Murnen, Alice; Kreitzer, Faith; Bravo, Verenice; Czeisler, Catherine; Gokozan, Hamza Numan; Gygli, Patrick; Bush, Sean; Weese-Mayer, Debra E; Conklin, Bruce; Yee, Siu-Pok; Huang, Eric J; Gray, Paul A; Rowitch, David; Otero, José Javier. Dysregulation of locus coeruleus development in congenital central hypoventilation syndrome.2015Acta Neuropathol 2015 Aug; 130(2):171-83 PMID: 25975378 PMC ID: 4503865
Guimier A, Gabriel GC, Bajolle F, Tsang M, Liu H, Noll A, Schwartz M, El Malti R, Smith LD, Klena NT, Jimenez G, Miller NA, Oufadem M, Moreau de Bellaing A, Yagi H, Saunders CJ, Baker CN, Di Filippo S, Peterson KA, Thiffault I, Bole-Feysot C, Cooley LD, Farrow EG, Masson C, Schoen P, Deleuze J-F, Nitschké P, Lyonnet S, de Pontual L, Murray SA, Bonnet D, Kingsmore SF, Amiel J, Bouvagnet P, Lo CW & Gordon CT. MMP21 is mutated in human heterotaxy and is required for normal left-right asymmetry in vertebrates2015Nat Genet. 2015 Nov;47(11):1260-3. doi: 10.1038/ng.3376. Epub 2015 Oct 5. PMID: 26437028; PMCID: in process.
Musunuru, Kiran; Hickey, Kathleen T; Al-Khatib, Sana M; Delles, Christian; Fornage, Myriam; Fox, Caroline S; Frazier, Lorraine; Gelb, Bruce D; Herrington, David M; Lanfear, David E; Rosand, Jonathan; American Heart Association Council on Functional Genomics and Translational Biology,Council on Clinical Cardiology, Council on Cardiovascular Disease in the Young, Council on Cardiovascular and Stroke Nursing, Council on Epidemiology and Prevention, Council on Hypertension, Council on Lifestyle and Cardiometabolic Health, Council on Quality of Care and Outcomes Research, and Stroke Council. Basic concepts and potential applications of genetics and genomics for cardiovascular and stroke clinicians: a scientific statement from the American Heart Association.2015Circ Cardiovasc Genet 2015 Feb; 8(1):216-42 PMID: 25561044 PMC ID: 4887701
Theodoris CV, Li M, White MP, Liu L, He D, Pollard KS, Bruneau BG, Srivastava D. Human disease modeling reveals integrated transcriptional and epigenetic mechanisms of NOTCH1 haploinsufficiency.2015Cell. 2015 Mar 12;160(6):1072-86. doi: 10.1016/j.cell.2015.02.035. PMID: 25768904; PMCID: PMC4359747.
Abou Hassan, Ossama K; Fahed, Akl C; Batrawi, Manal; Arabi, Mariam; Refaat, Marwan M; DePalma, Steven R; Seidman, J G; Seidman, Christine E; Bitar, Fadi F; Nemer, Georges M. NKX2-5 mutations in an inbred consanguineous population: genetic and phenotypic diversity.2015Sci Rep 2015 Mar 6; 5:8848 PMID: 25742962 PMC ID: 4351524
Percival, Stefanie M; Thomas, Holly R; Amsterdam, Adam; Carroll, Andrew J; Lees, Jacqueline A; Yost, H Joseph; Parant, John M. Variations in dysfunction of sister chromatid cohesion in esco2 mutant zebrafish reflect the phenotypic diversity of Roberts syndrome.2015Dis Model Mech 2015 Aug 1; 8(8):941-55 PMID: 26044958 PMC ID: 4527282
Czarnecki PG, Gabriel GC, Manning DK, Sergeev M, Lemke K, Klena NT, Liu X, Chen y, Li Y, San Agustin JT, Garnaas MK, Francis RJ, Tobita K, Goessling W, Pazour GJ, Lo CW, Beier DR, and Shah JV. ANKS6 is the critical activator of NEK8 kinase in embryonic situs determination and organ patterning.2015Nat Comms, 2015, 20 Jan. DOI: 10.1038/ncomms7023. PMID: 25599650; PMCID: PMC4361001.
Li Y, Klena NT, Gabriel GC, Liu X, Kim AJ, Lemke K, Chen Y, Chatterjee B, Devine W, Damerla RR., Chang C-F, Yagi H, San Agustin JT, Thahir M, Anderton S, Lawhead C, Vescovi A., Pratt H, Morgan J, Haynes L, Smith CL, Eppig JT, Reinholdt L, Francis R, Leatherbury L, Ganapathiraju MK, Tobita K, Pazour GJ, Lo CW. Global genetic analysis in mice unveils central role for cilia in congenital heart disease.2015Nature. 2015 May 28;521(7553):520-4. doi: 10.1038/nature14269. Epub 2015 Mar 25. PMID: 25807483; PMCID: PMC4617540.
Kostka D, Friedrich T, Holloway AK, Pollard KS. motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences2015Statistics and Its Interface. 2015; 8(4): 463-476. PMID: 26709360; PMCID: PMC4689439.
Nash, Dustin; Arrington, Cammon B; Kennedy, Brett J; Yandell, Mark; Wu, Wilfred; Zhang, Wenying; Ware, Stephanie; Jorde, Lynn B; Gruber, Peter J; Yost, H Joseph; Bowles, Neil E; Bleyl, Steven B. Shared Segment Analysis and Next-Generation Sequencing Implicates the Retinoic Acid Signaling Pathway in Total Anomalous Pulmonary Venous Return (TAPVR).2015PLoS One 2015 Jun 29; 10(6): PMID: 26121141 PMC ID: 4485409
Erwin GD, Oksenberg N, Truty RM, Kosta K, Murphy KK, Ahituv N, Pollard KS, Capra JA. Integrating diverse datasets improves developmental enhancer prediction2014PLoS Computational Biology 2014; 10(6):e1003677. PMID: 24967590; PMCI: PMC4072507.
Li K, Wang G, Andersen T, Zhou P, Pu WT. Optimization of genome engineering approaches with the CRISPR/Cas9 system2014PLos One 2014; 9(8):e105779. PMID: 25166277; PMCID: PMC4148324.
Backenroth D, Homsy J, Murillo L, Glessner J, Lin E, Brueckner M, Lifton R, Goldmuntz E, Chung W, Shen Y.CANOES: detecting rare copy number variants from whole exome sequencing data2014Nucleic Acids Research 2014; 42(12):e97. PMID: 24771342; PMCID: PMC4081054.
Dickel DE, Zhu Y, Nord AS, Wylie JN, Akiyama JA, Afzal V, Plajzer-Frick I, Kirkpatrick A, Gottgens B, Bruneau BG, Visel A, Pennacchio LA. Function-based identification of mammalian enhancers using site-specific integration2014Nat Methods 2014; 11(5):566-571. PMID: 24658141; PMCID: PMC4008384.
Lyozin GT, Bressloff PC, Kumar A, Kosaka Y, Demarest BL, Yost HJ, Kuehn MR, Brunelli L. Isolation of rare recombinants without using selectable markers for one-step seamless BAC mutagenesis2014Nat Methods 2014; 11(9):966-970. PMID: 25028895; PMCID: PMC4149595.
Devine WP, Wythe JD, George M, Koshiba-Takeuchi K, Bruneau BG. Early patterning and specification of cardiac progenitors in gastrulating mesoderm2014eLife 2014; Oct 8; 3. doi: 10.7665/eLife.03848. PMID: 25296024; PMCID: PMC4356145.
Delgado-Olguin PD, Dang LT, He D, Thomas S, Chi L, Sukonnik T, Khyzha N, Dobenecker M-W, Fish JE, Bruneau BG. Ezh2-mediated repression of a transcriptional pathway upstream of Mmp9 maintains integrity of the developing vasculature2014Development 2014; 141(23):4610-7. PMID: 25359725; PMCID: PMC4302930.
Thomas S, Underwood JG, Tseng E, Holloway AK. Long-read sequencing of chicken transcripts and identification of new transcript isoforms2014PLoS One 2014; 9(4):e94650. PMID: 24736250; PMCID: PMC3988055.
Williams AG, Thomas S, Wyman SK, Holloway, AK. RNA-seq data: challenges in and recommendations for experimental design and analysis2014Curr Protoc Hum Genet 2014; 83:11.13.1-11.13.20. PMID: 25271838; PMCID: PMC25271838.
Oksenberg, N; Haliburton, G D E; Eckalbar, W L; Oren, I; Nishizaki, S; Murphy, K; Pollard, K S; Birnbaum, R Y; Ahituv, N. Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes.2014Transl Psychiatry 2014 Sep 2; 4:e431  PMID: 25180570 PMC ID: 4199417
Gelb, Bruce D; Chung, Wendy K. Complex genetics and the etiology of human congenital heart disease
2014Cold Spring Harb Perspect Med 2014 Jul 1; 4(7):a013953 PMID: 24985128 PMC ID: 4066638
Hill JT, Demarest BL, Bisgrove BW, Su YC, Smith M, Yost HJ. Poly peak parser: Method and software for identification of unknown indels using sanger sequencing of polymerase chain reaction products.2014Dev Dyn., 2014, Dec;243(12):1632-6. doi: 10.1002/dvdy.24183. Epub 2014 Sep 30.  PMID: 25160973; PMCID: PMC4525701 [Available on 2015-12-01].
Glessner J, Bick AG, Ito K, Homsy J, Rodriguez-Murillo L, Fromer M, Mazaika E, Vardarajan B, Italia MJ, Leipzig J, DePalma S, Golhar R, Sanders SJ, Yamrom B, Ronemus M, Iossifov I, Willsey AJ, State MW, Kaltman JR, White PS, Shen Y, Warburton D, Brueckner M, Seidman C, Goldmuntz E, Gelb BD, Lifton R, Seidman JG, Hakonarson H, Chung WK. Increased frequency of de novo copy number variants in congenital heart disease by integrative analysis of single nucleotide polymorphism array and exome sequence data2014Circ Res 2014;  115(10):884-896. PMID: 25205790; PMCID: PMC4209190.
Brown JR, Zetsche B, Jackson-Grusby L. RUSH & CRUSH: a rapid and conditional RNA interference method in mice2014Genesis 2014; 52(1):39-48. PMID: 24166816; PMCID: PMC3985430.
Liu X, Francis R, Kim A, Ramirez R, Chen G, Subramanian R, Anderton S, Kim Y, Wang L, Morgan J, Pratt CH, Reinholdt L, Devine W, Leatherbury L, Tobita K, Lo CW. Interrogating congenital heart defects with noninvasive fetal echocardiography in a mouse forward genetic screen2014Circ Cardiovasc Imaging 2014; 7(1):31-42. PMID: 24319090; PMCID: PMC3962690.
He A, Gu F, Hu Y, Ma Q, Ye LY, Akiyama JA, Visel A, Pennachio LA, Pu WT. Dynamic GATA4 enhancers shape the chromatin landscape central to heart development and disease2014Nature Comms 2014; 5;4907. PMID: 25249388; PMCID: PMC4236193.
Damerla RR, Chatterjee B, Li Y, Francis JB, Fatakia SN, Lo CW. Ion Torrent sequencing for conducting genome-wide scans for mutation mapping analysis2014Mamm Genome 2014; 25(3-4):120-128. PMID: 24306492; NIHMSID: NIHMS546518.
Eminaga S, Christodoulou DC, Vigneault F, Church GM, Seidman JG. Quantification of microRNA expression with next-generation sequencing2013Curr Protoc Mol Biol 2013; Chapter 4:Unit 4.17. PMID: 23821442; NIHMSID: NIHMS506236.
Klattenhoff C, Scheuermann JC, Surface LE, Bradley RK, Fields PA, Steinhauser ML, Ding H, Butty VL, Torrey L, Haas S, Abo R, Tabebordbar M, Lee RT, Burge CB, Boyer LA. Braveheart, a long non-coding RNA required for cardiovascular lineage commitment2013Cell 2013; 152(3):570-583. PMID: 23352431; PMCID: PMC3563769.
Liu X, Tobita K, Francis RJ, Lo CW. Imaging techniques for visualizing and phenotyping congenital heart defects in murine models2013Birth Defects Res C Embryo Today 2013 Jun; 99(2):93-105. PMID: 23897594; PMCID: PMC3962687.
Lui KO, Zangi L, Silva EA, Bu L, Sahara M, Li RA, Mooney DJ, Chien KR. Driving vascular endothelial cell fate of human multipotent Isl1+ heart progenitors with VEGF modified mRNA2013Cell Res 2013; 23(10):1172-1186. PMID: 24018375; PMCID: PMC3790234.
Zhang B, Day DS, Ho JW, Song L, Cao J, Christodoulou D, Seidman JG, Crawford GE, Park PJ, Pu WT. A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity2013Genome Res 2013; 23(6):917-927. PMID: 23547170; PMCID: PMC3668360.
Zaidi S, Choi M, Wakimoto H, Ma L, Jiang J, Overton JD, Romano-Adesman A, Bjornson RD, Breitbart RE, Brown KK, Carriero NJ, Cheung YH, Deanfield J, DePalma S, Fakhro KA, Glessner J, Hakonarson H, Italia M, Kaltman JR, Kaski J, Kim R, Kline JK, Lee T, Leipzig J, Lopez A, Mane SM, Mitchell LE, Newburger JW, Parfenov M, Pe'er I, Porter G, Roberts A, Sachidanandam R, Sanders SJ, Seiden HS, State MW, Subramanian S, Tikhonova IR, Wang W, Warburton D, White PS, Williams IA, Zhao H, Seidman JG, Brueckner M, Chung WK, Gelb BD, Goldmuntz E, Seidman CE, Lifton RP. De novo mutations in histone modifying genes in congenital heart disease2013Nature 2013; 498(7453):220-223. PMID: 23665959; PMCID: PMC2706629.
Jiang J, Wakimoto H, Seidman JG, Seidman CE. Allele-specific silencing of mutant Myh6 transcripts in mice suppresses hypertrophic cardiomyopathy2013Science 2013; 342(6154):111-114. PMID: 24092743; PMCID: PMC4100553.
Maguire CT, Demarest BL, Hill JT, Palmer JD, Brothman AR, Yost HJ, Condic ML. Genome-wide analysis reveals the unique stem cell identity of human amniocytes2013PLoS One 2013; 8(1):e53372. PMID: 23326421; PMCID: PMC3542377.
Yuan S, Zaidi S, Brueckner M. Congenital heart disease: emerging themes linking genetics and development2013Curr Opin Genet Dev 2013; 23(3):352-359. PMID: 23790954; PMCID: PMC Journal in process.
Francis R, Lo C. Ex vivo method for high resolution imaging of cilia motility in rodent airway epithelia2013J Vis Exp. 2013; (78), e50343. PMID: 23963287; PMCID: Unavailable - Video article.
DeLaughter DM, Christodoulou DC, Robinson JY, Seidman CE, Baldwin HS, Seidman JG, Barnett JV. Spatial transcriptional profile of the chick and mouse endocardial cushions identify novel regulators of endocardial EMT in vitro2013J Mol Cell Cardiol 2013; 59:196-204. PMID: 23557753; PMCID: PMC3659811.
Wythe JD, Dang LTH, Devine WP, Boudreau E, Artap ST, He D, Schachterle W, Stainier DYR, Oettgen P, Black BL, Bruneau BG, Fish JE. ETS factors regulate Vegf-dependent arterial specification2013Dev Cell 2013; 26(1):45-58. PMID: 23830865; PMCID: PMC3754838.
Kim AJ, Francis R, Liu X, Devine WA, Ramirez R, Anderton SJ, Wong LY, Faruque F, Gabriel GC, Chung W, Leatherbury L, Tobita K, Lo CW. Microcomputed tomography provides high accuracy congenital heart disease diagnosis in neonatal and fetal mice2013Cir Cardiovasc Imaging 2013; 6(4):551-559. PMID: 23759365; PMCID: 505948.
Capra JA, Erwin GD, McKinsey G, Rubenstein JLR, Pollard KS. Many human accelerated regions are developmental enhancers2013Philos Trans R Soc Lond B Biol Sci 2013; 368(1632):20130025. PMID: 24218637; PMCID: PMC3826498.
Pediatric Cardiac Genomics Consortium: Gelb B, Brueckner M, Chung W, Goldmuntz E, Kaltman J, Kaski JP, Kim R, Kline J, Mercer-Rosa L, Porter G, Roberts A, Rosenberg E, Seiden H, Seidman C, Sleeper L, Tennstedt S, Kaltman J, Schramm C, Burns K, Pearson G, Rosenberg E. The Congenital Heart Disease Genetic Network Study (CHD GENES): rationale, design, and early results2013Circ Res 2013; 112(4):698-706. PMID: 23410879; PMCID: PMC3679175.
Fahed AC, Gelb BD, Seidman JG, Seidman CE. Genetics of congenital heart disease: the glass half empty2013Circ Res 2013; 112(4):707-720. PMID: 23410880; PMCID: PMC3827691.
Potok ME, Nix DA, Parnell TJ, Cairns BR. Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern2013Cell 2013; 153:759-772. PMID: 23663776; PMCID: PMC3600721.
Capra JA, Stolzer M, Durand D, Pollard KS. How old is my gene?2013Trends Genet 2013; 29(11):659–668. PMID: 23915718; PMCID: PMC3812327.
Costa MW, Guo G, Wolstein O, Vale M, Castro ML, Wang Libin, Otway R, Riek P, Cochrane N, Furtado M, Semsarian C, Weintraub RG, Yeoh T, Hayward C, Keogh A, Macdonald P, Feneley M, Graham RM, Seidman JG, Seidman CE, Rosenthal N, Fatkin D, Harvey RP. Functional characterization of a novel mutation in NKX2-5 associated with congenital heart disease and adult-onset cardiomyopathy2013Circ Cardiovasc Genet 2013; 6(3):238-247. PMID: 23661673; PMCID: PMC3816146.
Tarkar A, Loges NT, Slagle CE, Francis R, Dougherty GW, Tamayo JV, Shook B, Cantino M, Schwartz D, Jahnke C, Olbrich H, Werner C, Raidt J, Pennekamp P, Abouhamed M, Hjeij R, Köhler G, Griese M, Li Y, Lemke K, Klena N, Liu X, Gabriel G, Tobita K, Jaspers M, Morgan LC, Shapiro AJ, Letteboer SJF, Mans DA, Carson JL, Leigh MW, Wolf WE, Chen S, Lucas JS, Onoufriadis A, Plagnol V, Schmidts M, Boldt K, UK10K16, Roepman R, Zariwala M, Lo CW, Mitchison HM, Knowles MR, Burdine RD, Loturco JJ, Omran H. DYX1C1 is required for axonemal dynein assembly and ciliary motility2013Nature Genetics 2013; 45(9):995-1003; PMID: 23872636; PMCID: PMC4000444.
Tarczy-Hornoch P, Amendola L, Aronson SJ, Garraway L, Gray S, Grundmeier RW, Hindorff LA, Jarvik G, Karavite D, Lebo M, Plon SE, Van Allen E, Weck KE, White PS, Yang Y. A survey of informatics approaches to whole-exome and whole-genome clinical reporting in the electronic health record2013Genet Med 2013; 15(10):824-832. PMID: 24071794; PMCID: PMC3951437.
Scheuermann JC; Boyer LA.Getting to the heart of the matter: long non-coding RNAs in cardiac development and disease2013EMBO J 2013; 32(13):1805-1816; PMID: 23756463; PMCID:PMC3981183.
Schröder S, Herker E, Itzen F, He D, Thomas S, Gilchrist DA, Kaehlcke K, Cho S, Pollard KS, Capra JA, Schnölzer M, Cole PA, Geyer M, Bruneau BG, Adelan K, Ott M. Acetylation of RNA polymerase II regulates growth factor-induced gene transcription in mammalian cells2013Mol Cell 2013; 52(3):314-324. PMID: 24207025; NIHMSID: NIHMS562451.
Subramanian S, Di Pierro V, Shah H, Jayaprakash AD, Weisberger I, Shim J, George A, Gelb BD, Sachidanandam R. MiST: a new approach to variant detection in deep sequencing datasets2013Nucleic Acids Res 2013; 41(16):e154. PMID: 23828039; PMCID: PMC3763541.
Smith RP, Riesenfeld SJ, Holloway AK, Li Q, Murphy KK, Feliciano NM, Orecchia L, Oksenberg N, Pollard KS, Ahituv N. A compact, in vivo screen of all 6-mers revelas drivers of tissue-specific expression and guides synthetic regulatory element design.2013Genome Biology 2013; 14(7):R72. PMID: 23867016; NIHMSID: NIHMS512991.
Srivastava D, Berry EC. Cardiac reprogramming: from mouse toward man2013Curr Opin Genet 2013; 23(5):574-578. PMID: 23993230; PMCID: PMC3782415.
Srivastava D, Cordes Metzler KR. Fending for a Braveheart2013EMBO J 2013; 32(9):1211-1213. PMID: 23524853; PMCID: PMC3642680.
Srivastava D, Heidersbach AJ. Small solutions to big problems: microRNAs for cardiac regeneration2013Circ Res 2013; 112(11):1412-1414. PMID: 23704215; PMCID: PMC3760376.
Cui C, Chatterjee B, Lozito TP, Zhang Z, Francis RJ, Yagi H, Swanhart LM, Sanker S, Francis D, Yu Q, San Agustin JT, Puligilla C, Chatterjee T, Tansey T, Liu X, Kelley MW, Spiliotis ET, Kwiatkowski AV, Tuan R, Pazour GJ, Hukriede NA, Lo CW. Wdpcp, a PCP protein required for ciliogenesis, regulates directional cell migration and cell polarity by direct modulation of the actin cytoskeleton2013PLoS Biol 2013; 11(11):e1001720. PMID: 24302887; PMCID: PMC3841097.
Worringer KA, Rand TA, Hayashi Y, Sami S, Takahashi K, Tanabe K, Narita M, Srivastava D, Yamanaka S. The let-7/LIN-41 pathway regulates reprogramming to human induced pluripotent stem cells by controlling expression of prodifferentiation genes2013Cell Stem Cell 2013; 14(1):40-52. PMID: 24239284; PMCID: NIHMSID: NIHMS538439.
Hill JT, Demarest BL, Bisgrove BW, Gorsi B, Yost HJ. MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq2013Genome Res 2013; 23(4):687-697. PMID: 23299975; PMCID: PMC3613585.
White MP, Rufaihah AJ, Liu L, Ghebremariam YT, Ivey KN, Cooke JP, Srivastava D. Limited gene expression variation in human embryonic stem cell and induced pluripotent stem cell-derived endothelial cells2013Stem Cells 2013; 31(1):92-103. PMID: 23079999; PMCID: PMC3528812.
Zhou P, Zhang Y, Ma Q, Gu F, Day DS, He A, Zhou B, Li J, Stevens S, Romo D, Park PJ, Pu WT. Interrogating translational efficiency and lineage-specific transcriptomes using ribosome affinity purification2013Proc Natl Acad Sci U S A 2013; 110(38):15395-15400. PMID: 24003143; PMCID: PMC3780890.
Hjeij R, Lindstrand A, Francis R, Zariwala MA, Liu X, Li Y, Damerla R, Dougherty GW, Abouhamed M, Olbrich H, Loges NT, Pennekamp P, Davis EE, Carvalho CM, Pehlivan D, Werner C, Raidt J, Koehler G, Haeffner K, Reyes-Mugica M, Lupski JR, Leigh MW, Rosenfeld M, Morgan LC, Knowles MR, Lo C, Katsanis N, Omran H. ARMC4 mutations cause primary ciliary dyskinesia with randomization of left/right body asymmetry2013Am J Hum Genet 2013; 93(2):357-367. PMID: 23849778; PMCID: PMC3738828.
He A, Shen X, Ma Q, Cao J, von Gise A, Zhou P, Wang G, Marquez VE, Orkin SH, Pu WT. PRC2 directly methylates GATA4 and represses its transcriptional activity2012Genes Dev 2012; 26(1):37-42. PMID: 22215809; PMC3258964.
Tomoda K, Takahashi K, Leung K, Okada A, Narita M, Yamada NA, Eilertson KE, Tsang P, Baba S, White MP, Sami S, Srivastava D, Conklin BR, Panning B, Yamanaka S. Derivation conditions impact X-inactivation status in female human induced pluripotent stem cells2012Cell Stem Cell 2012; 11(1):91-99. PMID: 22770243; PMC3396435.
Gelb BD, Seidman CE. The Good SHP2 association: a porthole into the genetics of congenital heart disease2012Circ Cardiovasc Genet 2012; 5(3):271-273. PMID: 22715277; PMCID: PMC3380280.
Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, Erwin G, Kattman SJ, Keller GM, Srivastava D, Levine SS, Pollard KS, Holloway AK, Boyer LA, Bruneau BG. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage2012Cell 2012; 151(1):206-220. PMID: 22981692; PMCID: PMC3462286.
Bruneau BG.Direct reprogramming for cardiac regeneration: from dream to reality2012Circ Res 2012; 110(11):1392-1394. PMID: 22628569; PMCID: PMC3391590.
Lahti AL, Kujala VJ, Chapman H, Koivisto AP, Pekkanen-Mattila M, Kerkelä E, Hyttinen J, Kontula K, Swan H, Conklin BR, Yamanaka S, Silvennoinen O, Aalto-Setälä K. Model for long QT syndrome type 2 using human iPS cells demonstrates arrhythmogenic characteristics in cell culture2012Dis Model Mech 2012; 5(2):220-30. PMID: 22052944; PMC3291643.
Keady BT, Samtani R, Tobita K, Tsuchya M, San Agustin JT, Follit JA, Jonassen JA, Subramanian R, Lo CW, Pazour GJ. IFT25 links the signal-dependent movement of hedgehog components to intraflagellar transport2012Dev Cell 2012; 22(5):940-951. PMID: 22595669; PMC3366633.
Lage K, Greenway SC, Rosenfeld JA, Wakimoto H, Gorham JM, Segre AV, Roberts AE, Smoot LB, Pu WT, Pereira AC, Mesquita SM, Tommerup N, Brunak S, Ballif BC, Shaffer LG, Donahoe PK, Daly MJ, Seidman JG, Seidman CE, Larsen LA. Genetic and environmental risk factors in congenital heart disease functionally converge in protein networks driving heart development2012PNAS 2012; 109(35):14035-14040. PMID: 22904188; PMC3435181.
Chin AJ, Saint-Jeannet J-P, Lo CW. How insights from cardiovascular developmental biology have impacted the care of infants and children with congenital heart disease2012Mech Dev 2012; 129:75-97. PMID: 22640994; PMC3409324.
Hassel D, Cheng P, White MP, Ivey KN, Kroll J, Augustin HG, Katus HA, Stainier DYR, Srivastava D. MicroRNA-10 regulates the angiogenic behavior of zebrafish and human endothelial cells by promoting vascular endothelial growth factor signaling2012Circ Res2012; 111(11):1421-1433. PMID: 22955733; PMCID: PMC3525481.
He A, Ma Q, Cao J, von Gise A, Zhou P, Xie H, Zhang B, Hsing M, Christodoulou DC, Cahan P, Daley GQ, Kong SW, Orkin SH, Seidman CE, Seidman JG, Pu WT. Polycomb repressive complex 2 regulates normal development of the mouse heart2012Circ Res 2012; 110(3):406-415. PMID: 22158708;. PMC3282145.
Zhou P, He A, Pu WT. Regulation of GATA4 transcriptional activity in cardiovascular development and disease2012Curr Top Dev Biol 2012; 100:143-169. PMID: 22449843; PMCID # unavailable; part of a book series.
Delgado-Olguín P, Huang Y, Li X, Christodoulou D, Seidman CE, Seidman JG, Tarakhovsky A, Bruneau BG. Epigenetic repression of cardiac progenitor gene expression by Ezh2 is required for postnatal cardiac homeostasis2012Nat Genet 2012; 44(3):343-347. PMID: 22267199; PMC3288669.
Cui C, Chatterjee B, Francis D, Yu Q, SanAgustin JT, Francis R, Tansey T, Henry C, Wang B, Lemley B, Pazour GJ, Lo CW. Disruption of Mks1 localization to the mother centriole causes cilia defects and developmental malformations in Meckel-Gruber syndrome2012Dis Model Mech 2012; 4(1):43-56. PMID: 21045211; PMC3008963.
Ostrowski LE, Dutcher SK, Lo CW. Cilia and models for studying structure and function2011Proc Am Thorac Soc 2011; 8(5):423-429. PMID: 21926393; PMC3209580.
Christodoulou DC, Gorham JM, Herman DS, Seidman JG. Construction of normalized RNA-seq libraries for next-generation sequencing using the crab duplex-specific nuclease2011Curr Protoc Mol Biol 2011; Chapter: Unit 4.12. PMID: 21472699; PMC3152986; NIHMSID: NIHMS286089.
Kuttippurathu L, Hsing M, Liu Y, Schmidt B, Maskell DL, Lee K, He A, Pu WT, Kong SW. CompleteMOTIFs: DNA motif discovery platform for transcription2011Bioinformatics 2011; 27(5):715-717. Epub 2010 Dec 23. PMID: 21183585; PMC3105477.
Alcalai R, Wakimoto H, Arad M, Planer D, Konno T, Wang L, Seidman JG, Seidman CE, Berul CI. Prevention of ventricular arrhythmia and calcium dysregulation in a catecholaminergic polymorphic ventricular tachycardia mouse model carrying calsequestrin-2 mutation2011Cardiovasc Electrophysiol 2011; 22(3):316-324. PMID: 20807279; PMC3053436.
He A, Kong SW, Ma Q, Pu WT. Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart2011Proc Natl Acad Sci U S A 2011; 108(4):5632-5637. PMID: 21415370; PMC3078411.
Hsiao EC, Nguyen TD, Ng JK, Scott MJ, Chang WC, Zahed H, Conklin BR. Constitutive Gs activation using a single-construct2011Stem Cell Res Ther 2011; 2(2):11. PMID: 21375737; PMC3226282.
Salomonis N, Schlieve CR, Pereira L, Wahlquist C, Colas A, Zambon AC, Vranizan K, Spindler MJ, Pico AR, Cline MS, Clark TA, Williams A, Blume JE, Samal E, Mercola M, Merrill BJ, Conklin BR. Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation2010Proc Natl Acad Sci U S A 2010; 107(23):10514-10519. PMID: 20498046; PMC2890851.
Salomonis N, Conklin BR. Stem cell pluripotency: alternative modes of transcription regulation2010Cell Cycle. 2010; 9(16):3133-3134. PMID: 20814242; PMC3866144.
Yamada S, Samtani RR, Lee ES, Lockett E, Uwabe C, Shiota K, Anderson SA, Lo CW. Developmental atlas of the early first trimester human embryo2010Dev Dyn 2010; 239(6):1585-1595. PMID: 20503356; PMC3401072.
van Laake LW, Qian L, Cheng P, Huang Y, Hsiao EC, Conklin BR, Srivastava D. Reporter-based isolation of induced pluripotent stem cell- and embryonic stem cell-derived cardiac progenitors reveals limited gene expression variance2010Circ Res 2010; 107(3):340-347. PMID: 20558827; PMC2919280.
He A, Pu WT. Genome-wide location analysis by pull down of in vivo biotinylated transcription factors2010Curr Protoc Mol Biol 2010; Chapter: Unit-21.20. PMID: 20890903; PMC3004968.