A benchmark for microRNA quantification algorithms using the OpenArray platform. Matthew N. McCall, Alexander S. Baras, Alexander Crits-Christoph, Roxann Ingersoll, Melissa A. McAlexander, Kenneth W. Witwer, Marc K. Halushka. BMC Bioinformatics 2016 17:138

Phylodynamic Analysis of Clinical and Environmental Vibrio cholerae Isolates from Haiti Reveals Diversification Driven by Positive Selection.Taj Azarian, Afsar Ali, Judith A. Johnson, David Mohr, Mattia Prosperi, Nazle M. Veras, Mohammed Jubair, Samantha L. Strickland, Mohammad H. Rashid, Meer T. Alam, Thomas A. Weppelmann, Lee S. Katz, Cheryl L. Tarr, Rita R. Colwell, J. Glenn Morris, Jr., and Marco Salemi. mBio. 2014;5(6):e01824-14. doi:10.1128/mBio.01824-14.

Identification of an HMGB3 Frameshift Mutation in a Family With an X-linked Colobomatous Microphthalmia Syndrome Using Whole-Genome and X-Exome Sequencing.  Scott AF, Mohr DW, Kasch LM, Barton JA, Pittiglio R, Ingersoll R, Craig B, Marosy BA, Doheny KF, Bromley WC, Roderick TH, Chassaing N, Calvas P, Prabhu SS, Jabs EW. JAMA Ophthalmol. 2014 Jul 3 PMID: 24993872

Characterization of the genomic architecture and mutational spectrum of a small cell prostate carcinoma. Scott AF, Mohr DW, Ling H, Scharpf RB, Zhang P, Liptak GS. Genes (Basel). 2014 May 12;5(2):366-84. PMID: 24823478

Whole Exome Sequencing of Distant Relatives in Multiplex Families Implicates Rare Variants in Candidate Genes for Oral Clefts. Bureau A, Parker MM, Ruczinski I, Taub MA, Marazita ML, Murray JC, Mangold E, Noethen MM, Ludwig KU, Hetmanski JB, Bailey-Wilson JE, Cropp CD, Li Q, Szymczak S, Albacha-Hejazi H, Alqosayer K, Field LL, Wu-Chou YH, Doheny KF, Ling H, Scott AF, Beaty TH.Genetics. 2014 May 2. PMID:  24793288

Mutations in Alström protein impair terminal differentiation of cardiomyocytes. Lincoln T. Shenje, Peter Andersen, Marc K. Halushka, Cecillia Lui, Laviel Fernandez, Gayle B. Collin, Nuria Amat-Alarcon, Wendy Meschino, Ernest Cutz, Kenneth Chang, Raluca Yonescu, Denise A. S. Batista, Yan Chen, Stephen Chelko, Jane E. Crosson, Janet Scheel, Luca Vricella, Brian D. Craig, Beth A. Marosy, David W. Mohr, Kurt N. Hetrick, Jane M. Romm, Alan F. Scott, David Valle, Jürgen K. Naggert, Chulan Kwon, Kimberly F. Doheny & Daniel P. Judge. Nature Communications 5, Article number: 3416 doi:10.1038/ncomms4416 (2014).

Mutations in the TGF-ß repressor SKI cause Shprintzen-Goldberg syndrome with aortic aneurysm. Doyle AJ, Doyle JJ, Bessling SL, Maragh S, Lindsay ME, Schepers D, Gillis E, Mortier G, Homfray T, Sauls K, Norris RA, Huso ND, Leahy D, Mohr DW, Caulfield MJ, Scott AF, Destrée A, Hennekam RC, Arn PH, Curry CJ, Van Laer L, McCallion AS, Loeys BL, Dietz HC. Nature genetics 44, 1249?54 (2012).

Analysis of polymorphisms and haplotype structure of the human thymidylate synthase genetic region: a tool for pharmacogenetic studies.  Ghosh S, Hossain MZ, Borges M, Goggins MG, Ingersoll RG, Eshleman JR, Klein AP, Kern SE.  PLoS One. 2012;7(4):e34426. Epub 2012 Apr 5.  PMID: 22496803

Polymorphisms in Toll-like receptor genes influence antibody responses to cytomegalovirus glycoprotein B vaccine.  Arav-Boger R, Wojcik GL, Duggal P, Ingersoll RG, Beaty T, Pass RF, Yolken RH.  BMC Res Notes. 2012 Mar 13;5:140. PMID: 22414065

Slower Clearance of Nevirapine Resistant Virus in Infants Failing Extended Nevirapine Prophylaxis for Prevention of Mother-to-Child HIV Transmission. Persaud D, Bedri A, Ziemniak C, Moorthy A, Gudetta B, Abashawl A, Mengistu Y, Omer SB, Isehak A, Kumbi S, Adamu R, Lulseged S, Ashworth R, Hassen E, Ruff And The Ethiopian Swen Study Team A. AIDS Res Hum Retroviruses. 2011 Aug;27(8):823-9. Epub 2011 Feb 25.

Disruption of the ASXL1 gene is frequent in primary, post-essential thrombocytosis and post-polycythemia vera myelofibrosis, but not essential thrombocytosis or polycythemia vera: analysis of molecular genetics and clinical phenotypes. Stein BL, Williams DM, O’Keefe C, Rogers O, Ingersoll RG, Spivak JL, Verma A, Maciejewski JP, McDevitt MA, Moliterno AR.  Haematologica. 2011 Jun 28.

Evidence of gene-environment interaction for the IRF6 gene and maternal multivitamin supplementation in controlling the risk of cleft lip with/without cleft palate. Wu T, Liang KY, Hetmanski JB, Ruczinski I, Fallin MD, Ingersoll RG, Wang H, Huang S, Ye X, Wu-Chou YH, Chen PK, Jabs EW, Shi B, Redett R, Scott AF, Beaty TH. Hum Genet. 2010 Oct;128(4):401-10. Epub 2010 Jul 23.

Association between genes on chromosome 4p16 and non-syndromic oral clefts in four populations. Ingersoll RG, Hetmanski J, Park JW, Fallin MD, McIntosh I, Wu-Chou YH, Chen PK, Yeow V, Chong SS, Cheah F, Sull JW, Jee SH, Wang H, Wu T, Murray T, Huang S, Ye X, Jabs EW, Redett R, Raymond G, Scott AF, Beaty TH.  Eur J Hum Genet. 2010 Jun;18(6):726-32. Epub 2010 Jan 20.

 A genome-wide association study on African-ancestry populations for asthma. Rasika A. Mathias, ScD, Audrey V. Grant, PhD, Nicholas Rafaels, MS, Tracey Hand, MS, Li Gao, MD, PhD, Candelaria Vergara, MSc, Yuhjung J. Tsai, MD, Mao Yang, MS, Monica Campbell, BS, Cassandra Foster, Peisong Gao, MD, PhD, A. Togias, MD, Nadia N. Hansel, MD, MPH, Gregory Diette, MD, N. Franklin Adkinson, MD, Mark C. Liu, MD, Mezbah Faruque, MD, PhD, Georgia M. Dunston, PhD, Harold R. Watson, MD, Michael B. Bracken, PhD, Josephine Hoh, PhD, Pissamai Maul, RN, Trevor Maul, RN, Anne E. Jedlicka, MS, Tanda Murray, MS, Jacqueline B. Hetmanski, MS, Roxann Ashworth, MHS, Chrissie M. Ongaco, BS, Kurt N. Hetrick, MS, Kimberly F. Doheny, PhD, Elizabeth W. Pugh, PhD, MPH, Charles N. Rotimi, PhD, Jean Ford, MD, Celeste Eng, BS, Esteban G. Burchard, MD, Patrick M. A. Sleiman, PhD, Hakon Hakonarson, MD, PhD, Erick Forno, MD, Benjamin A. Raby, MD, Scott T. Weiss, MD, Alan F. Scott, PhD, Michael Kabesch, MD, Liming Liang, MS, Goncxalo Abecasis, PhD, Miriam F. Moffatt, PhD, William O. C. Cookson, MD, Ingo Ruczinski, PhD, Terri H. Beaty, PhD, and Kathleen C. Barnes, PhD. J ALLERGY CLIN IMMUNOL 2009

Using a 1.5K ovine SNP array to expand the sheep linkage map. Jillian F. Maddox, Allan M. Crawford, Roxann Ingersoll, James W. Kijas, Brian P. Dalrymple, Ian R. W. Evans, Frank W. Nicholas, John McEwan, Tracey van Stijn, Herman Raadsa and the International Sheep Genomics Consortium. 

An Integrated Genomic Analysis of Human Glioblastoma Multiforme . D. Williams Parsons, Siân Jones, Xiaosong Zhang, Jimmy Cheng-Ho Lin, Rebecca J. Leary, Philipp Angenendt, Parminder Mankoo, Hannah Carter, I-Mei Siu, Gary L. Gallia, Alessandro Olivi, Roger McLendon, B. Ahmed Rasheed, Stephen Keir, Tatiana Nikolskaya,6 Yuri Nikolsky, Dana A. Busam, Hanna Tekleab, Luis A. Diaz Jr., James Hartigan, Doug R. Smith, Robert L. Strausberg, Suely Kazue Nagahashi Marie, Sueli Mieko Oba Shinjo, Hai Yan, Gregory J. Riggins, Darell D. Bigner, Rachel Karchin, Nick Papadopoulos, Giovanni Parmigiani, Bert Vogelstein, Victor E. Velculescu, Kenneth W. Kinzler, Science, 4 September 2008 (10.1126/science.11643820).

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses. Siân Jones, Xiaosong Zhang, D. Williams Parsons, Jimmy Cheng-Ho Lin, Rebecca J. Leary, Philipp Angenendt, Parminder Mankoo, Hannah Carter, Hirohiko Kamiyama, Antonio Jimeno, Seung-Mo Hong, Baojin Fu, Ming-Tseh Lin, Eric S. Calhoun, Mihoko Kamiyama, Kimberly Walter, Tatiana Nikolskaya, Yuri Nikolsky, James Hartigan, Douglas R. Smith, Manuel Hidalgo, Steven D. Leach, Alison P. Klein, Elizabeth M. Jaffee, Michael Goggins, Anirban Maitra, Christine Iacobuzio-Donahue, James R. Eshleman, Scott E.Kern, Ralph H. Hruban, Rachel Karchin, Nickolas Papadopoulos, Giovanni Parmigiani, Bert Vogelstein, Victor E. Velculescu, Kenneth W. Kinzler,Science, 4 September 2008 (10.1126/science.1164368).

Excess Maternal Transmission of Markers in TCOF1 Among Cleft Palate Case-Parent Trios From Three Populations. Sull JW, Liang KY, Hetmanski JB, Fallin MD, Ingersoll RG, Park JW, Wu-Chou YH, Chen PK, Chong SS, Cheah F, Yeouw V, Park BY, Jee SH, Jabs EW, Redett R, Scott AF, Beaty TH. American Journal of Medical Genetics Part A 146A:2327–2331 (2008)

A Novel Variant in the Platelet Endothelial Aggregation Receptor-1 Gene Is Associated With Increased Platelet Aggregability. Herrera-Galeano JE, Becker DM, Wilson AF, Yanek LR, Bray P, Vaidya D, Faraday N, Becker LC. Arterioscler Thromb Vasc Biol. 2008 May 29.

Differential parental transmission of markers in RUNX2 among cleft case-parent trios from four populations. Sull JW, Liang KY, Hetmanski JB, Fallin MD, Ingersoll RG, Park J, Wu-Chou YH, Chen PK, Chong SS, Cheah F, Yeow V, Park BY, Jee SH, Jabs EW, Redett R, Jung E, Ruczinski I, Scott AF, Beaty TH. Genet Epidemiol. 2008 Mar 20.

Heritability of platelet function in families with premature coronary artery disease. Bray PF, Mathias RA, Faraday N, Yanek LR, Fallin MD, Herrera-Galeano JE, Wilson AF, Becker LC, Becker DM. J Thromb Haemost. 2007 Aug;5(8):1617-23.

Reliability of high-throughput genotyping of whole genome amplified DNA in SNP genotyping studies. Berthier-Schaad Y, Kao WH, Coresh J, Zhang L, Ingersoll RG, Stephens R, Smith MW. Electrophoresis 2007 Aug 14;28(16):2812-2817. Click to view Pubmed entry

Dense SNP association study for bipolar I disorder on chromosome 18p11 suggests two loci with excess paternal transmission.Mulle JG, Fallin MD, Lasseter VK, McGrath JA, Wolyniec PS, Pulver AE. Mol Psychiatry. 2007 Apr;12(4):367-75. Epub 2006 Oct 31.  PMID: 17389904

Factors Associated with Success of Custom SNP Assays Factors Associated with Success of Custom SNP Assays.  R. Ingersoll, I.A. McMullen, G. Ingersoll, E.W. Pugh, A.F. Scott. 2006 Mar 10  Download (.pdf format, 2 MB )

A graphical assessment of p-values from sliding window haplotype tests of association to identify asthma susceptibility loci on chromosome 11q. Mathias RA, Gao P, Goldstein JL, Wilson AF, Pugh EW, Furbert-Harris P, Dunston G, Malveaux F, Togias A, Barnes KC, Beaty TH, Huang SK.  BMC Genet. 2006 Jun 14;7(1):38.

Comparison of SNP tagging methods using empirical data: association study of 713 SNPs on chromosome 12q14.3-12q24.21 for asthma and total serum IgE in an African Caribbean population. Chi PB, Duggal P, Kao WH, Mathias RA, Grant AV, Stockton ML, Garcia JG, Ingersoll RG, Scott AF, Beaty TH, Barnes KC, Fallin MD. Genet Epidemiol. 2006 Jul 7.

Analysis of candidate genes on chromosome 2 in oral cleft case-parent trios from three populations. Beaty TH, Hetmanski JB, Fallin MD, Park JW, Sull JW, McIntosh I, Liang KY, Vanderkolk CA, Redett RJ, Boyadjiev SA, Jabs EW, Chong SS, Cheah FS, Wu-Chou YH, Chen PK, Chiu YF, Yeow V, Ng IS, Cheng J, Huang S, Ye X, Wang H, Ingersoll R, Scott AF. Hum Genet. 2006 Nov;120(4):501-18. Epub 2006 Sep 5.

High Throughput SNP and Expression Analyses of Candidate Genes for Non-syndromic Oral Clefts. Park JW, Cai J, McIntosh I, Jabs EW, Fallin MD, Ingersoll R, Hetmanski JB, Vekemans M, Attie-Bitach T, Michael L, Scott AF, Beaty TH. J Med Genet. 2006 Jul;43(7):598-608. Epub 2006 Jan 13.

Susceptibility Genes for Age-Related Maculopathy on Chromosome 10q26. Johanna Jakobsdottir, Yvette P. Conley, Daniel E. Weeks, Tammy S. Mah, Robert E. Ferrell, and Michael B. Gorin. Am. J. Hum. Genet.,77:389-407, 2005.

Variants in the gene encoding C3 are associated with asthma and related phenotypes among African Caribbean families, Barnes KC, Grant AV, Baltadzhieva D, Zhang S, Berg T, Shao L, Zambelli-Weiner A, Anderson W, Nelsen A, Pillai S, Yarnall DP, Dienger K, Ingersoll RG, Scott AF, Fallin MD, Mathias RA, Beaty TH, Garcia JG, Wills-Karp M, Genes Immun. 2005 Dec 15.

Haplotype diversity in 11 candidate genes across 4 populationsBeaty TH, Fallin MD, Hetmanski JB, McIntosh I, Chong SS, Ingersoll R, Sheng X, Chakraborty R, Scott AF. Genetics. 2005 Jun 18

Assembly and Initial Characterization of a Panel of 85 Genomically Validated Cell Lines from Diverse Head and Neck Tumor Sites. Mei Zhao, Daisuke Sano, Curtis R. Pickering, Samar A. Jasser, Ying C. Henderson, Gary L. Clayman, Erich M. Sturgis, Thomas J. Ow, Reuben Lotan, Thomas E. Carey, Peter G. Sacks, Jennifer R. Grandis, David Sidransky, Nils Erik Heldin, and Jeffrey N. Myers. Clin Cancer Res 2011;17:7248-7264.

Inherited surfactant deficiency due to uniparental disomy of rare mutations in the surfactant protein-B and ATP binding cassette, subfamily A, member 3 genes. Aaron Hamvas, MD, Lawrence M. Nogee, MD, Daniel J. Wegner, MS , Kelcey DePass, BA, John Christodoulou, MBBS, PhD, Bruce Bennetts, PhD, Leon R. McQuade, PhD,Peter H. Gray, MD,  Robin R. Deterding, MD, Travis R. Carroll, MD, Anja Kammesheidt, PhD, Laura M. Kasch, BA, Shashikant Kulkarni, PhD, F. Sessions Cole, MD. The Journal of Pediatrics December 2009, Vol. 155, No. 6

Telomerase Mutations in Families with Idiopathic Pulmonary Fibrosis. Mary Y. Armanios, M.D., Julian J.-L. Chen, Ph.D., Joy D. Cogan, Ph.D., Jonathan K. Alder, B.A., Roxann G. Ingersoll, B.S., Cheryl Markin, B.S., William E. Lawson, M.D., Mingyi Xie, B.S., Irma Vulto, B.S., John A. Phillips III, M.D., Peter M. Lansdorp, M.D., Ph.D., Carol W. Greider, Ph.D., and James E. Loyd, M.D. N Engl J Med 2007;356:1317-26.

Hypoxia-Inducible Factor 1 Polymorphism and Coronary Collateralsin Patients With Ischemic Heart Disease. Jon R. Resar, MD; Ariel Roguin, MD, PhD; Jeffery Voner, PA; Khurram Nasir, MD; Thomas A. Hennebry, MB, BCh, BAO; Julie M. Miller, MD; Roxann Ingersoll; Laura M. Kasch; and Gregg L. Semenza, MD, PhD. CHEST / 128 / 2 / AUGUST, 2005

Platelet Gene Polymorphisms and Cardiac Risk Assessment in Vascular Surgical Patients. Nauder Faraday, M.D., Elizabeth A. Martinez, M.D., Robert B. Scharpf, M.S., Laura Kasch-Semenza, M.S.,Todd Dorman, M.D., Peter J. Pronovost, M.D., Ph.D., Bruce Perler, M.D., Gary Gerstenblith, M.D., Paul F. Bray, M.D., Lee A. Fleisher, M.D.   Anesthesiology 2004; 101:1291–7