Publications

Kevin Judd McKernan, Heather E. Peckham, Gina L. Costa, Stephen F. McLaughlin, Yutao Fu, Eric F. Tsung, Christopher R. Clouser, Cisyla Duncan, Jeffrey K. Ichikawa, Clarence C. Lee, Zheng Zhang, Swati S. Ranade, Eileen T. Dimalanta, Fiona C. Hyland, Tanya D. Sokolsky, Lei Zhang, Andrew Sheridan, Haoning Fu, Cynthia L. Hendrickson, Bin Li, Lev Kotler, Jeremy R. Stuart, Joel A. Malek, Jonathan M. Manning, Alena A. Antipova, Damon S. Perez, Michael P. Moore, Kathleen C. Hayashibara, Michael R. Lyons, Robert E. Beaudoin, Brittany E. Coleman, Michael W. Laptewicz, Adam E. Sannicandro, Michael D. Rhodes, Rajesh K. Gottimukkala, Shan Yang, Vineet Bafna, Ali Bashir, Andrew MacBride, Can Alkan, Jeffrey M. Kidd, Evan E. Eichler, Martin G. Reese, Francisco M. De La Vega, Alan P. Blanchard

Genome Res. 2009 Sep;19(9):1527-41. doi: 10.1101/gr.091868.109.
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Francisco M. De La Vega , Shimul Chowdhury, Barry Moore, Erwin Frise, Jeanette McCarthy, Edgar Javier Hernandez, Terence Wong, Kiely James, Lucia Guidugli, Pankaj B. Agrawal, Casie A. Genetti, Catherine A. Brownstein, Alan H. Beggs, Britt-Sabina Löscher, Andre Franke, Braden Boone, Shawn E. Levy, Katrin Õunap, Sander Pajusalu, Matt Huentelman, Keri Ramsey, Marcus Naymik, Vinodh Narayanan, Narayanan Veeraraghavan, Paul Billings, Martin G. Reese, Mark Yandell and Stephen F. Kingsmore

Fabric GEM ranks >90% of causal genes in top 2 candidates and breaks ground by incorporating SVs and phenotypes in automated AI-driven analysis.

Genome Medicine; October 14, 2021
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Hao Hu, Jared C. Roach, Hilary Coon, Stephen L. Guthery, Karl V. Voelkerding, Rebecca L. Margraf, Jacob D. Durtschi, Sean V. Tavtigian, Shankaracharya, Wilfred Wu, Paul Scheet, Shuoguo Wang, Jinchuan Xing, Gustavo Glusman, Robert Hubley, Hong Li, Vidu Garg, Barry Moore, Leroy Hood, David J Galas, Deepak Srivastava, Martin G Reese, Lynn B Jorde, Mark Yandell, Chad D. Huff

Nat Biotechnol. 2014 May 18. doi: 10.1038/nbt.2895.
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Alan F. Rope, Kai Wang, Rune Evjenth, Jinchuan Xing, Jennifer J. Johnston, Jeffrey J. Swensen, W. Evan Johnson, Barry Moore, Chad D. Huff, Lynne M. Bird, John C. Carey, John M. Opitz, Cathy A. Stevens, Tao Jiang, Christa Schank, Heidi Deborah Fain, Reid Robison, Brian Dalley, Steven Chin, Sarah T. South, Theodore J. Pysher, Lynn B. Jorde, Hakon Hakonarson, Johan R. Lillehaug, Leslie G. Biesecker, Mark Yandell, Thomas Arnesen, Gholson J. Lyon

Am J Hum Genet. 2011 Jul 15;89(1):28-43. doi: 10.1016/j.ajhg.2011.05.017.
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Amy S. Gargis, Lisa Kalman, Meredith W Berry, David P. Bick, David P. Dimmock, Tina Hambuch, Fei Lu, Elaine Lyon, Karl V. Voelkerding, Barbara A. Zehnbauer, Richa Agarwala, Sarah F. Bennett, Bin Chen, Ephrem L. H. Chin, John G. Compton, Soma Das, Daniel H. Farkas, Matthew J. Ferber, Birgit H. Funke, Manohar R. Furtado, Lilia M. Ganova-Raeva, Ute Geigenmüller, Sandra J. Gunselman, Madhuri R. Hegde, Philip L. F. Johnson, Andrew Kasarskis, Shashikant Kulkarni, Thomas Lenk, C. S. Jonathan Liu, Megan Manion, Teri A. Manolio, Elaine R. Mardis, Jason D. Merker, Mangalathu S. Rajeevan, Martin G. Reese, Heidi L. Rehm, Birgitte B. Simen, Joanne M. Yeakley, Justin M. Zook, Ira M. Lubin

Nat Biotechnol. 2012 Nov;30(11):1033-6. doi: 10.1038/nbt.2403.
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Roderic Guigó, Paul Flicek, Josep F. Abril1, Alexandre Reymond, Julien Lagarde, France Denoeud, Stylianos Antonarakis, Michael Ashburner, Vladimir B. Bajic, Ewan Birney, Robert Castelo, Eduardo Eyras, Catherine Ucla, Thomas R. Gingeras, Jennifer Harrow, Tim Hubbard, Suzanna E. Lewis, Martin G. Reese

Genome Biol. 2006;7 Suppl 1:S2.1-31.
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Mika Moriwaki, Barry Moore, Timothy Mosbruger, Deborah W. Neklason, Mark Yandell, Lynn B. Jorde, Corrine K. Welt

Data was analyzed using Omicia Opal (now known as Fabric Genomics) in a three-person cohort analysis including the proband, mother, and daughter. The software prioritizes variants using the Variant Annotation, Analysis and Search Tool (VAAST)...Mutations were prioritized by the Fabric Genomics' score (aka Omicia score) which ranks variants according to expected protein effects using SIFT (http://sift.jcvi.org/), Mutation Taster (http://www.mutationtaster.org/), PolyPhen (http://genetics.bwh.harvard.edu/pph2), and phyloP [17–19]. In both analyses, the Phenotype Driven Variant Ontological Re-ranking tool (Phevor) feature was used to further prioritize genes for analysis using premature ovarian failure and POI as filters [8, 20].

J. Endocr. Soc. (2017) 1 (3): 162-173, Feb. 2017
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Lauge Farnaes, Shareef A Nahas, Shimul Chowdhury, James Nelson, Serge Batalov, David Dimmock, Stephen F. Kingsmore, and RCIGM Investigators

Variants were annotated and analyzed in Opal Clinical (Fabric Genomics - formerly Omicia.) Clinical analysis of genome next-generation sequencing data used the Fabric Genomics- formerly Omicia platform.

Cold Spring Harbor Molecular Case Studies; May 2017
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Amber Hildreth, Kristen Wigby, Shimul Chowdhury, Shareef Nahas, Jaime Barea, Paulina Ordonez, Serge Batalov, David M Dimmock, RCIGM Investigators and Stephen F Kingsmore

Variants were annotated and analyzed in Opal Clinical (Fabric Genomics- formerly Omicia.)

Cold Spring Harbor Molecular Case Studies; May 2017
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