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Tyson Clark

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Oligonucleotide Array Sequence Analysis

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TOP 3
Tyson A Clark; Qing Dai; Chuan He; Xingyu Lu; Khai Luong; Stephen W Turner; Matthew Boitano; Jonas Korlach
Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation.
Maria Lluch-Senar; Khai Luong; Eric Schadt; Tyson A Clark; Javier Delgado; Gang Fang; Jonas Korlach; Verónica Lloréns-Rico; Kristi Spittle; Stephen W P Turner; Luis Serrano
Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution.
Eric E Schadt; Neal Sondheimer; Wing H Wong; Xuegong Zhang; Onureena Banerjee; Alice Chen-Plotkin; Andrew Chess; Tyson A Clark; Gang Fang; Zhixing Feng; Alona Keren-Paz; Andrey Kislyuk; Jonas Korlach; Vipin Kumar; Khai Luong; Andrew Kasarskis
Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases.

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All Publications

2013: Tyson A Clark; Qing Dai; Chuan He; Xingyu Lu; Khai Luong; Stephen W Turner; Matthew Boitano; Jonas Korlach
Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation.
BMC biology 2013;11():4.
2013: Maria Lluch-Senar; Khai Luong; Eric Schadt; Tyson A Clark; Javier Delgado; Gang Fang; Jonas Korlach; Verónica Lloréns-Rico; Kristi Spittle; Stephen W P Turner; Luis Serrano
Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution.
PLoS genetics 2013;9(1):e1003191.
2013: Eric E Schadt; Neal Sondheimer; Wing H Wong; Xuegong Zhang; Onureena Banerjee; Alice Chen-Plotkin; Andrew Chess; Tyson A Clark; Gang Fang; Zhixing Feng; Alona Keren-Paz; Andrey Kislyuk; Jonas Korlach; Vipin Kumar; Khai Luong; Andrew Kasarskis
Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases.
Genome research 2013;23(1):129-41.
2012: Gang Fang; Zhixing Feng; David I Friedman; Omar J Jabado; Alona Keren-Paz; Jonas Korlach; Vipin Kumar; Bojan Losic; Khai Luong; Milind C Mahajan; Anjali Mandlik; Diana Munera; Iain A Murray; Richard J Roberts; Onureena Banerjee; Michael C Chao; Andrew Chess; Tyson A Clark; Brigid M Davis; Gintaras Deikus; Steve W Turner; Matthew K Waldor; Eric E Schadt
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing.
Nature biotechnology 2012;30(12):1232-9.
2012: Iain A Murray; Stephen W P Turner; Brian P Anton; Matthew Boitano; Tyson A Clark; Alexey Fomenkov; Jonas Korlach; Khai Luong; Richard D Morgan; Richard J Roberts
The methylomes of six bacteria.
Nucleic acids research 2012;40(22):11450-62.
2012: Tyson A Clark; Alexey Fomenkov; Andrey O Kislyuk; Richard D Morgan; Iain A Murray; Richard J Roberts; Kristi E Spittle; Matthew Boitano; Jonas Korlach
Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing.
Nucleic acids research 2012;40(4):e29.
2011: James R Tollervey; Zhen Wang; Joshua T Witten; Kathi Zarnack; Blaz Zupan; Tyson A Clark; Tomaz Curk; Tibor Hortobágyi; Melis Kayikci; Boris Rogelj; Gregor Rot; Anthony C Schweitzer; Christopher E Shaw; Jernej Ule
Analysis of alternative splicing associated with aging and neurodegeneration in the human brain.
Genome research 2011;21(10):1572-82.
2011: Tyson A Clark; Kristi E Spittle; Stephen W Turner; Jonas Korlach
Direct detection and sequencing of damaged DNA bases.
Genome integrity 2011;2():10.
2010: Miriam Llorian; Schraga Schwartz; Tyson A Clark; Dror Hollander; Lit-Yeen Tan; Rachel Spellman; Adele Gordon; Anthony C Schweitzer; Pierre DE LA GRANGE; Gil Ast; Christopher W J Smith
Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB.
Nature structural & molecular biology 2010;17(9):1114-23.
2010: Anna Lapuk; Henry Marr; Lakshmi Jakkula; Helder Pedro; Sanchita Bhattacharya; Elizabeth Purdom; Zhi Hu; Ken Simpson; Lior Pachter; Steffen Durinck; Nicholas Wang; Bahram Parvin; Gerald Fontenay; Terence P Speed; James Garbe; Martha Stampfer; Hovig Bayandorian; Shannon Dorton; Tyson A Clark; Anthony Schweitzer; Andrew Wyrobek; Heidi Feiler; Paul Spellman; John G Conboy; Joe Gray
Exon-level microarray analyses identify alternative splicing programs in breast cancer.
Molecular cancer research : MCR 2010;8(7):961-74.
2010: Nathan Salomonis; Christopher R Schlieve; Laura Pereira; Christine Wahlquist; Alexandre Colas; Alexander C Zambon; Karen Vranizan; Matthew J Spindler; Alexander R Pico; Melissa S Cline; Tyson A Clark; Alan Williams; John E Blume; Eva Samal; Mark Mercola; Bradley J. Merrill; Bruce R Conklin
Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(23):10514-9.
2010: Benjamin A Flusberg; Dale R Webster; Jessica H Lee; Kevin J Travers; Eric C Olivares; Tyson A Clark; Jonas Korlach; Stephen W P Turner
Direct detection of DNA methylation during single-molecule, real-time sequencing.
Nature methods 2010;7(6):461-5.
2010: Hongqing Du; Melissa S Cline; Robert J Osborne; Daniel L Tuttle; Tyson A Clark; John Paul Donohue; Megan P Hall; Lily Shiue; Maurice S Swanson; Charles A Thornton; Manuel Ares
Aberrant alternative splicing and extracellular matrix gene expression in mouse models of myotonic dystrophy.
Nature structural & molecular biology 2010;17(2):187-93.
2009: Andy Pohl; Charles W Sugnet; Tyson A Clark; Kayla Smith; Pauline A Fujita; Melissa S Cline
Affy exon tissues: exon levels in normal tissues in human, mouse and rat.
Bioinformatics (Oxford, England) 2009;25(18):2442-3.
2009: Miki L Yamamoto; Tyson A Clark; Sherry L Gee; Jeong-Ah Kang; Anthony C Schweitzer; Amittha Wickrema; John G Conboy
Alternative pre-mRNA splicing switches modulate gene expression in late erythropoiesis.
Blood 2009;113(14):3363-70.
2009: Wei Zhang; Shiwei Duan; Wasim K Bleibel; Steven A Wisel; Rong Stephanie Huang; Xiaolin Wu; Lijun He; Tyson A Clark; Tina X Chen; Anthony Schweitzer; John E Blume; M Eileen Dolan; Nancy J Cox
Identification of common genetic variants that account for transcript isoform variation between human populations.
Human genetics 2009;125(1):81-93.
2008: Donny D Licatalosi; Aldo Mele; John J Fak; Jernej Ule; Melis Kayikci; Sung Wook Chi; Tyson A Clark; Anthony C Schweitzer; John E Blume; Xuning Wang; Jennifer C Darnell; Robert B Darnell
HITS-CLIP yields genome-wide insights into brain alternative RNA processing.
Nature 2008;456(7221):464-9.
2008: Shiwei Duan; Rong Stephanie Huang; Wei Zhang; Wasim K Bleibel; Cheryl Roe; Tyson A Clark; Tina X Chen; Anthony Schweitzer; John E Blume; Nancy J Cox; M Eileen Dolan
Genetic architecture of transcript-level variation in humans.
American journal of human genetics 2008;82(5):1101-13.
2008: Wei Zhang; Shiwei Duan; Emily O Kistner; Wasim K Bleibel; Rong Stephanie Huang; Tyson A Clark; Tina X Chen; Anthony Schweitzer; John E Blume; Nancy J Cox; M Eileen Dolan
Evaluation of genetic variation contributing to differences in gene expression between populations.
American journal of human genetics 2008;82(3):631-40.
2007: Rong Stephanie Huang; Shiwei Duan; Sunita J Shukla; Emily O Kistner; Tyson A Clark; Tina X Chen; Anthony Schweitzer; John E Blume; M Eileen Dolan
Identification of genetic variants contributing to cisplatin-induced cytotoxicity by use of a genomewide approach.
American journal of human genetics 2007;81(3):427-37.
2007: Tony Kwan; David Benovoy; Christel Dias; Scott Gurd; david serre; Harry Zuzan; Tyson A Clark; Anthony Schweitzer; Michelle K Staples; Hui Wang; John E Blume; Thomas J Hudson; Robert Sladek; Jacek Majewski
Heritability of alternative splicing in the human genome.
Genome research 2007;17(8):1210-8.
2007: Rong Stephanie Huang; Shiwei Duan; Wasim K Bleibel; Emily O Kistner; Wei Zhang; Tyson A Clark; Tina X Chen; Anthony Schweitzer; John E Blume; Nancy J Cox; M Eileen Dolan
A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(23):9758-63.
2007: Julie Z Ni; Leslie Grate; John Paul Donohue; Christine Preston; Naomi Nobida; Georgeann O'Brien; Lily Shiue; Tyson A Clark; John E Blume; Manuel Ares
Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay.
Genes & development 2007;21(6):708-18.
2007: Debopriya Das; Tyson A Clark; Anthony Schweitzer; Miki Yamamoto; Henry Marr; Josh Arribere; Simon Minovitsky; Alexander Poliakov; Inna Dubchak; John E Blume; John G Conboy
A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing.
Nucleic acids research 2007;35(14):4845-57.
2007: Tyson A Clark; Anthony Schweitzer; Tina X Chen; Michelle K Staples; Gang Lu; Hui Wang; Alan Williams; John E Blume
Discovery of tissue-specific exons using comprehensive human exon microarrays.
Genome biology 2007;8(4):R64.
2006: Paul J Gardina; Tyson A Clark; Brian Shimada; Michelle K Staples; Qing Yang; James Veitch; Anthony Schweitzer; Tarif Awad; Charles Sugnet; Suzanne Dee; Christopher Davies; Alan Williams; Yaron Turpaz
Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array.
BMC genomics 2006;7():325.
2006: Charles W Sugnet; Karpagam Srinivasan; Tyson A Clark; Georgeann O'Brien; Melissa Cline; Hui Wang; Alan Williams; David Kulp; John E Blume; David Haussler; Manuel Ares
Unusual intron conservation near tissue-regulated exons found by splicing microarrays.
PLoS computational biology 2006;2(1):e4.
2005: Karpagam Srinivasan; Lily Shiue; Justin D Hayes; Ross Centers; Sean PATRICK Fitzwater; Rebecca Loewen; Lillian R Edmondson; Jessica Bryant; Michael Smith; Claire Rommelfanger; Valerie Welch; Tyson A Clark; Charles W Sugnet; Kenneth James Howe; Yael Mandel-Gutfreund; Manuel Ares
Detection and measurement of alternative splicing using splicing-sensitive microarrays.
Methods (San Diego, Calif.) 2005;37(4):345-59.
2005: Melissa Cline; John E Blume; Simon Cawley; Tyson A Clark; Jing-Shan Hu; Gang Lu; Nathan Salomonis; Hui Wang; Alan Williams
ANOSVA: a statistical method for detecting splice variation from expression data.
Bioinformatics (Oxford, England) 2005;21 Suppl 1():i107-15.
2005: Todd A Burckin; Roland Nagel; Yael Mandel-Gutfreund; Lily Shiue; Tyson A Clark; Jean-Leon Chong; Tien-Hsien Chang; Sharon Squazzo; Grant A Hartzog; Manuel Ares
Exploring functional relationships between components of the gene expression machinery.
Nature structural & molecular biology 2005;12(2):175-82.
2002: Tyson A Clark; Charles W Sugnet; Manuel Ares
Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays.
Science (New York, N.Y.) 2002;296(5569):907-10.
2002: C Geoffrey Burns; Ryoma Ohi; Sapna Mehta; Eileen T O'Toole; Mark Winey; Tyson A Clark; Charles W Sugnet; Manuel Ares; Kathleen L Gould
Removal of a single alpha-tubulin gene intron suppresses cell cycle arrest phenotypes of splicing factor mutations in Saccharomyces cerevisiae.
Molecular and cellular biology 2002;22(3):801-15.