A
Andrew Hollinger
Researcher at Broad Institute
Publications - 7
Citations - 3788
Andrew Hollinger is an academic researcher from Broad Institute. The author has contributed to research in topics: Ion semiconductor sequencing & Genomics. The author has an hindex of 6, co-authored 7 publications receiving 3570 citations.
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Journal ArticleDOI
Evolution of genes and genomes on the Drosophila phylogeny.
Andrew G. Clark,Michael B. Eisen,Michael B. Eisen,Douglas Smith,Casey M. Bergman,Brian Oliver,Therese A. Markow,Thomas C. Kaufman,Manolis Kellis,Manolis Kellis,William M. Gelbart,Venky N. Iyer,Daniel A. Pollard,Timothy B. Sackton,Amanda M. Larracuente,Nadia D. Singh,José P. Abad,Dawn N. Abt,Boris Adryan,Montserrat Aguadé,Hiroshi Akashi,Wyatt W. Anderson,Charles F. Aquadro,David H. Ardell,Roman Arguello,Carlo G. Artieri,Daniel A. Barbash,Daniel Barker,Paolo Barsanti,Phil Batterham,Serafim Batzoglou,Dave Begun,Arjun Bhutkar,Arjun Bhutkar,Enrico Blanco,Stephanie Bosak,Robert K. Bradley,Adrianne Brand,Michael R. Brent,Angela N. Brooks,Randall H. Brown,Roger K. Butlin,Corrado Caggese,Brian R. Calvi,A. Bernardo Carvalho,Anat Caspi,Sergio Castrezana,Susan E. Celniker,Jean L. Chang,Charles Chapple,Sourav Chatterji,Sourav Chatterji,Asif T. Chinwalla,Alberto Civetta,Sandra W. Clifton,Josep M. Comeron,James C. Costello,Jerry A. Coyne,Jennifer Daub,Robert David,Arthur L. Delcher,Kim D. Delehaunty,Chuong B. Do,Heather Ebling,Kevin A. Edwards,Thomas H. Eickbush,Jay D. Evans,Alan Filipski,Sven Findeiß,Sven Findeiß,Eva Freyhult,Lucinda Fulton,Robert S. Fulton,Ana Cristina Lauer Garcia,Anastasia Gardiner,David A. Garfield,Barry E. Garvin,Greg Gibson,Don Gilbert,Sante Gnerre,Jennifer Godfrey,Robert T. Good,Valer Gotea,Brenton Gravely,Anthony J. Greenberg,Sam Griffiths-Jones,Sam Griffiths-Jones,Samuel R. Gross,Roderic Guigó,Erik Gustafson,Wilfried Haerty,Matthew W. Hahn,Daniel L. Halligan,Aaron L. Halpern,Gillian M. Halter,Mira V. Han,Andreas Heger,LaDeana W. Hillier,Angie S. Hinrichs,Ian Holmes,Roger A. Hoskins,Melissa J. Hubisz,Dan Hultmark,Melanie A. Huntley,David B. Jaffe,Santosh Jagadeeshan,William R. Jeck,Justin Johnson,Corbin D. Jones,William C. Jordan,Gary H. Karpen,Gary H. Karpen,Eiko Kataoka,Peter D. Keightley,Pouya Kheradpour,Ewen F. Kirkness,Leonardo Koerich,Karsten Kristiansen,Dave Kudrna,Rob J. Kulathinal,Sudhir Kumar,Roberta Kwok,Eric S. Lander,Charles H. Langley,Richard T. Lapoint,Brian P. Lazzaro,So Jeong Lee,Lisa Levesque,Ruiqiang Li,Ruiqiang Li,Chiao-Feng Lin,Michael F. Lin,Michael F. Lin,Kerstin Lindblad-Toh,Ana Llopart,Manyuan Long,Lloyd Low,Elena R. Lozovsky,Jian Lu,Meizhong Luo,Carlos A. Machado,Wojciech Makalowski,Mar Marzo,Muneo Matsuda,Luciano M. Matzkin,Bryant F. McAllister,Carolyn S. McBride,Brendan McKernan,Kevin McKernan,Maria Mendez-Lago,Patrick Minx,Michael U. Mollenhauer,Kristi L. Montooth,Stephen M. Mount,Xu Mu,Eugene W. Myers,Bárbara Negre,Stuart J. Newfeld,Rasmus Nielsen,Mohamed A. F. Noor,Patrick M. O’Grady,Lior Pachter,Montserrat Papaceit,Matthew J. Parisi,Michael Parisi,Leopold Parts,Jakob Skou Pedersen,Jakob Skou Pedersen,Graziano Pesole,Adam M. Phillippy,Chris P. Ponting,Mihai Pop,Damiano Porcelli,Jeffrey R. Powell,Sonja J. Prohaska,Kim D. Pruitt,Marta Sabariego Puig,Hadi Quesneville,Kristipati Ravi Ram,David M. Rand,Matthew D. Rasmussen,Laura K. Reed,Robert A. Reenan,Amy Denise Reily,Karin A. Remington,Tania Tassinari Rieger,Michael G. Ritchie,Charles Robin,Yu-Hui Rogers,Claudia Rohde,Julio Rozas,Marc Rubenfield,Alfredo Ruiz,Susan M. Russo,Steven L. Salzberg,Alejandro Sánchez-Gracia,Alejandro Sánchez-Gracia,David J. Saranga,Hajime Sato,Stephen W. Schaeffer,Michael C. Schatz,Todd A. Schlenke,Russell Schwartz,Carmen Segarra,Rama S. Singh,Laura K. Sirot,Marina Sirota,Nicholas Sisneros,Christopher D. Smith,Christopher D. Smith,Temple F. Smith,John Spieth,Deborah E. Stage,Alexander Stark,Alexander Stark,Wolfgang Stephan,Robert L. Strausberg,Sebastian Strempel,David Sturgill,Granger G. Sutton,Granger G. Sutton,Wei Tao,Sarah A. Teichmann,Yoshiko N. Tobari,Yoshihiko Tomimura,Jason M. Tsolas,Vera L. S. Valente,Eli Venter,J. Craig Venter,Saverio Vicario,Filipe G. Vieira,Albert J. Vilella,Alfredo Villasante,Brian P. Walenz,Jun Wang,Jun Wang,Marvin Wasserman,Thomas D. Watts,Derek Wilson,Richard K. Wilson,Rod A. Wing,Mariana F. Wolfner,Alex Wong,Gane Ka-Shu Wong,Gane Ka-Shu Wong,Chung-I Wu,Gabriel C. Wu,Daisuke Yamamoto,Hsiao Pei Yang,Shiaw Pyng Yang,James A. Yorke,Kiyohito Yoshida,Evgeny M. Zdobnov,Peili Zhang,Yu Zhang,Aleksey V. Zimin,Jennifer Baldwin,Amr Abdouelleil,Jamal Abdulkadir,Adal Abebe,Brikti Abera,Justin Abreu,St Christophe Acer,Lynne Aftuck,Allen Alexander,Peter An,Erica Anderson,Scott Anderson,Harindra Arachi,Marc Azer,Pasang Bachantsang,Andrew Barry,Tashi Bayul,Aaron M. Berlin,Daniel Bessette,Toby Bloom,Jason Blye,Leonid Boguslavskiy,Claude Bonnet,Boris Boukhgalter,Imane Bourzgui,Adam Brown,Patrick Cahill,Sheridon Channer,Yama Cheshatsang,Lisa Chuda,Mieke Citroen,Alville Collymore,Patrick Cooke,Maura Costello,Katie D'Aco,Riza M. Daza,Georgius De Haan,Stuart DeGray,Christina Demaso,Norbu Dhargay,Kimberly Dooley,Erin E. Dooley,Missole Doricent,Passang Dorje,Kunsang Dorjee,Alan Dupes,Richard Elong,Jill Falk,Abderrahim Farina,Susan Faro,Diallo Ferguson,Sheila Fisher,Chelsea D. Foley,Alicia Franke,Dennis C. Friedrich,Loryn Gadbois,Gary Gearin,Christina R. Gearin,Georgia Giannoukos,Tina Goode,Joseph Graham,Edward Grandbois,Sharleen Grewal,Kunsang Gyaltsen,Nabil Hafez,Birhane Hagos,Jennifer L. Hall,Charlotte Henson,Andrew Hollinger,Tracey Honan,Monika D. Huard,Leanne Hughes,Brian Hurhula,M. Erii Husby,Asha Kamat,Ben Kanga,Seva Kashin,Dmitry Khazanovich,Peter Kisner,Krista Lance,Marcia Lara,William Lee,Niall J. Lennon,Frances Letendre,Rosie Levine,Alex Lipovsky,Xiaohong Liu,Jinlei Liu,Shangtao Liu,Tashi Lokyitsang,Yeshi Lokyitsang,Rakela Lubonja,Annie Lui,Pen MacDonald,Vasilia Magnisalis,Kebede Maru,Charles Matthews,William McCusker,Susan McDonough,Teena Mehta,James Meldrim,Louis Meneus,Oana Mihai,Atanas Mihalev,Tanya Mihova,Rachel Mittelman,Valentine Mlenga,Anna Montmayeur,Leonidas Mulrain,Adam Navidi,Jerome Naylor,Tamrat Negash,Thu Nguyen,Nga Nguyen,Robert Nicol,Choe Norbu,Nyima Norbu,Nathaniel Novod,Barry O'Neill,Sahal Osman,Eva Markiewicz,Otero L. Oyono,Christopher Patti,Pema Phunkhang,Fritz Pierre,Margaret Priest,Sujaa Raghuraman,Filip Rege,Rebecca Reyes,Cecil Rise,Peter Rogov,Keenan Ross,Elizabeth P. Ryan,Sampath Settipalli,Terry Shea,Ngawang Sherpa,Lu Shi,Diana Shih,Todd Sparrow,Jessica Spaulding,John Stalker,Nicole Stange-Thomann,Sharon Stavropoulos,Catherine Stone,Christopher Strader,Senait Tesfaye,Talene Thomson,Yama Thoulutsang,Dawa Thoulutsang,Kerri Topham,Ira Topping,Tsamla Tsamla,Helen Vassiliev,Andy Vo,Tsering Wangchuk,Tsering Wangdi,Michael Weiand,Jane Wilkinson,Adam Wilson,Shailendra Yadav,Geneva Young,Qing Yu,Lisa Zembek,Danni Zhong,Andrew Zimmer,Zac Zwirko,Pablo Alvarez,William Brockman,Jonathan Butler,Cheewhye Chin,Manfred Grabherr,Michael Kleber,Evan Mauceli,Iain MacCallum +429 more
TL;DR: These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution.
Journal ArticleDOI
Characterizing and measuring bias in sequence data
Michael G. Ross,Carsten Russ,Maura Costello,Andrew Hollinger,Niall J. Lennon,Ryan Hegarty,Chad Nusbaum,David B. Jaffe +7 more
TL;DR: The assays presented in this paper provide a comprehensive view of sequencing bias, which can be used to drive laboratory improvements and to monitor production processes, and indicate that combining data from two technologies can reduce coverage bias.
Journal ArticleDOI
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
Tarjei S. Mikkelsen,Tarjei S. Mikkelsen,Matthew Wakefield,Bronwen Aken,Chris T. Amemiya,Jean L. Chang,Shannon E. Duke,Manuel Garber,Andrew J. Gentles,Andrew J. Gentles,Leo Goodstadt,Andreas Heger,Jerzy Jurka,Michael Kamal,Evan Mauceli,Stephen M. J. Searle,Ted Sharpe,Michelle L. Baker,Mark A. Batzer,Panayiotis V. Benos,Katherine Belov,Michele Clamp,April Cook,James Cuff,Radhika Das,Lance S. Davidow,Janine E. Deakin,Melissa Fazzari,Jacob L. Glass,Manfred Grabherr,John M. Greally,Wanjun Gu,Timothy A. Hore,Gavin A. Huttley,Michael Kleber,Randy L. Jirtle,Edda Koina,Jeannie T. Lee,Shaun Mahony,Marco A. Marra,Robert D. Miller,Robert D. Nicholls,Mayumi Oda,Anthony T. Papenfuss,Zuly E. Parra,David D. Pollock,David A. Ray,Jacqueline E. Schein,Terence P. Speed,Katherine Thompson,John L. VandeBerg,Claire M. Wade,Claire M. Wade,Jerilyn A. Walker,Paul D. Waters,Caleb Webber,Jennifer R. Weidman,Xiaohui Xie,Michael C. Zody,Jennifer Baldwin,Amr Abdouelleil,Jamal Abdulkadir,Adal Abebe,Brikti Abera,Justin Abreu,St Christophe Acer,Lynne Aftuck,Allen Alexander,Peter An,Erica Anderson,Scott Anderson,Harindra Arachi,Marc Azer,Pasang Bachantsang,Andrew Barry,Tashi Bayul,Aaron M. Berlin,Daniel Bessette,Toby Bloom,Jason Blye,Leonid Boguslavskiy,Claude Bonnet,Boris Boukhgalter,Imane Bourzgui,Adam Brown,Patrick Cahill,Sheridon Channer,Yama Cheshatsang,Lisa Chuda,Mieke Citroen,Alville Collymore,Patrick Cooke,Maura Costello,Katie D'Aco,Riza M. Daza,Georgius De Haan,Stuart DeGray,Christina Demaso,Norbu Dhargay,Kimberly Dooley,Erin E. Dooley,Missole Doricent,Passang Dorje,Kunsang Dorjee,Alan Dupes,Richard Elong,Jill Falk,Abderrahim Farina,Susan Faro,Diallo Ferguson,Sheila Fisher,Chelsea D. Foley,Alicia Franke,Dennis C. Friedrich,Loryn Gadbois,Gary Gearin,Christina R. Gearin,Georgia Giannoukos,Tina Goode,Joseph Graham,Edward Grandbois,Sharleen Grewal,Kunsang Gyaltsen,Nabil Hafez,Birhane Hagos,Jennifer L. Hall,Charlotte Henson,Andrew Hollinger,Tracey Honan,Monika D. Huard,Leanne Hughes,Brian Hurhula,M. Erii Husby,Asha Kamat,Ben Kanga,Seva Kashin,Dmitry Khazanovich,Peter Kisner,Krista Lance,Marcia Lara,William Lee,Niall J. Lennon,Frances Letendre,Rosie Levine,Alex Lipovsky,Xiaohong Liu,Jinlei Liu,Shangtao Liu,Tashi Lokyitsang,Yeshi Lokyitsang,Rakela Lubonja,Annie Lui,Pen MacDonald,Vasilia Magnisalis,Kebede Maru,Charles Matthews,William McCusker,Susan McDonough,Teena Mehta,James Meldrim,Louis Meneus,Oana Mihai,Atanas Mihalev,Tanya Mihova,Rachel Mittelman,Valentine Mlenga,Anna Montmayeur,Leonidas Mulrain,Adam Navidi,Jerome Naylor,Tamrat Negash,Thu Nguyen,Nga Nguyen,Robert Nicol,Choe Norbu,Nyima Norbu,Nathaniel Novod,Barry O'Neill,Sahal Osman,Eva Markiewicz,Otero L. Oyono,Christopher Patti,Pema Phunkhang,Fritz Pierre,Margaret Priest,Sujaa Raghuraman,Filip Rege,Rebecca Reyes,Cecil Rise,Peter Rogov,Keenan Ross,Elizabeth P. Ryan,Sampath Settipalli,Terry Shea,Ngawang Sherpa,Lu Shi,Diana Shih,Todd Sparrow,Jessica Spaulding,John Stalker,Nicole Stange-Thomann,Sharon Stavropoulos,Catherine Stone,Christopher Strader,Senait Tesfaye,Talene Thomson,Yama Thoulutsang,Dawa Thoulutsang,Kerri Topham,Ira Topping,Tsamla Tsamla,Helen Vassiliev,Andy Vo,Tsering Wangchuk,Tsering Wangdi,Michael Weiand,Jane Wilkinson,Adam Wilson,Shailendra Yadav,Geneva Young,Qing Yu,Lisa Zembek,Danni Zhong,Andrew Zimmer,Zac Zwirko,David B. Jaffe,Pablo Alvarez,William Brockman,Jonathan Butler,Chee Whye Chin,Sante Gnerre,Iain MacCallum,Jennifer A. Marshall Graves,Chris P. Ponting,Matthew Breen,Paul B. Samollow,Eric S. Lander,Eric S. Lander,Kerstin Lindblad-Toh +238 more
TL;DR: A high-quality draft of the genome sequence of the grey, short-tailed opossum is reported, indicating a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation.
Journal ArticleDOI
A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454
Niall J. Lennon,Robert E. Lintner,Scott Anderson,Pablo Alvarez,Andrew Barry,William Brockman,Riza M. Daza,Rachel L. Erlich,Georgia Giannoukos,Lisa Green,Andrew Hollinger,Cindi A. Hoover,David B. Jaffe,Frank Juhn,Danielle McCarthy,Danielle Perrin,Karen Ponchner,Taryn L Powers,Kamran Rizzolo,Dana Robbins,Elizabeth M. Ryan,Carsten Russ,Todd Sparrow,John Stalker,Scott Steelman,Michael Weiand,Andrew Zimmer,Matthew R. Henn,Chad Nusbaum,Robert Nicol +29 more
TL;DR: An automated, high throughput library construction process for 454 technology, where one technician can create 96 sequence-ready 454 libraries in 2 days, a dramatic improvement over the standard method.
Journal ArticleDOI
Semiconductor-based DNA sequencing of histone modification states
Christine S. Cheng,Kunal Rai,Manuel Garber,Manuel Garber,Andrew Hollinger,Dana Robbins,Scott Anderson,Alyssa Macbeth,Austin Tzou,Mauricio O. Carneiro,Raktima Raychowdhury,Carsten Russ,Nir Hacohen,Nir Hacohen,Jeffrey E. Gershenwald,Niall J. Lennon,Chad Nusbaum,Lynda Chin,Aviv Regev,Aviv Regev,Ido Amit,Ido Amit +21 more
TL;DR: The utility of Ion Torrent semiconductor-based sequencing for sensitive, efficient and rapid chromatin immunoprecipitation followed by sequencing (ChIP-seq) through the application of sample preparation methods that are optimized for ChIP- sequencing on the Ion Torrent platform is demonstrated.