Publications by authors named "Maika Malig"

38Publications

An evolutionary driver of interspersed segmental duplications in primates.

Authors:
Stuart Cantsilieris Susan M Sunkin Matthew E Johnson Fabio Anaclerio John Huddleston Carl Baker Max L Dougherty Jason G Underwood Arvis Sulovari PingHsun Hsieh Yafei Mao Claudia Rita Catacchio Maika Malig AnneMarie E Welch Melanie Sorensen Katherine M Munson Weihong Jiang Santhosh Girirajan Mario Ventura Bruce T Lamb Ronald A Conlon Evan E Eichler

Genome Biol 2020 08 10;21(1):202. Epub 2020 Aug 10.

Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.

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August 2020

Characterization of R-Loop Structures Using Single-Molecule R-Loop Footprinting and Sequencing.

Authors:
Maika Malig Frederic Chedin

Methods Mol Biol 2020 ;2161:209-228

Department of Molecular and Cellular Biology and Genome Center, University of California Davis, Davis, CA, USA.

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January 2020

Ultra-deep Coverage Single-molecule R-loop Footprinting Reveals Principles of R-loop Formation.

Authors:
Maika Malig Stella R Hartono Jenna M Giafaglione Lionel A Sanz Frederic Chedin

J Mol Biol 2020 03 24;432(7):2271-2288. Epub 2020 Feb 24.

Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA. Electronic address:

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March 2020

Interplay between DNA sequence and negative superhelicity drives R-loop structures.

Authors:
Robert Stolz Shaheen Sulthana Stella R Hartono Maika Malig Craig J Benham Frederic Chedin

Proc Natl Acad Sci U S A 2019 03 8;116(13):6260-6269. Epub 2019 Mar 8.

Department of Molecular and Cellular Biology, University of California, Davis, CA 95616;

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March 2019

The evolution and population diversity of human-specific segmental duplications.

Authors:
Megan Y Dennis Lana Harshman Bradley J Nelson Osnat Penn Stuart Cantsilieris John Huddleston Francesca Antonacci Kelsi Penewit Laura Denman Archana Raja Carl Baker Kenneth Mark Maika Malig Nicolette Janke Claudia Espinoza Holly A F Stessman Xander Nuttle Kendra Hoekzema Tina A Lindsay-Graves Richard K Wilson Evan E Eichler

Nat Ecol Evol 2017 17;1(3):69. Epub 2017 Feb 17.

Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.

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February 2017

Epigenetic origin of evolutionary novel centromeres.

Authors:
Doron Tolomeo Oronzo Capozzi Roscoe R Stanyon Nicoletta Archidiacono Pietro D'Addabbo Claudia R Catacchio Stefania Purgato Giovanni Perini Werner Schempp John Huddleston Maika Malig Evan E Eichler Mariano Rocchi

Sci Rep 2017 02 3;7:41980. Epub 2017 Feb 3.

Department of Biology, University of Bari, Bari, Italy.

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February 2017

Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.

Authors:
Xander Nuttle Giuliana Giannuzzi Michael H Duyzend Joshua G Schraiber Iñigo Narvaiza Peter H Sudmant Osnat Penn Giorgia Chiatante Maika Malig John Huddleston Chris Benner Francesca Camponeschi Simone Ciofi-Baffoni Holly A F Stessman Maria C N Marchetto Laura Denman Lana Harshman Carl Baker Archana Raja Kelsi Penewit Nicolette Janke W Joyce Tang Mario Ventura Lucia Banci Francesca Antonacci Joshua M Akey Chris T Amemiya Fred H Gage Alexandre Reymond Evan E Eichler

Nature 2016 08 3;536(7615):205-9. Epub 2016 Aug 3.

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August 2016

Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies.

Authors:
Nima Rafati Lisa S Andersson Sofia Mikko Chungang Feng Terje Raudsepp Jessica Pettersson Jan Janecka Ove Wattle Adam Ameur Gunilla Thyreen John Eberth John Huddleston Maika Malig Ernest Bailey Evan E Eichler Göran Dalin Bhanu Chowdary Leif Andersson Gabriella Lindgren Carl-Johan Rubin

G3 (Bethesda) 2016 07 7;6(7):2213-23. Epub 2016 Jul 7.

Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden 751 23

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July 2016

Long-read sequence assembly of the gorilla genome.

Authors:
David Gordon John Huddleston Mark J P Chaisson Christopher M Hill Zev N Kronenberg Katherine M Munson Maika Malig Archana Raja Ian Fiddes LaDeana W Hillier Christopher Dunn Carl Baker Joel Armstrong Mark Diekhans Benedict Paten Jay Shendure Richard K Wilson David Haussler Chen-Shan Chin Evan E Eichler

Science 2016 Apr;352(6281):aae0344

Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.

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April 2016

Bovine NK-lysin: Copy number variation and functional diversification.

Authors:
Junfeng Chen John Huddleston Reuben M Buckley Maika Malig Sara D Lawhon Loren C Skow Mi Ok Lee Evan E Eichler Leif Andersson James E Womack

Proc Natl Acad Sci U S A 2015 Dec 14;112(52):E7223-9. Epub 2015 Dec 14.

Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843;

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December 2015

An integrated map of structural variation in 2,504 human genomes.

Authors:
Peter H Sudmant Tobias Rausch Eugene J Gardner Robert E Handsaker Alexej Abyzov John Huddleston Yan Zhang Kai Ye Goo Jun Markus Hsi-Yang Fritz Miriam K Konkel Ankit Malhotra Adrian M Stütz Xinghua Shi Francesco Paolo Casale Jieming Chen Fereydoun Hormozdiari Gargi Dayama Ken Chen Maika Malig Mark J P Chaisson Klaudia Walter Sascha Meiers Seva Kashin Erik Garrison Adam Auton Hugo Y K Lam Xinmeng Jasmine Mu Can Alkan Danny Antaki Taejeong Bae Eliza Cerveira Peter Chines Zechen Chong Laura Clarke Elif Dal Li Ding Sarah Emery Xian Fan Madhusudan Gujral Fatma Kahveci Jeffrey M Kidd Yu Kong Eric-Wubbo Lameijer Shane McCarthy Paul Flicek Richard A Gibbs Gabor Marth Christopher E Mason Androniki Menelaou Donna M Muzny Bradley J Nelson Amina Noor Nicholas F Parrish Matthew Pendleton Andrew Quitadamo Benjamin Raeder Eric E Schadt Mallory Romanovitch Andreas Schlattl Robert Sebra Andrey A Shabalin Andreas Untergasser Jerilyn A Walker Min Wang Fuli Yu Chengsheng Zhang Jing Zhang Xiangqun Zheng-Bradley Wanding Zhou Thomas Zichner Jonathan Sebat Mark A Batzer Steven A McCarroll Ryan E Mills Mark B Gerstein Ali Bashir Oliver Stegle Scott E Devine Charles Lee Evan E Eichler Jan O Korbel

Nature 2015 Oct;526(7571):75-81

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.

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October 2015

Resolving the complexity of the human genome using single-molecule sequencing.

Authors:
Mark J P Chaisson John Huddleston Megan Y Dennis Peter H Sudmant Maika Malig Fereydoun Hormozdiari Francesca Antonacci Urvashi Surti Richard Sandstrom Matthew Boitano Jane M Landolin John A Stamatoyannopoulos Michael W Hunkapiller Jonas Korlach Evan E Eichler

Nature 2015 Jan 10;517(7536):608-11. Epub 2014 Nov 10.

1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.

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January 2015

Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity.

Authors:
Corey T Watson Karyn Meltz Steinberg Tina A Graves Rene L Warren Maika Malig Jacqueline Schein Richard K Wilson Robert A Holt Evan E Eichler Felix Breden

Genes Immun 2015 Jan-Feb;16(1):24-34. Epub 2014 Oct 23.

Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada.

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August 2015

Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability.

Authors:
Francesca Antonacci Megan Y Dennis John Huddleston Peter H Sudmant Karyn Meltz Steinberg Jill A Rosenfeld Mattia Miroballo Tina A Graves Laura Vives Maika Malig Laura Denman Archana Raja Andrew Stuart Joyce Tang Brenton Munson Lisa G Shaffer Chris T Amemiya Richard K Wilson Evan E Eichler

Nat Genet 2014 Dec 19;46(12):1293-302. Epub 2014 Oct 19.

1] Department of Genome Sciences, University of Washington, Seattle, Washington, USA. [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA.

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December 2014

Whole-genome sequencing of individuals from a founder population identifies candidate genes for asthma.

Authors:
Catarina D Campbell Kiana Mohajeri Maika Malig Fereydoun Hormozdiari Benjamin Nelson Gaixin Du Kristen M Patterson Celeste Eng Dara G Torgerson Donglei Hu Catherine Herman Jessica X Chong Arthur Ko Brian J O'Roak Niklas Krumm Laura Vives Choli Lee Lindsey A Roth William Rodriguez-Cintron Jose Rodriguez-Santana Emerita Brigino-Buenaventura Adam Davis Kelley Meade Michael A LeNoir Shannon Thyne Daniel J Jackson James E Gern Robert F Lemanske Jay Shendure Mark Abney Esteban G Burchard Carole Ober Evan E Eichler

PLoS One 2014 12;9(8):e104396. Epub 2014 Aug 12.

Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America; Howard Hughes Medical Institute, Seattle, Washington, United States of America.

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April 2015

Reconstructing complex regions of genomes using long-read sequencing technology.

Authors:
John Huddleston Swati Ranade Maika Malig Francesca Antonacci Mark Chaisson Lawrence Hon Peter H Sudmant Tina A Graves Can Alkan Megan Y Dennis Richard K Wilson Stephen W Turner Jonas Korlach Evan E Eichler

Genome Res 2014 Apr 13;24(4):688-96. Epub 2014 Jan 13.

Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA;

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April 2014

Hominoid fission of chromosome 14/15 and the role of segmental duplications.

Authors:
Giuliana Giannuzzi Michele Pazienza John Huddleston Francesca Antonacci Maika Malig Laura Vives Evan E Eichler Mario Ventura

Genome Res 2013 Nov 27;23(11):1763-73. Epub 2013 Sep 27.

Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy;

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November 2013

Rates and patterns of great ape retrotransposition.

Authors:
Fereydoun Hormozdiari Miriam K Konkel Javier Prado-Martinez Giorgia Chiatante Irene Hernando Herraez Jerilyn A Walker Benjamin Nelson Can Alkan Peter H Sudmant John Huddleston Claudia R Catacchio Arthur Ko Maika Malig Carl Baker Tomas Marques-Bonet Mario Ventura Mark A Batzer Evan E Eichler

Proc Natl Acad Sci U S A 2013 Aug 24;110(33):13457-62. Epub 2013 Jul 24.

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.

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August 2013

Evolution and diversity of copy number variation in the great ape lineage.

Authors:
Peter H Sudmant John Huddleston Claudia R Catacchio Maika Malig Ladeana W Hillier Carl Baker Kiana Mohajeri Ivanela Kondova Ronald E Bontrop Stephan Persengiev Francesca Antonacci Mario Ventura Javier Prado-Martinez Tomas Marques-Bonet Evan E Eichler

Genome Res 2013 Sep 3;23(9):1373-82. Epub 2013 Jul 3.

Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA.

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September 2013

Great ape genetic diversity and population history.

Authors:
Javier Prado-Martinez Peter H Sudmant Jeffrey M Kidd Heng Li Joanna L Kelley Belen Lorente-Galdos Krishna R Veeramah August E Woerner Timothy D O'Connor Gabriel Santpere Alexander Cagan Christoph Theunert Ferran Casals Hafid Laayouni Kasper Munch Asger Hobolth Anders E Halager Maika Malig Jessica Hernandez-Rodriguez Irene Hernando-Herraez Kay Prüfer Marc Pybus Laurel Johnstone Michael Lachmann Can Alkan Dorina Twigg Natalia Petit Carl Baker Fereydoun Hormozdiari Marcos Fernandez-Callejo Marc Dabad Michael L Wilson Laurie Stevison Cristina Camprubí Tiago Carvalho Aurora Ruiz-Herrera Laura Vives Marta Mele Teresa Abello Ivanela Kondova Ronald E Bontrop Anne Pusey Felix Lankester John A Kiyang Richard A Bergl Elizabeth Lonsdorf Simon Myers Mario Ventura Pascal Gagneux David Comas Hans Siegismund Julie Blanc Lidia Agueda-Calpena Marta Gut Lucinda Fulton Sarah A Tishkoff James C Mullikin Richard K Wilson Ivo G Gut Mary Katherine Gonder Oliver A Ryder Beatrice H Hahn Arcadi Navarro Joshua M Akey Jaume Bertranpetit David Reich Thomas Mailund Mikkel H Schierup Christina Hvilsom Aida M Andrés Jeffrey D Wall Carlos D Bustamante Michael F Hammer Evan E Eichler Tomas Marques-Bonet

Nature 2013 Jul 3;499(7459):471-5. Epub 2013 Jul 3.

Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.

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July 2013