Publications by authors named "Niall J Lennon"

35Publications

Best practices for the analytical validation of clinical whole-genome sequencing intended for the diagnosis of germline disease.

Authors:
Christian R Marshall Shimul Chowdhury Ryan J Taft Mathew S Lebo Jillian G Buchan Steven M Harrison Ross Rowsey Eric W Klee Pengfei Liu Elizabeth A Worthey Vaidehi Jobanputra David Dimmock Hutton M Kearney David Bick Shashikant Kulkarni Stacie L Taylor John W Belmont Dimitri J Stavropoulos Niall J Lennon

NPJ Genom Med 2020 23;5:47. Epub 2020 Oct 23.

Broad Institute of MIT and Harvard, Cambridge, MA USA.

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October 2020

Sensitive Detection of Minimal Residual Disease in Patients Treated for Early-Stage Breast Cancer.

Authors:
Heather A Parsons Justin Rhoades Sarah C Reed Gregory Gydush Priyanka Ram Pedro Exman Kan Xiong Christopher C Lo Tianyu Li Mark Fleharty Gregory J Kirkner Denisse Rotem Ofir Cohen Fangyan Yu Mariana Fitarelli-Kiehl Ka Wai Leong Melissa E Hughes Shoshana M Rosenberg Laura C Collins Kathy D Miller Brendan Blumenstiel Lorenzo Trippa Carrie Cibulskis Donna S Neuberg Matthew DeFelice Samuel S Freeman Niall J Lennon Nikhil Wagle Gavin Ha Daniel G Stover Atish D Choudhury Gad Getz Eric P Winer Matthew Meyerson Nancy U Lin Ian Krop J Christopher Love G Mike Makrigiorgos Ann H Partridge Erica L Mayer Todd R Golub Viktor A Adalsteinsson

Clin Cancer Res 2020 06 13;26(11):2556-2564. Epub 2020 Mar 13.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts.

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June 2020

Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial.

Authors:
Derin B Keskin Annabelle J Anandappa Jing Sun Itay Tirosh Nathan D Mathewson Shuqiang Li Giacomo Oliveira Anita Giobbie-Hurder Kristen Felt Evisa Gjini Sachet A Shukla Zhuting Hu Letitia Li Phuong M Le Rosa L Allesøe Alyssa R Richman Monika S Kowalczyk Sara Abdelrahman Jack E Geduldig Sarah Charbonneau Kristine Pelton J Bryan Iorgulescu Liudmila Elagina Wandi Zhang Oriol Olive Christine McCluskey Lars R Olsen Jonathan Stevens William J Lane Andres M Salazar Heather Daley Patrick Y Wen E Antonio Chiocca Maegan Harden Niall J Lennon Stacey Gabriel Gad Getz Eric S Lander Aviv Regev Jerome Ritz Donna Neuberg Scott J Rodig Keith L Ligon Mario L Suvà Kai W Wucherpfennig Nir Hacohen Edward F Fritsch Kenneth J Livak Patrick A Ott Catherine J Wu David A Reardon

Nature 2019 01 19;565(7738):234-239. Epub 2018 Dec 19.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.

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January 2019

Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms.

Authors:
Maura Costello Mark Fleharty Justin Abreu Yossi Farjoun Steven Ferriera Laurie Holmes Brian Granger Lisa Green Tom Howd Tamara Mason Gina Vicente Michael Dasilva Wendy Brodeur Timothy DeSmet Sheila Dodge Niall J Lennon Stacey Gabriel

BMC Genomics 2018 May 8;19(1):332. Epub 2018 May 8.

Broad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA.

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May 2018

Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing.

Authors:
D Lee Taylor William A Walters Niall J Lennon James Bochicchio Andrew Krohn J Gregory Caporaso Taina Pennanen

Appl Environ Microbiol 2016 12 21;82(24):7217-7226. Epub 2016 Nov 21.

Natural Resources Institute Finland (Luke), Vantaa, Finland.

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December 2016

Technological considerations for genome-guided diagnosis and management of cancer.

Authors:
Niall J Lennon Viktor A Adalsteinsson Stacey B Gabriel

Genome Med 2016 10 26;8(1):112. Epub 2016 Oct 26.

Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA.

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October 2016

Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus.

Authors:
Damien C Tully Colin B Ogilvie Rebecca E Batorsky David J Bean Karen A Power Musie Ghebremichael Hunter E Bedard Adrianne D Gladden Aaron M Seese Molly A Amero Kimberly Lane Graham McGrath Suzane B Bazner Jake Tinsley Niall J Lennon Matthew R Henn Zabrina L Brumme Philip J Norris Eric S Rosenberg Kenneth H Mayer Heiko Jessen Sergei L Kosakovsky Pond Bruce D Walker Marcus Altfeld Jonathan M Carlson Todd M Allen

PLoS Pathog 2016 05 10;12(5):e1005619. Epub 2016 May 10.

Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America.

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May 2016

Development and Validation of a Mass Spectrometry-Based Assay for the Molecular Diagnosis of Mucin-1 Kidney Disease.

Authors:
Brendan Blumenstiel Matthew DeFelice Ozge Birsoy Anthony J Bleyer Stanislav Kmoch Todd A Carter Andreas Gnirke Kendrah Kidd Heidi L Rehm Lucienne Ronco Eric S Lander Stacey Gabriel Niall J Lennon

J Mol Diagn 2016 07 5;18(4):566-71. Epub 2016 May 5.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts.

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July 2016

Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus.

Authors:
Kristian G Andersen B Jesse Shapiro Christian B Matranga Rachel Sealfon Aaron E Lin Lina M Moses Onikepe A Folarin Augustine Goba Ikponmwonsa Odia Philomena E Ehiane Mambu Momoh Eleina M England Sarah Winnicki Luis M Branco Stephen K Gire Eric Phelan Ridhi Tariyal Ryan Tewhey Omowunmi Omoniwa Mohammed Fullah Richard Fonnie Mbalu Fonnie Lansana Kanneh Simbirie Jalloh Michael Gbakie Sidiki Saffa Kandeh Karbo Adrianne D Gladden James Qu Matthew Stremlau Mahan Nekoui Hilary K Finucane Shervin Tabrizi Joseph J Vitti Bruce Birren Michael Fitzgerald Caryn McCowan Andrea Ireland Aaron M Berlin James Bochicchio Barbara Tazon-Vega Niall J Lennon Elizabeth M Ryan Zach Bjornson Danny A Milner Amanda K Lukens Nisha Broodie Megan Rowland Megan Heinrich Marjan Akdag John S Schieffelin Danielle Levy Henry Akpan Daniel G Bausch Kathleen Rubins Joseph B McCormick Eric S Lander Stephan Günther Lisa Hensley Sylvanus Okogbenin Stephen F Schaffner Peter O Okokhere S Humarr Khan Donald S Grant George O Akpede Danny A Asogun Andreas Gnirke Joshua Z Levin Christian T Happi Robert F Garry Pardis C Sabeti

Cell 2015 Aug;162(4):738-50

FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, MA 02115, USA. Electronic address:

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August 2015

Clinical Acquired Resistance to RAF Inhibitor Combinations in BRAF-Mutant Colorectal Cancer through MAPK Pathway Alterations.

Authors:
Leanne G Ahronian Erin M Sennott Eliezer M Van Allen Nikhil Wagle Eunice L Kwak Jason E Faris Jason T Godfrey Koki Nishimura Kerry D Lynch Craig H Mermel Elizabeth L Lockerman Anuj Kalsy Joseph M Gurski Samira Bahl Kristin Anderka Lisa M Green Niall J Lennon Tiffany G Huynh Mari Mino-Kenudson Gad Getz Dora Dias-Santagata A John Iafrate Jeffrey A Engelman Levi A Garraway Ryan B Corcoran

Cancer Discov 2015 Apr 11;5(4):358-67. Epub 2015 Feb 11.

Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts.

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April 2015

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.

Authors:
Cole Trapnell Davide Cacchiarelli Jonna Grimsby Prapti Pokharel Shuqiang Li Michael Morse Niall J Lennon Kenneth J Livak Tarjei S Mikkelsen John L Rinn

Nat Biotechnol 2014 Apr 23;32(4):381-386. Epub 2014 Mar 23.

Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.

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April 2014

Characterizing and measuring bias in sequence data.

Authors:
Michael G Ross Carsten Russ Maura Costello Andrew Hollinger Niall J Lennon Ryan Hegarty Chad Nusbaum David B Jaffe

Genome Biol 2013 May 29;14(5):R51. Epub 2013 May 29.

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May 2013

Whole genome pyrosequencing of rare hepatitis C virus genotypes enhances subtype classification and identification of naturally occurring drug resistance variants.

Authors:
Ruchi M Newman Thomas Kuntzen Brian Weiner Andrew Berical Patrick Charlebois Carla Kuiken Donald G Murphy Peter Simmonds Phil Bennett Niall J Lennon Bruce W Birren Michael C Zody Todd M Allen Matthew R Henn

J Infect Dis 2013 Jul 6;208(1):17-31. Epub 2012 Nov 6.

Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.

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July 2013

De novo assembly of highly diverse viral populations.

Authors:
Xiao Yang Patrick Charlebois Sante Gnerre Matthew G Coole Niall J Lennon Joshua Z Levin James Qu Elizabeth M Ryan Michael C Zody Matthew R Henn

BMC Genomics 2012 Sep 13;13:475. Epub 2012 Sep 13.

The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

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September 2012

Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations.

Authors:
Trevor J Pugh Shyamal Dilhan Weeraratne Tenley C Archer Daniel A Pomeranz Krummel Daniel Auclair James Bochicchio Mauricio O Carneiro Scott L Carter Kristian Cibulskis Rachel L Erlich Heidi Greulich Michael S Lawrence Niall J Lennon Aaron McKenna James Meldrim Alex H Ramos Michael G Ross Carsten Russ Erica Shefler Andrey Sivachenko Brian Sogoloff Petar Stojanov Pablo Tamayo Jill P Mesirov Vladimir Amani Natalia Teider Soma Sengupta Jessica Pierre Francois Paul A Northcott Michael D Taylor Furong Yu Gerald R Crabtree Amanda G Kautzman Stacey B Gabriel Gad Getz Natalie Jäger David T W Jones Peter Lichter Stefan M Pfister Thomas M Roberts Matthew Meyerson Scott L Pomeroy Yoon-Jae Cho

Nature 2012 Aug;488(7409):106-10

Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.

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August 2012

Reemergence and decline of dengue virus serotype 3 in Puerto Rico.

Authors:
Gilberto A Santiago Kate McElroy-Horne Niall J Lennon Luis M Santiago Bruce W Birren Matthew R Henn Jorge L Muñoz-Jordán

J Infect Dis 2012 Sep 27;206(6):893-901. Epub 2012 Jun 27.

Division of Vector-borne Infectious Diseases, Dengue Branch, Centers for Disease Control and Prevention, San Juan, Puerto Rico.

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September 2012

Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African Americans.

Authors:
Paul J McLaren Stephan Ripke Kimberly Pelak Amy C Weintrob Nikolaos A Patsopoulos Xiaoming Jia Rachel L Erlich Niall J Lennon Carl M Kadie David Heckerman Namrata Gupta David W Haas Steven G Deeks Florencia Pereyra Bruce D Walker Paul I W de Bakker

Hum Mol Genet 2012 Oct 19;21(19):4334-47. Epub 2012 Jun 19.

Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA.

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October 2012

Complex dynamic of dengue virus serotypes 2 and 3 in Cambodia following series of climate disasters.

Authors:
Veasna Duong Matthew R Henn Cameron Simmons Chantha Ngan Bunthin Y Laurent Gavotte Alain Viari Sivuth Ong Rekol Huy Niall J Lennon Sowath Ly Sirenda Vong Bruce W Birren Jeremy J Farrar Vincent Deubel Roger Frutos Philippe Buchy

Infect Genet Evol 2013 Apr 5;15:77-86. Epub 2012 Jun 5.

Institut Pasteur in Cambodia, Réseau International des Instituts Pasteur, 5 Monivong Boulevard, PO Box 983, Phnom Penh, Cambodia.

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April 2013

Genome-wide patterns of intrahuman dengue virus diversity reveal associations with viral phylogenetic clade and interhost diversity.

Authors:
Poornima Parameswaran Patrick Charlebois Yolanda Tellez Andrea Nunez Elizabeth M Ryan Christine M Malboeuf Joshua Z Levin Niall J Lennon Angel Balmaseda Eva Harris Matthew R Henn

J Virol 2012 Aug 30;86(16):8546-58. Epub 2012 May 30.

Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, USA.

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August 2012

Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data.

Authors:
Alexander R Macalalad Michael C Zody Patrick Charlebois Niall J Lennon Ruchi M Newman Christine M Malboeuf Elizabeth M Ryan Christian L Boutwell Karen A Power Doug E Brackney Kendra N Pesko Joshua Z Levin Gregory D Ebel Todd M Allen Bruce W Birren Matthew R Henn

PLoS Comput Biol 2012 15;8(3):e1002417. Epub 2012 Mar 15.

Broad Institute of MIT & Harvard, Cambridge, Massachusetts, USA.

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June 2012

Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection.

Authors:
Matthew R Henn Christian L Boutwell Patrick Charlebois Niall J Lennon Karen A Power Alexander R Macalalad Aaron M Berlin Christine M Malboeuf Elizabeth M Ryan Sante Gnerre Michael C Zody Rachel L Erlich Lisa M Green Andrew Berical Yaoyu Wang Monica Casali Hendrik Streeck Allyson K Bloom Tim Dudek Damien Tully Ruchi Newman Karen L Axten Adrianne D Gladden Laura Battis Michael Kemper Qiandong Zeng Terrance P Shea Sharvari Gujja Carmen Zedlack Olivier Gasser Christian Brander Christoph Hess Huldrych F Günthard Zabrina L Brumme Chanson J Brumme Suzane Bazner Jenna Rychert Jake P Tinsley Ken H Mayer Eric Rosenberg Florencia Pereyra Joshua Z Levin Sarah K Young Heiko Jessen Marcus Altfeld Bruce W Birren Bruce D Walker Todd M Allen

PLoS Pathog 2012 8;8(3):e1002529. Epub 2012 Mar 8.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

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July 2012

Internally deleted WNV genomes isolated from exotic birds in New Mexico: function in cells, mosquitoes, and mice.

Authors:
Kendra N Pesko Kelly A Fitzpatrick Elizabeth M Ryan Pei-Yong Shi Bo Zhang Niall J Lennon Ruchi M Newman Matthew R Henn Gregory D Ebel

Virology 2012 May 23;427(1):10-7. Epub 2012 Feb 23.

Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM, USA.

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May 2012

Dynamics of dengue disease severity determined by the interplay between viral genetics and serotype-specific immunity.

Authors:
Molly OhAinle Angel Balmaseda Alexander R Macalalad Yolanda Tellez Michael C Zody Saira Saborío Andrea Nuñez Niall J Lennon Bruce W Birren Aubree Gordon Matthew R Henn Eva Harris

Sci Transl Med 2011 Dec;3(114):114ra128

Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720-7354, USA.

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December 2011

High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections.

Authors:
Khoa T D Thai Matthew R Henn Michael C Zody Vianney Tricou Nguyen Minh Nguyet Patrick Charlebois Niall J Lennon Lisa Green Peter J de Vries Tran Tinh Hien Jeremy Farrar H Rogier van Doorn Menno D de Jong Bruce W Birren Edward C Holmes Cameron P Simmons

J Virol 2012 Jan 16;86(2):835-43. Epub 2011 Nov 16.

Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.

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January 2012

Genetic diversity and lineage dynamic of dengue virus serotype 1 (DENV-1) in Cambodia.

Authors:
Veasna Duong Cameron Simmons Laurent Gavotte Alain Viari Sivuth Ong Ngan Chantha Niall J Lennon Bruce W Birren Sirenda Vong Jeremy J Farrar Matthew R Henn Vincent Deubel Roger Frutos Philippe Buchy

Infect Genet Evol 2013 Apr 2;15:59-68. Epub 2011 Jul 2.

Institut Pasteur in Cambodia, Réseau International des Instituts Pasteur, 5 Monivong Boulevard, PO Box 983, Phnom Penh, Cambodia.

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April 2013

Molecular evolution of West Nile virus in a northern temperate region: Connecticut, USA 1999-2008.

Authors:
Philip M Armstrong Charles R Vossbrinck Theodore G Andreadis John F Anderson Kendra N Pesko Ruchi M Newman Niall J Lennon Bruce W Birren Gregory D Ebel Mathew R Henn

Virology 2011 Aug 1;417(1):203-10. Epub 2011 Jul 1.

Center for Vector Biology and Zoonotic Diseases, The Connecticut Agricultural Experiment Station, New Haven, CT 06504, USA.

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August 2011

Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission.

Authors:
Jayna Raghwani Andrew Rambaut Edward C Holmes Vu Ty Hang Tran Tinh Hien Jeremy Farrar Bridget Wills Niall J Lennon Bruce W Birren Matthew R Henn Cameron P Simmons

PLoS Pathog 2011 Jun 2;7(6):e1002064. Epub 2011 Jun 2.

University of Edinburgh, Institute of Evolutionary Biology, Ashworth Laboratories, United Kingdom.

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June 2011

Next-generation sequencing for HLA typing of class I loci.

Authors:
Rachel L Erlich Xiaoming Jia Scott Anderson Eric Banks Xiaojiang Gao Mary Carrington Namrata Gupta Mark A DePristo Matthew R Henn Niall J Lennon Paul I W de Bakker

BMC Genomics 2011 Jan 18;12:42. Epub 2011 Jan 18.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

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January 2011

Endurance, refuge, and reemergence of dengue virus type 2, Puerto Rico, 1986-2007.

Authors:
Kate L McElroy Gilberto A Santiago Niall J Lennon Bruce W Birren Matthew R Henn Jorge L Muñoz-Jordán

Emerg Infect Dis 2011 Jan;17(1):64-71

Dengue Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico.

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January 2011

PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes.

Authors:
Qing Yu Elizabeth M Ryan Todd M Allen Bruce W Birren Matthew R Henn Niall J Lennon

Bioinformatics 2011 Jan 9;27(2):266-7. Epub 2010 Nov 9.

Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA.

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January 2011

The early whole-blood transcriptional signature of dengue virus and features associated with progression to dengue shock syndrome in Vietnamese children and young adults.

Authors:
Long Truong Hoang David J Lynn Matt Henn Bruce W Birren Niall J Lennon Phuong Thi Le Kien Thi Hue Duong Tham Thi Hong Nguyen Lanh Ngoc Mai Jeremy J Farrar Martin L Hibberd Cameron P Simmons

J Virol 2010 Dec 13;84(24):12982-94. Epub 2010 Oct 13.

Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 190 Ben Ham Tu, District 5, Ho Chi Minh City, Vietnam.

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December 2010

Emergence of the Asian 1 genotype of dengue virus serotype 2 in viet nam: in vivo fitness advantage and lineage replacement in South-East Asia.

Authors:
Thi Ty Hang Vu Edward C Holmes Veasna Duong Thien Quy Nguyen Tinh Hien Tran Michael Quail Carol Churcher Julian Parkhill Jane Cardosa Jeremy Farrar Bridget Wills Niall J Lennon Bruce W Birren Philippe Buchy Matthew R Henn Cameron P Simmons

PLoS Negl Trop Dis 2010 Jul 20;4(7):e757. Epub 2010 Jul 20.

Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam.

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July 2010

A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454.

Authors:
Niall J Lennon Robert E Lintner Scott Anderson Pablo Alvarez Andrew Barry William Brockman Riza 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 Ryan Carsten Russ Todd Sparrow John Stalker Scott Steelman Michael Weiand Andrew Zimmer Matthew R Henn Chad Nusbaum Robert Nicol

Genome Biol 2010 5;11(2):R15. Epub 2010 Feb 5.

Genome Sequencing Platform, Broad Institute of MIT and Harvard, 320 Charles St, Cambridge, MA 02141, USA.

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August 2010

Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach.

Authors:
D Lee Taylor Michael G Booth Jack W McFarland Ian C Herriott Niall J Lennon Chad Nusbaum Thomas G Marr

Mol Ecol Resour 2008 Jul;8(4):742-52

Institute of Arctic Biology, 311 Irving I Building, University of Alaska, Fairbanks, AK 99775, USA, Broad Institute, Massachusetts Institute of Technology, 320 Charles Street, Cambridge, MA 02141, USA.

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July 2008

Dysferlin interacts with annexins A1 and A2 and mediates sarcolemmal wound-healing.

Authors:
Niall J Lennon Alvin Kho Brian J Bacskai Sarah L Perlmutter Bradley T Hyman Robert H Brown

J Biol Chem 2003 Dec 23;278(50):50466-73. Epub 2003 Sep 23.

Day Neuromuscular Research Laboratory, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA.

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December 2003