Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
Chen-Shan Chin, David H Alexander, Patrick Marks, Aaron A Klammer, James Drake, Cheryl Heiner, Alicia Clum, Alex Copeland, John Huddleston, Evan E Eichler, Stephen W Turner & Jonas Korlach
Marc W. Allard, Tim Muruvanda, Errol Strain, Ruth Timme, Yan Luo, Charles Wang, Christine E. Keys, Justin Payne, Tony Cooper, Khai Luong, Yi Song, Chen-Shan Chin, Jonas Korlach, Rich J. Roberts, Peter Evans, Steven M. Musser, Eric W. Brown
Aluminum tolerance in maize is associated with higher MATE1 gene copy number
Authors: Lyza G. Maron, Claudia T. Guimares, Matias Kirst, Patrice S. Albert, James A. Birchler, Peter J. Bradbury, Edward S. Buckler, Alison E. Coluccio, Tatiana V. Danilova, David Kudrna, Jurandir V. Magalhaes, Miguel A. Pieros, Michael C. Schatz, Rod A. Wing, and Leon V. Kochian
The impact of aminoglycosides on the dynamics of translation elongation
Albert Tsai, Sotaro Uemura, Magnus Johansson, Elisabetta Viani Puglisi, R. Andrew Marshall, Colin Echeverria Aitken, Jonas Korlach, Mans Ehrenberg, Joseph D. Puglisi
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution
Daniël P Melters, Keith R Bradnam, Hugh A Young3, Natalie Telis, Michael R May, J Graham Ruby, Robert Sebra, Paul Peluso, John Eid, David Rank, José Fernando Garcia, Joseph L DeRisi, Timothy Smith, Christian Tobias, Jeffrey Ross-Ibarra, Ian Korf and Simon W-L Chan
Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at Single-Base Resolution
Maria Lluch-Senar, Khai Luong, Verónica Lloréns-Rico, Javier Delgado, Gang Fang, Kristi Spittle, Tyson A. Clark, Eric Schadt, Stephen W. Turner, Jonas Korlach, Luis Serrano
Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology
Adam C. English, Stephen Richards, Yi Han, Min Wang, Vanesa Vee, Jiaxin Qu, Xiang Qin, Donna M. Muzny, Jeffrey G. Reid, Kim C. Worley, Richard A. Gibbs
PLoS ONE 7(11): e47768. doi:10.1371/journal.pone.0047768
Use of Four Next-generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism
John Archer, Jan Weber, Kenneth Henry, Dane Winner, Richard Gibson, Lawrence Lee, Ellen Paxinos, Eric J. Arts, David L. Robertson, Larry Mimms, Miguel E. Quiñones-Mateu
PLOS ONE 7(11): e49602. doi:10.1371/journal.pone.0049602
Inv(16)(p13.3q24.3)-Encoded CBFA2T3-GLIS2 Fusion Protein Defines an Aggressive Subtype of Pediatric Acute Megakaryoblastic Leukemia
Tanja A. Gruber, Amanda Larson Gedman, Jinghui Zhang, Cary S. Koss, Suresh Marada, Huy Q. Ta, Shann-Ching Chen, Xiaoping Su, Stacey K. Ogden, Jinjun Dang, Gang Wu, Vedant Gupta, Anna K. Andersson, Stanley Pounds, Lei Shi, John Easton, Michael I. Barbato, Heather L. Mulder, Jayanthi Manne, Jianmin Wang, Michael Rusch, Swati Ranade, Ramapriya Ganti, Matthew Parker, Jing Ma, Ina Radtke, Li Ding, Giovanni Cazzaniga, Andrea Biondi, Steven M. Kornblau, Farhad Ravandi, Hagop Kantarjian, Stephen D. Nimer, Konstanze Döhner, Hartmut Döhner, Timothy J. Ley, Paola Ballerini, Sheila Shurtleff, Daisuke Tomizawa, Souichi Adachi, Yasuhide Hayashi, Akio Tawa, Lee-Yung Shih, Der-Cherng Liang, Jeffrey E. Rubnitz, Ching-Hon Pui, Elaine R. Mardis, Richard K. Wilson, James R. Downing
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing
Gang Fang, Diana Munera, David I Friedman, Anjali Mandlik, Michael C Chao, Onureena Banerjee, Zhixing Feng, Bojan Losic, Milind C Mahajan, Omar J Jabado, Gintaras Deikus, Tyson A Clark, Khai Luong, Iain A Murray, Brigid M Davis, Alona Keren-Paz, Andrew Chess, Richard J Roberts, Jonas Korlach, Steve W Turner, Vipin Kumar, Matthew K Waldor & Eric E Schadt
Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases
Eric Schadt, Onureena Banerjee, Gang Fang, Zhixing Feng, Wing Wong, Xuegong Zhang, Andrey Kislyuk, Tyson Clark, Khai Luong, Alona Keren-Paz, Andrew Chess, Vipin Kumar, Alice Chen-Plotkin, Neal Sondheimer, Jonas Korlach and Andrew Kasarskis
Iain A. Murray, Tyson A. Clark, Richard D. Morgan, Matthew Boitano, Brian P. Anton, Khai Luong, Alexey Fomenkov, Stephen W. Turner, Jonas Korlach, and Richard J. Roberts
Feasibility of real time next generation sequencing of cancer genes linked to drug response: Results from a clinical trial
Ben Tran, Andrew M.K. Brown, Philippe L. Bedard, Eric Winquist, Glenwood D. Goss, Sebastien J. Hotte, Stephen A. Welch, Hal W. Hirte, Tong Zhang, Lincoln D. Stein, Vincent Ferretti, Stuart Watt, Wei Jiao, Karen Ng, Sangeet Ghai, Patricia Shaw, Teresa Petrocelli, Thomas J. Hudson, Benjamin G. Neel, Nicole Onetto, Lillian L. Siu, John D. McPherson, Suzanne Kamel-Reid, Janet E. Dancey
International Journal of Cancer DOI: 10.1002/ijc.27817
Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing
Karen E. Ocwieja, Scott Sherrill-Mix, Rithun Mukherjee, Rebecca Custers-Allen, Patricia David, Michael Brown, Susana Wang, Darren R. Link, Jeff Olson, Kevin Travers, Eric Schadt and Frederic D. Bushman
Finished bacterial genomes from shotgun sequence data
Filipe Ribeiro, Dariusz Przybylski, Shuangye Yin, Ted Sharpe, Sante Gnerre, Amr Abouelleil, Aaron M Berlin, Anna Montmayeur, Terrance P Shea, Bruce J Walker, Sarah K Young, Carsten Russ, Iain MacCallum, Chad Nusbaum and David B Jaffe
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
Improving genome assemblies by sequencing PCR products with PacBio
Xiaojing Zhang, Karen W. Davenport, Wei Gu, Hajnalka E. Daligault, A. Christine Munk, Hazuki Tashima, Krista Reitenga, Lance D. Green, and Cliff S. Han
BioTechniques 53:61-62 (July 2012) doi 10.2144/0000113891
A hybrid approach for the automated finishing of bacterial genomes
Ali Bashir, Aaron A Klammer, William P Robins, Chen-Shan Chin, Dale Webster, Ellen Paxinos, David Hsu, Meredith Ashby, Susana Wang, Paul Peluso, Robert Sebra, Jon Sorenson, James Bullard, Jackie Yen, Marie Valdovino, Emilia Mollova, Khai Luong, Steven Lin, Brianna LaMay, Amruta Joshi, Lori Rowe, Michael Frace, Cheryl L Tarr, Maryann Turnsek, Brigid M Davis, Andrew Kasarskis, John J Mekalanos, Matthew K Waldor & Eric E Schadt
Hybrid error correction and de novo assembly of single-molecule sequencing reads
Sergey Koren, Michael C. Schatz, Brian P. Walenz, Jeffrey Martin,Jason Howard, Ganeshkumar Ganapathy, Zhong Wang, David A.Rasko , W. Richard McCombie, Erich D. Jarvis, and Adam M. Phillippy
Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia
Manuel Martinez-Garcia, David M. Brazel, Brandon K. Swan, Carol Arnosti, Patrick S. G. Chain, Krista G. Reitenga, Gary Xie, Nicole J. Poulton, Monica Lluesma Gomez, Dashiell E. D. Masland, Brian Thompson, Wendy K. Bellows, Kai Ziervogel, Chien-Chi Lo, Sanaa Ahmed, Cheryl D. Gleasner, Chris J. Detter, Ramunas Stepanauskas
PLoS ONE 7(4): e35314. doi:10.1371/journal.pone.0035314
Validation of FLT3-ITD as a therapeutic target in human acute myeloid leukemia
Catherine C. Smith, Qi Wang, Chen-Shan Chin, Sara Salerno1, Lauren E. Damon, Mark J. Levis, Alexander E. Perl, Kevin J. Travers, SusanaWang, Jeremy P. Hunt, Patrick P. Zarrinkar, Eric E. Schadt, Andrew Kasarskis, John Kuriyan & Neil P. Shah
Journal of Clinical Oncology – Cancer Genomics: Technology, Discovery and Translation
Ben Tran, Janet E. Dancey, Suzanne Kamel-Reid, John D. McPherson, Philippe L. Bedard, Andrew M.K. Brown, Tong Zhang, Patricia Shaw, Nicole Onetto, Lincoln Stein, Thomas J. Hudson, Benjamin G. Neel and Lillian L. Siu
Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011
Yonatan H. Grad, Marc Lipsitch, Michael Feldgarden, Harindra M. Arachchid, Gustavo C. Cerqueira, Michael FitzGerald, Paul Godfrey, Brian J. Haas, Cheryl I. Murphy, Carsten Russ, Sean Sykes, Bruce J. Walker, Jennifer R. Wortman, Sarah Young, Qiandong Zeng, Amr Abouelleil, James Bochicchio, Sara Chauvin, Timothy DeSmet, Sharvari Gujja, Caryn McCowan, Anna Montmayeur, Scott Steelman, Jakob Frimodt-Møller, Andreas M. Petersen, Carsten Struve, Karen A. Krogfelt, Edouard Bingen, François-Xavier Weill, Eric S. Lander, Chad Nusbaum, Bruce W. Birren, Deborah T. Hung, William P. Hanage
Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing
Tyson A. Clark, Iain A. Murray, Richard D. Morgan, Andrey O. Kislyuk, Kristi E. Spittle, Matthew Boitano, Alexey Fomenkov, Richard J. Roberts, and Jonas Korlach
Origins of the E. coli Strain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany
David A. Rasko, Ph.D., Dale R. Webster, Ph.D., Jason W. Sahl, Ph.D., Ali Bashir, Ph.D., Nadia Boisen, Ph.D., Flemming Scheutz, Ph.D., Ellen E. Paxinos, Ph.D., Robert Sebra, Ph.D., Chen-Shan Chin, Ph.D., Dimitris Iliopoulos, Ph.D., Aaron Klammer, Ph.D., Paul Peluso, Ph.D., Lawrence Lee, Ph.D., Andrey O. Kislyuk, Ph.D., James Bullard, Ph.D., Andrew Kasarskis, Ph.D., Susanna Wang, B.S., John Eid, Ph.D., David Rank, Ph.D., Julia C. Redman, Ph.D., Susan R. Steyert, Ph.D., Jakob Frimodt-Møller, B.S., Carsten Struve, Ph.D., Andreas M. Petersen, Ph.D., Karen A. Krogfelt, Ph.D., James P. Nataro, M.D., Ph.D., M.B.A., Eric E. Schadt, Ph.D., and Matthew K. Waldor, M.D., Ph.D.
The New England Journal of Medicine 10.1056/NEJMoa1106920
Chen-Shan Chin, Ph.D., Jon Sorenson, Ph.D., Jason B. Harris, M.D., William P. Robins, Ph.D., Richelle C. Charles, M.D., Roger R. Jean-Charles, M.D., James Bullard, Ph.D., Dale R. Webster, Ph.D., Andrew Kasarskis, Ph.D., Paul Peluso, Ph.D., Ellen E. Paxinos, Ph.D., Yoshiharu Yamaichi, Ph.D., Stephen B. Calderwood, M.D., John J. Mekalanos, Ph.D., Eric E. Schadt, Ph.D., and Matthew K. Waldor, M.D., Ph.D.
The New England Journal of Medicine 10.1056/NEJMoa1012928
Real-time DNA sequencing from single polymerase molecules
Jonas Korlach, Keith Bjornson, Bidhan Chaudhuri, Ron Cicero, Benjamin Flusberg, Jeremy Gray, David Holden, Ravi Saxena, Jeffrey Wegener, Stephen W. Turner.
Methods in Enzymology Volume 472, 2010, Pages 431-455
Real-Time DNA Sequencing from Single Polymerase Molecules
John Eid, Adrian Fehr, Jeremy Gray, Khai Lyong, John Lyle, Geoff Otto, Paul Peluso, David Rank, Primo Baybayan, Brad Bettman, Arakadiusz Bibillo, Keith Bjornson, Bidhan Chaudhuri, Frederick Christians, Ronald Cicero, Sonya Clark, Ravindra Dalal, Alex deWinter, John Dixon, Mathieu Foquet, Alfred Gaertner, Paul Hardenbol, Cheryl Heiner, Kevin Hester, David Holden, Gregory Kearns, Xiangxu Hong, Ronald Kuse, Yves Lacroix, Steven Lin, Paul Lunquist, Congcong Ma, Patrick Marks, Mark Maxham, Devon Murphy, Insil Park, Thang Pham, Michael Phillips, Joy Roy, Robert Sebra, Gene Shen, Jon Sorenson, Austin Tomaney, Kevin Travers, Mark Trulson, John Vieceli, Jeffrey Wegener, Dawn Wu, Alicia Yang, Denis Zaccarin, Peter Zhao, Frank Zhong, Jonas Korlach, Stephen Turner
Parallel confocal detection of single molecules in real time
Paul M. Lundquist, Cheng F. Zhong, Peiqian Zhao, Austin B. Tomaney, Paul S. Peluso, John Dixon, Brad Bettman, Yves Lacroix, Deborah P. Kwo, Etienne McCullough, Mark Maxham, Kevin Hester, Paul McNitt, Donald M. Grey, Carlos Henriquez, Mathieu Foquet, Stephen W. Turner, and Denis Zaccarin
