2012 Sequencing archive


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2012 Sequencing


De novo derivation of proteomes from transcriptomes for transcript and protein identification pp1207 - 1211

Vanessa C Evans, Gary Barker, Kate J Heesom, Jun Fan, Conrad Bessant & David A Matthews

doi:10.1038/nmeth.2227


DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution pp1107 - 1112

Ester Falconer, Mark Hills, Ulrike Naumann, Steven S S Poon, Elizabeth A Chavez, Ashley D Sanders, Yongjun Zhao, Martin Hirst & Peter M Lansdorp

doi:10.1038/nmeth.2206



Metagenomic microbial community profiling using unique clade-specific marker genes pp811 - 814

Nicola Segata, Levi Waldron, Annalisa Ballarini, Vagheesh Narasimhan, Olivier Jousson & Curtis Huttenhower

doi:10.1038/nmeth.2066

See also: News and Views by Haft & Tovchigrechko


High-speed microbial community profiling pp793 - 794

Daniel H Haft & Andrey Tovchigrechko

doi:10.1038/nmeth.2080

See also: Brief Communication by Segata et al.



Accurate identification of human Alu and non-Alu RNA editing sites pp579 - 581

Gokul Ramaswami, Wei Lin, Robert Piskol, Meng How Tan, Carrie Davis & Jin Billy Li

doi:10.1038/nmeth.1982


Systematic evaluation of factors influencing ChIP-seq fidelity pp609 - 614

Yiwen Chen, Nicolas Negre, Qunhua Li, Joanna O Mieczkowska, Matthew Slattery, Tao Liu, Yong Zhang, Tae-Kyung Kim, Housheng Hansen He, Jennifer Zieba, Yijun Ruan, Peter J Bickel, Richard M Myers, Barbara J Wold, Kevin P White, Jason D Lieb & X Shirley Liu

doi:10.1038/nmeth.1985


Counting stem cells: methodological constraints pp567 - 574

Leonid V Bystrykh, Evgenia Verovskaya, Erik Zwart, Mathilde Broekhuis & Gerald de Haan

doi:10.1038/nmeth.2043


Unsupervised pattern discovery in human chromatin structure through genomic segmentation pp473 - 476

Michael M Hoffman, Orion J Buske, Jie Wang, Zhiping Weng, Jeff A Bilmes & William Stafford Noble

doi:10.1038/nmeth.1937



Single-molecule mechanical identification and sequencing pp367 - 372

Fangyuan Ding, Maria Manosas, Michelle M Spiering, Stephen J Benkovic, David Bensimon, Jean-François Allemand & Vincent Croquette

doi:10.1038/nmeth.1925

See also: News and Views by Linnarsson


Genomics: A nanopore workhorse pp322 - 323

Nicole Rusk

doi:10.1038/nmeth.1962

Genomics

Sequencing

Single Molecule


Gene expression: In-depth functional dissection of enhancers pp322 - 323

Tal Nawy

doi:10.1038/nmeth.1963

Gene Expression

Sequencing


Library-free methylation sequencing with bisulfite padlock probes pp270 - 272

Dinh Diep, Nongluk Plongthongkum, Athurva Gore, Ho-Lim Fung, Robert Shoemaker & Kun Zhang

doi:10.1038/nmeth.1871


Detection of structural variants and indels within exome data pp176 - 178

Emre Karakoc, Can Alkan, Brian J O'Roak, Megan Y Dennis, Laura Vives, Kenneth Mark, Mark J Rieder, Debbie A Nickerson & Evan E Eichler

doi:10.1038/nmeth.1810



Gene expression: Ribosome profiling in bacteria p126

doi:10.1038/nmeth.1875


Sequencing: High-resolution chromatin immunoprecipitation p130

Tal Nawy

doi:10.1038/nmeth.1887

Sequencing

Genomics


Counting absolute numbers of molecules using unique molecular identifiers pp72 - 74

Teemu Kivioja, Anna Vähärautio, Kasper Karlsson, Martin Bonke, Martin Enge, Sten Linnarsson & Jussi Taipale

doi:10.1038/nmeth.1778


Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine pp75 - 77

Chun-Xiao Song, Tyson A Clark, Xing-Yu Lu, Andrey Kislyuk, Qing Dai, Stephen W Turner, Chuan He & Jonas Korlach

doi:10.1038/nmeth.1779



Optimal enzymes for amplifying sequencing libraries pp10 - 11

Michael A Quail, Thomas D Otto, Yong Gu, Simon R Harris, Thomas F Skelly, Jacqueline A McQuillan, Harold P Swerdlow & Samuel O Oyola

doi:10.1038/nmeth.1814


Sequencing:  Dark matter translation p17

doi:10.1038/nmeth.1832


Sequencing:  Peering deeper into the transcriptome pp14 - 15

Tal Nawy

doi:10.1038/nmeth.1844

Sequencing


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