A citation-based method for searching scientific literature

Steven R Head, H Kiyomi Komori, Sarah A LaMere, Thomas Whisenant, Filip Van Nieuwerburgh, Daniel R Salomon, Phillip Ordoukhanian. Biotechniques 2014
Times Cited: 228







List of co-cited articles
418 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
15

Coming of age: ten years of next-generation sequencing technologies.
Sara Goodwin, John D McPherson, W Richard McCombie. Nat Rev Genet 2016
13


Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
12

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
11

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
10

Sequencing technologies - the next generation.
Michael L Metzker. Nat Rev Genet 2010
9

Sequencing depth and coverage: key considerations in genomic analyses.
David Sims, Ian Sudbery, Nicholas E Ilott, Andreas Heger, Chris P Ponting. Nat Rev Genet 2014
591
9

Target-enrichment strategies for next-generation sequencing.
Lira Mamanova, Alison J Coffey, Carol E Scott, Iwanka Kozarewa, Emily H Turner, Akash Kumar, Eleanor Howard, Jay Shendure, Daniel J Turner. Nat Methods 2010
627
8

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly,[...]. Genome Res 2010
8

Library preparation methods for next-generation sequencing: tone down the bias.
Erwin L van Dijk, Yan Jaszczyszyn, Claude Thermes. Exp Cell Res 2014
191
8

TopHat: discovering splice junctions with RNA-Seq.
Cole Trapnell, Lior Pachter, Steven L Salzberg. Bioinformatics 2009
7

Accurate whole human genome sequencing using reversible terminator chemistry.
David R Bentley, Shankar Balasubramanian, Harold P Swerdlow, Geoffrey P Smith, John Milton, Clive G Brown, Kevin P Hall, Dirk J Evers, Colin L Barnes, Helen R Bignell,[...]. Nature 2008
7

Ten years of next-generation sequencing technology.
Erwin L van Dijk, Hélène Auger, Yan Jaszczyszyn, Claude Thermes. Trends Genet 2014
576
6

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
6

RNA-Seq: a revolutionary tool for transcriptomics.
Zhong Wang, Mark Gerstein, Michael Snyder. Nat Rev Genet 2009
6


Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries.
Daniel Aird, Michael G Ross, Wei-Sheng Chen, Maxwell Danielsson, Timothy Fennell, Carsten Russ, David B Jaffe, Chad Nusbaum, Andreas Gnirke. Genome Biol 2011
590
6

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.
Dinghua Li, Chi-Man Liu, Ruibang Luo, Kunihiko Sadakane, Tak-Wah Lam. Bioinformatics 2015
991
5


DNA sequencing with chain-terminating inhibitors.
F Sanger, S Nicklen, A R Coulson. Proc Natl Acad Sci U S A 1977
5

A framework for variation discovery and genotyping using next-generation DNA sequencing data.
Mark A DePristo, Eric Banks, Ryan Poplin, Kiran V Garimella, Jared R Maguire, Christopher Hartl, Anthony A Philippakis, Guillermo del Angel, Manuel A Rivas, Matt Hanna,[...]. Nat Genet 2011
5

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg. Genome Biol 2009
5

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
Cole Trapnell, Adam Roberts, Loyal Goff, Geo Pertea, Daehwan Kim, David R Kelley, Harold Pimentel, Steven L Salzberg, John L Rinn, Lior Pachter. Nat Protoc 2012
5

Comparison of Sample Preparation Methods Used for the Next-Generation Sequencing of Mycobacterium tuberculosis.
Andrea D Tyler, Sara Christianson, Natalie C Knox, Philip Mabon, Joyce Wolfe, Gary Van Domselaar, Morag R Graham, Meenu K Sharma. PLoS One 2016
26
19

Biases in small RNA deep sequencing data.
Carsten A Raabe, Thean-Hock Tang, Juergen Brosius, Timofey S Rozhdestvensky. Nucleic Acids Res 2014
119
5

Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing.
Anitha D Jayaprakash, Omar Jabado, Brian D Brown, Ravi Sachidanandam. Nucleic Acids Res 2011
148
5

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A Gurevich, Mikhail Dvorkin, Alexander S Kulikov, Valery M Lesin, Sergey I Nikolenko, Son Pham, Andrey D Prjibelski,[...]. J Comput Biol 2012
5

Systematic comparison of three methods for fragmentation of long-range PCR products for next generation sequencing.
Ellen Knierim, Barbara Lucke, Jana Marie Schwarz, Markus Schuelke, Dominik Seelow. PLoS One 2011
64
7

Comparison of next-generation sequencing systems.
Lin Liu, Yinhu Li, Siliang Li, Ni Hu, Yimin He, Ray Pong, Danni Lin, Lihua Lu, Maggie Law. J Biomed Biotechnol 2012
593
5

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.
Michael A Quail, Miriam Smith, Paul Coupland, Thomas D Otto, Simon R Harris, Thomas R Connor, Anna Bertoni, Harold P Swerdlow, Yong Gu. BMC Genomics 2012
971
5

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
Helga Thorvaldsdóttir, James T Robinson, Jill P Mesirov. Brief Bioinform 2013
5

Progress in ion torrent semiconductor chip based sequencing.
Barry Merriman, Jonathan M Rothberg. Electrophoresis 2012
146
5

A large genome center's improvements to the Illumina sequencing system.
Michael A Quail, Iwanka Kozarewa, Frances Smith, Aylwyn Scally, Philip J Stephens, Richard Durbin, Harold Swerdlow, Daniel J Turner. Nat Methods 2008
487
5

The Third Revolution in Sequencing Technology.
Erwin L van Dijk, Yan Jaszczyszyn, Delphine Naquin, Claude Thermes. Trends Genet 2018
209
5


Assembly algorithms for next-generation sequencing data.
Jason R Miller, Sergey Koren, Granger Sutton. Genomics 2010
496
4

PacBio Sequencing and Its Applications.
Anthony Rhoads, Kin Fai Au. Genomics Proteomics Bioinformatics 2015
643
4

The sequence read archive.
Rasko Leinonen, Hideaki Sugawara, Martin Shumway. Nucleic Acids Res 2011
937
4


Counting absolute numbers of molecules using unique molecular identifiers.
Teemu Kivioja, Anna Vähärautio, Kasper Karlsson, Martin Bonke, Martin Enge, Sten Linnarsson, Jussi Taipale. Nat Methods 2011
464
4

Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling.
Maria D Giraldez, Ryan M Spengler, Alton Etheridge, Paula M Godoy, Andrea J Barczak, Srimeenakshi Srinivasan, Peter L De Hoff, Kahraman Tanriverdi, Amanda Courtright, Shulin Lu,[...]. Nat Biotechnol 2018
51
7


RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries.
Markus Hafner, Neil Renwick, Miguel Brown, Aleksandra Mihailović, Daniel Holoch, Carolina Lin, John T G Pena, Jeffrey D Nusbaum, Pavel Morozov, Janos Ludwig,[...]. RNA 2011
225
4

Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation.
Sabrina Shore, Jordana M Henderson, Alexandre Lebedev, Michelle P Salcedo, Gerald Zon, Anton P McCaffrey, Natasha Paul, Richard I Hogrefe. PLoS One 2016
22
18

Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases.
Xi Chen, Yi Ba, Lijia Ma, Xing Cai, Yuan Yin, Kehui Wang, Jigang Guo, Yujing Zhang, Jiangning Chen, Xing Guo,[...]. Cell Res 2008
4

Toward reliable biomarker signatures in the age of liquid biopsies - how to standardize the small RNA-Seq workflow.
Dominik Buschmann, Anna Haberberger, Benedikt Kirchner, Melanie Spornraft, Irmgard Riedmaier, Gustav Schelling, Michael W Pfaffl. Nucleic Acids Res 2016
49
8

A reference human genome dataset of the BGISEQ-500 sequencer.
Jie Huang, Xinming Liang, Yuankai Xuan, Chunyu Geng, Yuxiang Li, Haorong Lu, Shoufang Qu, Xianglin Mei, Hongbo Chen, Ting Yu,[...]. Gigascience 2017
101
4

Genome sequencing in microfabricated high-density picolitre reactors.
Marcel Margulies, Michael Egholm, William E Altman, Said Attiya, Joel S Bader, Lisa A Bemben, Jan Berka, Michael S Braverman, Yi-Ju Chen, Zhoutao Chen,[...]. Nature 2005
4

Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists.
Marilyn M Li, Michael Datto, Eric J Duncavage, Shashikant Kulkarni, Neal I Lindeman, Somak Roy, Apostolia M Tsimberidou, Cindy L Vnencak-Jones, Daynna J Wolff, Anas Younes,[...]. J Mol Diagn 2017
468
4


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.