A citation-based method for searching scientific literature

Stephan Schmeing, Mark D Robinson. Genome Biol 2021
Times Cited: 2







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



Times Cited
  Times     Co-cited
Similarity


Sequence-specific error profile of Illumina sequencers.
Kensuke Nakamura, Taku Oshima, Takuya Morimoto, Shun Ikeda, Hirofumi Yoshikawa, Yuh Shiwa, Shu Ishikawa, Margaret C Linak, Aki Hirai, Hiroki Takahashi,[...]. Nucleic Acids Res 2011
363
50

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls.
Justin M Zook, Brad Chapman, Jason Wang, David Mittelman, Oliver Hofmann, Winston Hide, Marc Salit. Nat Biotechnol 2014
422
50

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.
Hongshan Jiang, Rong Lei, Shou-Wei Ding, Shuifang Zhu. BMC Bioinformatics 2014
550
50

First molecular cytogenetic high resolution characterization of the NIH 3T3 cell line by murine multicolor banding.
Christine Leibiger, Nadezda Kosyakova, Hasmik Mkrtchyan, Michael Glei, Vladimir Trifonov, Thomas Liehr. J Histochem Cytochem 2013
33
50

Characterizing and measuring bias in sequence data.
Michael G Ross, Carsten Russ, Maura Costello, Andrew Hollinger, Niall J Lennon, Ryan Hegarty, Chad Nusbaum, David B Jaffe. Genome Biol 2013
403
50

SOAP2: an improved ultrafast tool for short read alignment.
Ruiqiang Li, Chang Yu, Yingrui Li, Tak-Wah Lam, Siu-Ming Yiu, Karsten Kristiansen, Jun Wang. Bioinformatics 2009
50

A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE.
Kevin P Keegan, William L Trimble, Jared Wilkening, Andreas Wilke, Travis Harrison, Mark D'Souza, Folker Meyer. PLoS Comput Biol 2012
40
50

Comparison of the MGISEQ-2000 and Illumina HiSeq 4000 sequencing platforms for RNA sequencing.
Sol A Jeon, Jong Lyul Park, Jong-Hwan Kim, Jeong Hwan Kim, Yong Sung Kim, Jin Cheon Kim, Seon-Young Kim. Genomics Inform 2019
13
50

Single Nucleotide Polymorphism Identification in Polyploids: A Review, Example, and Recommendations.
Josh Clevenger, Carolina Chavarro, Stephanie A Pearl, Peggy Ozias-Akins, Scott A Jackson. Mol Plant 2015
68
50

Identification and correction of systematic error in high-throughput sequence data.
Frazer Meacham, Dario Boffelli, Joseph Dhahbi, David I K Martin, Meromit Singer, Lior Pachter. BMC Bioinformatics 2011
150
50

The SeqAn C++ template library for efficient sequence analysis: A resource for programmers.
Knut Reinert, Temesgen Hailemariam Dadi, Marcel Ehrhardt, Hannes Hauswedell, Svenja Mehringer, René Rahn, Jongkyu Kim, Christopher Pockrandt, Jörg Winkler, Enrico Siragusa,[...]. J Biotechnol 2017
31
50

Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation.
Michael I Love, John B Hogenesch, Rafael A Irizarry. Nat Biotechnol 2016
62
50

Summarizing and correcting the GC content bias in high-throughput sequencing.
Yuval Benjamini, Terence P Speed. Nucleic Acids Res 2012
426
50

Correcting Illumina data.
Michael Molnar, Lucian Ilie. Brief Bioinform 2015
18
50

Best practices for benchmarking germline small-variant calls in human genomes.
Peter Krusche, Len Trigg, Paul C Boutros, Christopher E Mason, Francisco M De La Vega, Benjamin L Moore, Mar Gonzalez-Porta, Michael A Eberle, Zivana Tezak, Samir Lababidi,[...]. Nat Biotechnol 2019
69
50

KMC 3: counting and manipulating k-mer statistics.
Marek Kokot, Maciej Dlugosz, Sebastian Deorowicz. Bioinformatics 2017
78
50

A better sequence-read simulator program for metagenomics.
Stephen Johnson, Brett Trost, Jeffrey R Long, Vanessa Pittet, Anthony Kusalik. BMC Bioinformatics 2014
20
50

DRISEE overestimates errors in metagenomic sequencing data.
A Murat Eren, Hilary G Morrison, Susan M Huse, Mitchell L Sogin. Brief Bioinform 2014
4
50

Systematic benchmarking of omics computational tools.
Serghei Mangul, Lana S Martin, Brian L Hill, Angela Ka-Mei Lam, Margaret G Distler, Alex Zelikovsky, Eleazar Eskin, Jonathan Flint. Nat Commun 2019
45
50

QUAST: quality assessment tool for genome assemblies.
Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler. Bioinformatics 2013
50

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
628
50


A comparison of tools for the simulation of genomic next-generation sequencing data.
Merly Escalona, Sara Rocha, David Posada. Nat Rev Genet 2016
67
50

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study.
Sheng Li, Scott W Tighe, Charles M Nicolet, Deborah Grove, Shawn Levy, William Farmerie, Agnes Viale, Chris Wright, Peter A Schweitzer, Yuan Gao,[...]. Nat Biotechnol 2014
130
50


Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data.
Melanie Schirmer, Rosalinda D'Amore, Umer Z Ijaz, Neil Hall, Christopher Quince. BMC Bioinformatics 2016
152
50

The present and future of de novo whole-genome assembly.
Jang-Il Sohn, Jin-Wu Nam. Brief Bioinform 2018
64
50


A broad survey of DNA sequence data simulation tools.
Shatha Alosaimi, Armand Bandiang, Noelle van Biljon, Denis Awany, Prisca K Thami, Milaine S S Tchamga, Anmol Kiran, Olfa Messaoud, Radia Ismaeel Mohammed Hassan, Jacquiline Mugo,[...]. Brief Funct Genomics 2020
4
50

Improved genome sequencing using an engineered transposase.
Amirali Kia, Christian Gloeckner, Trina Osothprarop, Niall Gormley, Erin Bomati, Michelle Stephenson, Igor Goryshin, Molly Min He. BMC Biotechnol 2017
13
50

Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
Bruce J Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K Young,[...]. PLoS One 2014
50

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
50

Systematic evaluation of error rates and causes in short samples in next-generation sequencing.
Franziska Pfeiffer, Carsten Gröber, Michael Blank, Kristian Händler, Marc Beyer, Joachim L Schultze, Günter Mayer. Sci Rep 2018
103
50

Assemblathon 1: a competitive assessment of de novo short read assembly methods.
Dent Earl, Keith Bradnam, John St John, Aaron Darling, Dawei Lin, Joseph Fass, Hung On Ken Yu, Vince Buffalo, Daniel R Zerbino, Mark Diekhans,[...]. Genome Res 2011
283
50


Simulating Next-Generation Sequencing Datasets from Empirical Mutation and Sequencing Models.
Zachary D Stephens, Matthew E Hudson, Liudmila S Mainzer, Morgan Taschuk, Matthew R Weber, Ravishankar K Iyer. PLoS One 2016
21
50

A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree.
Michael A Eberle, Epameinondas Fritzilas, Peter Krusche, Morten Källberg, Benjamin L Moore, Mitchell A Bekritsky, Zamin Iqbal, Han-Yu Chuang, Sean J Humphray, Aaron L Halpern,[...]. Genome Res 2017
157
50



GAGE: A critical evaluation of genome assemblies and assembly algorithms.
Steven L Salzberg, Adam M Phillippy, Aleksey Zimin, Daniela Puiu, Tanja Magoc, Sergey Koren, Todd J Treangen, Michael C Schatz, Arthur L Delcher, Michael Roberts,[...]. Genome Res 2012
351
50

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
Helga Thorvaldsdóttir, James T Robinson, Jill P Mesirov. Brief Bioinform 2013
50

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.
Keith R Bradnam, Joseph N Fass, Anton Alexandrov, Paul Baranay, Michael Bechner, Inanç Birol, Sébastien Boisvert, Jarrod A Chapman, Guillaume Chapuis, Rayan Chikhi,[...]. Gigascience 2013
365
50

Extensive sequencing of seven human genomes to characterize benchmark reference materials.
Justin M Zook, David Catoe, Jennifer McDaniel, Lindsay Vang, Noah Spies, Arend Sidow, Ziming Weng, Yuling Liu, Christopher E Mason, Noah Alexander,[...]. Sci Data 2016
252
50

pIRS: Profile-based Illumina pair-end reads simulator.
Xuesong Hu, Jianying Yuan, Yujian Shi, Jianliang Lu, Binghang Liu, Zhenyu Li, Yanxiang Chen, Desheng Mu, Hao Zhang, Nan Li,[...]. Bioinformatics 2012
106
50

Snakemake--a scalable bioinformatics workflow engine.
Johannes Köster, Sven Rahmann. Bioinformatics 2012
737
50

ART: a next-generation sequencing read simulator.
Weichun Huang, Leping Li, Jason R Myers, Gabor T Marth. Bioinformatics 2012
587
50

A synthetic-diploid benchmark for accurate variant-calling evaluation.
Heng Li, Jonathan M Bloom, Yossi Farjoun, Mark Fleharty, Laura Gauthier, Benjamin Neale, Daniel MacArthur. Nat Methods 2018
44
50

SeqPurge: highly-sensitive adapter trimming for paired-end NGS data.
Marc Sturm, Christopher Schroeder, Peter Bauer. BMC Bioinformatics 2016
54
50

Analysis of error profiles in deep next-generation sequencing data.
Xiaotu Ma, Ying Shao, Liqing Tian, Diane A Flasch, Heather L Mulder, Michael N Edmonson, Yu Liu, Xiang Chen, Scott Newman, Joy Nakitandwe,[...]. Genome Biol 2019
72
50

Long fragments achieve lower base quality in Illumina paired-end sequencing.
Ge Tan, Lennart Opitz, Ralph Schlapbach, Hubert Rehrauer. Sci Rep 2019
21
50


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.