A citation-based method for searching scientific literature

Adam Nunn, Christian Otto, Peter F Stadler, David Langenberger. Brief Bioinform 2021
Times Cited: 6







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



Times Cited
  Times     Co-cited
Similarity




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


BSMAP: whole genome bisulfite sequence MAPping program.
Yuanxin Xi, Wei Li. BMC Bioinformatics 2009
653
50

DNA methylation and its basic function.
Lisa D Moore, Thuc Le, Guoping Fan. Neuropsychopharmacology 2013
50

Nextflow enables reproducible computational workflows.
Paolo Di Tommaso, Maria Chatzou, Evan W Floden, Pablo Prieto Barja, Emilio Palumbo, Cedric Notredame. Nat Biotechnol 2017
505
33

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.
Shawn J Cokus, Suhua Feng, Xiaoyu Zhang, Zugen Chen, Barry Merriman, Christian D Haudenschild, Sriharsa Pradhan, Stanley F Nelson, Matteo Pellegrini, Steven E Jacobsen. Nature 2008
33

Ecological plant epigenetics: Evidence from model and non-model species, and the way forward.
Christina L Richards, Conchita Alonso, Claude Becker, Oliver Bossdorf, Etienne Bucher, Maria Colomé-Tatché, Walter Durka, Jan Engelhardt, Bence Gaspar, Andreas Gogol-Döring,[...]. Ecol Lett 2017
135
33

kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity.
Kevin D Murray, Christfried Webers, Cheng Soon Ong, Justin Borevitz, Norman Warthmann. PLoS Comput Biol 2017
24
33

Objective and comprehensive evaluation of bisulfite short read mapping tools.
Hong Tran, Jacob Porter, Ming-An Sun, Hehuang Xie, Liqing Zhang. Adv Bioinformatics 2014
24
33

Singularity: Scientific containers for mobility of compute.
Gregory M Kurtzer, Vanessa Sochat, Michael W Bauer. PLoS One 2017
280
33

A blind and independent benchmark study for detecting differeally methylated regions in plants.
Clemens Kreutz, Nilay S Can, Ralf Schulze Bruening, Rabea Meyberg, Zsuzsanna Mérai, Noe Fernandez-Pozo, Stefan A Rensing. Bioinformatics 2020
3
66

metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data.
Frank Jühling, Helene Kretzmer, Stephan H Bernhart, Christian Otto, Peter F Stadler, Steve Hoffmann. Genome Res 2016
165
33

Conservation and divergence of methylation patterning in plants and animals.
Suhua Feng, Shawn J Cokus, Xiaoyu Zhang, Pao-Yang Chen, Magnolia Bostick, Mary G Goll, Jonathan Hetzel, Jayati Jain, Steven H Strauss, Marnie E Halpern,[...]. Proc Natl Acad Sci U S A 2010
767
33


Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data.
Yaping Liu, Kimberly D Siegmund, Peter W Laird, Benjamin P Berman. Genome Biol 2012
156
33

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
33

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles.
Altuna Akalin, Matthias Kormaksson, Sheng Li, Francine E Garrett-Bakelman, Maria E Figueroa, Ari Melnick, Christopher E Mason. Genome Biol 2012
885
33

Transgenerational epigenetic inheritance: myths and mechanisms.
Edith Heard, Robert A Martienssen. Cell 2014
816
33

Highly integrated single-base resolution maps of the epigenome in Arabidopsis.
Ryan Lister, Ronan C O'Malley, Julian Tonti-Filippini, Brian D Gregory, Charles C Berry, A Harvey Millar, Joseph R Ecker. Cell 2008
33

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling.
Hongcang Gu, Zachary D Smith, Christoph Bock, Patrick Boyle, Andreas Gnirke, Alexander Meissner. Nat Protoc 2011
453
33

HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
33

The GEM mapper: fast, accurate and versatile alignment by filtration.
Santiago Marco-Sola, Michael Sammeth, Roderic Guigó, Paolo Ribeca. Nat Methods 2012
319
33

Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution.
Yibin Liu, Paulina Siejka-Zielińska, Gergana Velikova, Ying Bi, Fang Yuan, Marketa Tomkova, Chunsen Bai, Lei Chen, Benjamin Schuster-Böckler, Chun-Xiao Song. Nat Biotechnol 2019
137
33

Comparison of alignment software for genome-wide bisulphite sequence data.
Aniruddha Chatterjee, Peter A Stockwell, Euan J Rodger, Ian M Morison. Nucleic Acids Res 2012
85
33

Latest techniques to study DNA methylation.
Quentin Gouil, Andrew Keniry. Essays Biochem 2019
45
33

Analysing and interpreting DNA methylation data.
Christoph Bock. Nat Rev Genet 2012
344
33


Base resolution methylome profiling: considerations in platform selection, data preprocessing and analysis.
Zhifu Sun, Julie Cunningham, Susan Slager, Jean-Pierre Kocher. Epigenomics 2015
60
33

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome.
Claude Becker, Jörg Hagmann, Jonas Müller, Daniel Koenig, Oliver Stegle, Karsten Borgwardt, Detlef Weigel. Nature 2011
423
33


BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data.
Weilong Guo, Petko Fiziev, Weihong Yan, Shawn Cokus, Xueguang Sun, Michael Q Zhang, Pao-Yang Chen, Matteo Pellegrini. BMC Genomics 2013
233
33

A comprehensive evaluation of alignment software for reduced representation bisulfite sequencing data.
Xiwei Sun, Yi Han, Liyuan Zhou, Enguo Chen, Bingjian Lu, Yong Liu, Xiaoqing Pan, Allen W Cowley, Mingyu Liang, Qingbiao Wu,[...]. Bioinformatics 2018
14
33

Current challenges in de novo plant genome sequencing and assembly.
Michael C Schatz, Jan Witkowski, W Richard McCombie. Genome Biol 2012
91
16

Bioconda: sustainable and comprehensive software distribution for the life sciences.
Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A Chapman, Jillian Rowe, Christopher H Tomkins-Tinch, Renan Valieris, Johannes Köster. Nat Methods 2018
355
16

The nf-core framework for community-curated bioinformatics pipelines.
Philip A Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso, Sven Nahnsen. Nat Biotechnol 2020
275
16

Transgenerational response to stress in Arabidopsis thaliana.
Alex Boyko, Igor Kovalchuk. Plant Signal Behav 2010
69
16


A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.
M Frommer, L E McDonald, D S Millar, C M Collis, F Watt, G W Grigg, P L Molloy, C L Paul. Proc Natl Acad Sci U S A 1992
16

Estimating Global Methylation and Erasure Using Low-Coverage Whole-Genome Bisulfite Sequencing (WGBS ).
Oscar Ortega-Recalde, Julian R Peat, Donna M Bond, Timothy A Hore. Methods Mol Biol 2021
3
33

Antimicrobial and cytotoxic knotwood extracts and related pure compounds and their effects on food-associated microorganisms.
Anna-Liisa Välimaa, Ulla Honkalampi-Hämäläinen, Suvi Pietarinen, Stefan Willför, Bjarne Holmbom, Atte von Wright. Int J Food Microbiol 2007
44
16

Associating cellular epigenetic models with human phenotypes.
Tuuli Lappalainen, John M Greally. Nat Rev Genet 2017
161
16


Applications and potential of genome editing in crop improvement.
Yi Zhang, Karen Massel, Ian D Godwin, Caixia Gao. Genome Biol 2018
109
16

Epigenetics: the science of change.
Bob Weinhold. Environ Health Perspect 2006
241
16

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.
Lucia A Hindorff, Praveen Sethupathy, Heather A Junkins, Erin M Ramos, Jayashri P Mehta, Francis S Collins, Teri A Manolio. Proc Natl Acad Sci U S A 2009
16

The Genomics of Oryza Species Provides Insights into Rice Domestication and Heterosis.
Erwang Chen, Xuehui Huang, Zhixi Tian, Rod A Wing, Bin Han. Annu Rev Plant Biol 2019
37
16

Improving power and accuracy of genome-wide association studies via a multi-locus mixed linear model methodology.
Shi-Bo Wang, Jian-Ying Feng, Wen-Long Ren, Bo Huang, Ling Zhou, Yang-Jun Wen, Jin Zhang, Jim M Dunwell, Shizhong Xu, Yuan-Ming Zhang. Sci Rep 2016
188
16



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.