A citation-based method for searching scientific literature

Cole Trapnell, Lior Pachter, Steven L Salzberg. Bioinformatics 2009
Times Cited: 8420







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



Times Cited
  Times     Co-cited
Similarity


Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions.
Joshua N Burton, Andrew Adey, Rupali P Patwardhan, Ruolan Qiu, Jacob O Kitzman, Jay Shendure. Nat Biotechnol 2013
592
3

CAFE: a computational tool for the study of gene family evolution.
Tijl De Bie, Nello Cristianini, Jeffery P Demuth, Matthew W Hahn. Bioinformatics 2006
726
3

The variant call format and VCFtools.
Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A Albers, Eric Banks, Mark A DePristo, Robert E Handsaker, Gerton Lunter, Gabor T Marth, Stephen T Sherry,[...]. Bioinformatics 2011
3

TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.
W H Majoros, M Pertea, S L Salzberg. Bioinformatics 2004
694
3


PLINK: a tool set for whole-genome association and population-based linkage analyses.
Shaun Purcell, Benjamin Neale, Kathe Todd-Brown, Lori Thomas, Manuel A R Ferreira, David Bender, Julian Maller, Pamela Sklar, Paul I W de Bakker, Mark J Daly,[...]. Am J Hum Genet 2007
3

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
3


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
3

Repbase Update, a database of repetitive elements in eukaryotic genomes.
Weidong Bao, Kenji K Kojima, Oleksiy Kohany. Mob DNA 2015
3

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.
Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen White, C Robin Buell, Jennifer R Wortman. Genome Biol 2008
3

Using RepeatMasker to identify repetitive elements in genomic sequences.
Maja Tarailo-Graovac, Nansheng Chen. Curr Protoc Bioinformatics 2009
818
3

The Pfam protein families database.
Marco Punta, Penny C Coggill, Ruth Y Eberhardt, Jaina Mistry, John Tate, Chris Boursnell, Ningze Pang, Kristoffer Forslund, Goran Ceric, Jody Clements,[...]. Nucleic Acids Res 2012
3

AUGUSTUS: ab initio prediction of alternative transcripts.
Mario Stanke, Oliver Keller, Irfan Gunduz, Alec Hayes, Stephan Waack, Burkhard Morgenstern. Nucleic Acids Res 2006
909
3

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nucleic Acids Res 2009
3

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.
Daehwan Kim, Joseph M Paggi, Chanhee Park, Christopher Bennett, Steven L Salzberg. Nat Biotechnol 2019
3

NIH Image to ImageJ: 25 years of image analysis.
Caroline A Schneider, Wayne S Rasband, Kevin W Eliceiri. Nat Methods 2012
3


Comprehensive Integration of Single-Cell Data.
Tim Stuart, Andrew Butler, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M Mauck, Yuhan Hao, Marlon Stoeckius, Peter Smibert, Rahul Satija. Cell 2019
3

Full-length RNA-seq from single cells using Smart-seq2.
Simone Picelli, Omid R Faridani, Asa K Björklund, Gösta Winberg, Sven Sagasser, Rickard Sandberg. Nat Protoc 2014
3

Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Manfred G Grabherr, Brian J Haas, Moran Yassour, Joshua Z Levin, Dawn A Thompson, Ido Amit, Xian Adiconis, Lin Fan, Raktima Raychowdhury, Qiandong Zeng,[...]. Nat Biotechnol 2011
3

An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency.
Lena Ho, Jehnna L Ronan, Jiang Wu, Brett T Staahl, Lei Chen, Ann Kuo, Julie Lessard, Alexey I Nesvizhskii, Jeff Ranish, Gerald R Crabtree. Proc Natl Acad Sci U S A 2009
384
3

A Brg1 null mutation in the mouse reveals functional differences among mammalian SWI/SNF complexes.
S Bultman, T Gebuhr, D Yee, C La Mantia, J Nicholson, A Gilliam, F Randazzo, D Metzger, P Chambon, G Crabtree,[...]. Mol Cell 2000
628
3



The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools.
Philippe Lamesch, Tanya Z Berardini, Donghui Li, David Swarbreck, Christopher Wilks, Rajkumar Sasidharan, Robert Muller, Kate Dreher, Debbie L Alexander, Margarita Garcia-Hernandez,[...]. Nucleic Acids Res 2012
3

RNA-Seq: a revolutionary tool for transcriptomics.
Zhong Wang, Mark Gerstein, Michael Snyder. Nat Rev Genet 2009
3

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Damian Szklarczyk, Annika L Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic, Nadezhda T Doncheva, John H Morris, Peer Bork,[...]. Nucleic Acids Res 2019
3

Protein Kinase Ime2 Is Required for Mycelial Growth, Conidiation, Osmoregulation, and Pathogenicity in Nematode-Trapping Fungus Arthrobotrys oligospora.
Meihua Xie, Na Bai, Jiangliu Yang, Kexin Jiang, Duanxu Zhou, Yining Zhao, Dongni Li, Xuemei Niu, Ke-Qin Zhang, Jinkui Yang. Front Microbiol 2020
19
10

The Arf-GAP AoGlo3 regulates conidiation, endocytosis, and pathogenicity in the nematode-trapping fungus Arthrobotrys oligospora.
Yuxin Ma, Xuewei Yang, Meihua Xie, Guosheng Zhang, Le Yang, Na Bai, Yining Zhao, Dongni Li, Ke-Qin Zhang, Jinkui Yang. Fungal Genet Biol 2020
17
11

Two Rab GTPases play different roles in conidiation, trap formation, stress resistance, and virulence in the nematode-trapping fungus Arthrobotrys oligospora.
Xuewei Yang, Ni Ma, Le Yang, Yaqing Zheng, Zhengyi Zhen, Qing Li, Meihua Xie, Juan Li, Ke-Qin Zhang, Jinkui Yang. Appl Microbiol Biotechnol 2018
31
6

Genomic and proteomic analyses of the fungus Arthrobotrys oligospora provide insights into nematode-trap formation.
Jinkui Yang, Lei Wang, Xinglai Ji, Yun Feng, Xiaomin Li, Chenggang Zou, Jianping Xu, Yan Ren, Qili Mi, Junli Wu,[...]. PLoS Pathog 2011
133
2

Natural diversity in the predatory behavior facilitates the establishment of a robust model strain for nematode-trapping fungi.
Ching-Ting Yang, Guillermo Vidal-Diez de Ulzurrun, A Pedro Gonçalves, Hung-Che Lin, Ching-Wen Chang, Tsung-Yu Huang, Sheng-An Chen, Cheng-Kuo Lai, Isheng J Tsai, Frank C Schroeder,[...]. Proc Natl Acad Sci U S A 2020
27
7


AoStuA, an APSES transcription factor, regulates the conidiation, trap formation, stress resistance and pathogenicity of the nematode-trapping fungus Arthrobotrys oligospora.
Meihua Xie, Yunchuan Wang, Liyan Tang, Le Yang, Duanxu Zhou, Qing Li, Xuemei Niu, Ke-Qin Zhang, Jinkui Yang. Environ Microbiol 2019
23
8

The Velvet Proteins VosA and VelB Play Different Roles in Conidiation, Trap Formation, and Pathogenicity in the Nematode-Trapping Fungus Arthrobotrys oligospora.
Guosheng Zhang, Yaqing Zheng, Yuxin Ma, Le Yang, Meihua Xie, Duanxu Zhou, Xuemei Niu, Ke-Qin Zhang, Jinkui Yang. Front Microbiol 2019
16
12

Trapping devices of nematode-trapping fungi: formation, evolution, and genomic perspectives.
Hao Su, Yong Zhao, Jing Zhou, Huihua Feng, Dewei Jiang, Ke-Qin Zhang, Jinkui Yang. Biol Rev Camb Philos Soc 2017
35
5

MAP kinase Slt2 orthologs play similar roles in conidiation, trap formation, and pathogenicity in two nematode-trapping fungi.
Zhengyi Zhen, Xinjing Xing, Meihua Xie, Le Yang, Xuewei Yang, Yaqing Zheng, Yuanli Chen, Ni Ma, Qing Li, Ke-Qin Zhang,[...]. Fungal Genet Biol 2018
35
5



Gene finding in novel genomes.
Ian Korf. BMC Bioinformatics 2004
2

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
2

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Erez Lieberman-Aiden, Nynke L van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R Lajoie, Peter J Sabo, Michael O Dorschner,[...]. Science 2009
2

Methylation of histone H3 Lys 4 in coding regions of active genes.
Bradley E Bernstein, Emily L Humphrey, Rachel L Erlich, Robert Schneider, Peter Bouman, Jun S Liu, Tony Kouzarides, Stuart L Schreiber. Proc Natl Acad Sci U S A 2002
546
2


Pro-inflammatory CD11c+CD206+ adipose tissue macrophages are associated with insulin resistance in human obesity.
John M Wentworth, Gaetano Naselli, Wendy A Brown, Lisa Doyle, Belinda Phipson, Gordon K Smyth, Martin Wabitsch, Paul E O'Brien, Leonard C Harrison. Diabetes 2010
392
2

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool.
Edward Y Chen, Christopher M Tan, Yan Kou, Qiaonan Duan, Zichen Wang, Gabriela Vaz Meirelles, Neil R Clark, Avi Ma'ayan. BMC Bioinformatics 2013
2

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer.
Caryn S Ross-Innes, Rory Stark, Andrew E Teschendorff, Kelly A Holmes, H Raza Ali, Mark J Dunning, Gordon D Brown, Ondrej Gojis, Ian O Ellis, Andrew R Green,[...]. Nature 2012
944
2

Clustal W and Clustal X version 2.0.
M A Larkin, G Blackshields, N P Brown, R Chenna, P A McGettigan, H McWilliam, F Valentin, I M Wallace, A Wilm, R Lopez,[...]. Bioinformatics 2007
2

Near-optimal probabilistic RNA-seq quantification.
Nicolas L Bray, Harold Pimentel, Páll Melsted, Lior Pachter. Nat Biotechnol 2016
2


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.