A citation-based method for searching scientific literature

Guangchuang Yu, Li-Gen Wang, Qing-Yu He. Bioinformatics 2015
Times Cited: 699







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



Times Cited
  Times     Co-cited
Similarity


Variant Review with the Integrative Genomics Viewer.
James T Robinson, Helga Thorvaldsdóttir, Aaron M Wenger, Ahmet Zehir, Jill P Mesirov. Cancer Res 2017
277
2

Intron and gene size expansion during nervous system evolution.
Matthew J McCoy, Andrew Z Fire. BMC Genomics 2020
6
33

Chromatin remodelling during development.
Lena Ho, Gerald R Crabtree. Nature 2010
695
2

Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis.
Michael J Moore, Chaolin Zhang, Emily Conn Gantman, Aldo Mele, Jennifer C Darnell, Robert B Darnell. Nat Protoc 2014
163
2

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.
Ron Edgar, Michael Domrachev, Alex E Lash. Nucleic Acids Res 2002
2

BEDTools: The Swiss-Army Tool for Genome Feature Analysis.
Aaron R Quinlan. Curr Protoc Bioinformatics 2014
886
2

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
2


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
2

ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.
Jianhong Ou, Haibo Liu, Jun Yu, Michelle A Kelliher, Lucio H Castilla, Nathan D Lawson, Lihua Julie Zhu. BMC Genomics 2018
47
4

Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia.
Julien Bryois, Melanie E Garrett, Lingyun Song, Alexias Safi, Paola Giusti-Rodriguez, Graham D Johnson, Annie W Shieh, Alfonso Buil, John F Fullard, Panos Roussos,[...]. Nat Commun 2018
54
3

An expansive human regulatory lexicon encoded in transcription factor footprints.
Shane Neph, Jeff Vierstra, Andrew B Stergachis, Alex P Reynolds, Eric Haugen, Benjamin Vernot, Robert E Thurman, Sam John, Richard Sandstrom, Audra K Johnson,[...]. Nature 2012
516
2

DNase footprint signatures are dictated by factor dynamics and DNA sequence.
Myong-Hee Sung, Michael J Guertin, Songjoon Baek, Gordon L Hager. Mol Cell 2014
99
2

Global quantification of mammalian gene expression control.
Björn Schwanhäusser, Dorothea Busse, Na Li, Gunnar Dittmar, Johannes Schuchhardt, Jana Wolf, Wei Chen, Matthias Selbach. Nature 2011
2

F-Seq: a feature density estimator for high-throughput sequence tags.
Alan P Boyle, Justin Guinney, Gregory E Crawford, Terrence S Furey. Bioinformatics 2008
240
2

Ensembl 2018.
Daniel R Zerbino, Premanand Achuthan, Wasiu Akanni, M Ridwan Amode, Daniel Barrell, Jyothish Bhai, Konstantinos Billis, Carla Cummins, Astrid Gall, Carlos García Girón,[...]. Nucleic Acids Res 2018
2

A bivalent chromatin structure marks key developmental genes in embryonic stem cells.
Bradley E Bernstein, Tarjei S Mikkelsen, Xiaohui Xie, Michael Kamal, Dana J Huebert, James Cuff, Ben Fry, Alex Meissner, Marius Wernig, Kathrin Plath,[...]. Cell 2006
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


Mouse Genome Database (MGD) 2019.
Carol J Bult, Judith A Blake, Cynthia L Smith, James A Kadin, Joel E Richardson. Nucleic Acids Res 2019
228
2

MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens.
Wei Li, Han Xu, Tengfei Xiao, Le Cong, Michael I Love, Feng Zhang, Rafael A Irizarry, Jun S Liu, Myles Brown, X Shirley Liu. Genome Biol 2014
586
2

TGFβ drives immune evasion in genetically reconstituted colon cancer metastasis.
Daniele V F Tauriello, Sergio Palomo-Ponce, Diana Stork, Antonio Berenguer-Llergo, Jordi Badia-Ramentol, Mar Iglesias, Marta Sevillano, Sales Ibiza, Adrià Cañellas, Xavier Hernando-Momblona,[...]. Nature 2018
668
2

TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells.
Sanjeev Mariathasan, Shannon J Turley, Dorothee Nickles, Alessandra Castiglioni, Kobe Yuen, Yulei Wang, Edward E Kadel, Hartmut Koeppen, Jillian L Astarita, Rafael Cubas,[...]. Nature 2018
2

JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor.
Kenichi Yamane, Charalambos Toumazou, Yu-ichi Tsukada, Hediye Erdjument-Bromage, Paul Tempst, Jiemin Wong, Yi Zhang. Cell 2006
568
2


High-resolution profiling of histone methylations in the human genome.
Artem Barski, Suresh Cuddapah, Kairong Cui, Tae-Young Roh, Dustin E Schones, Zhibin Wang, Gang Wei, Iouri Chepelev, Keji Zhao. Cell 2007
2

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.
Maxim V Kuleshov, Matthew R Jones, Andrew D Rouillard, Nicolas F Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L Jenkins, Kathleen M Jagodnik, Alexander Lachmann,[...]. Nucleic Acids Res 2016
2

KRAS-IRF2 Axis Drives Immune Suppression and Immune Therapy Resistance in Colorectal Cancer.
Wenting Liao, Michael J Overman, Adam T Boutin, Xiaoying Shang, Di Zhao, Prasenjit Dey, Jiexi Li, Guocan Wang, Zhengdao Lan, Jun Li,[...]. Cancer Cell 2019
139
2

A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing.
Deng Pan, Aya Kobayashi, Peng Jiang, Lucas Ferrari de Andrade, Rong En Tay, Adrienne M Luoma, Daphne Tsoucas, Xintao Qiu, Klothilda Lim, Prakash Rao,[...]. Science 2018
310
2

IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.
Lam-Tung Nguyen, Heiko A Schmidt, Arndt von Haeseler, Bui Quang Minh. Mol Biol Evol 2015
2


Ballgown bridges the gap between transcriptome assembly and expression analysis.
Alyssa C Frazee, Geo Pertea, Andrew E Jaffe, Ben Langmead, Steven L Salzberg, Jeffrey T Leek. Nat Biotechnol 2015
305
2

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.
Mihaela Pertea, Daehwan Kim, Geo M Pertea, Jeffrey T Leek, Steven L Salzberg. Nat Protoc 2016
2

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals.
Vincent J Lynch, Robert D Leclerc, Gemma May, Günter P Wagner. Nat Genet 2011
234
2

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times.
Sudhir Kumar, Glen Stecher, Michael Suleski, S Blair Hedges. Mol Biol Evol 2017
771
2

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Cole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, Lior Pachter. Nat Biotechnol 2010
2

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
2

Silencing by plant Polycomb-group genes requires dispersed trimethylation of histone H3 at lysine 27.
Daniel Schubert, Lucia Primavesi, Anthony Bishopp, Gethin Roberts, John Doonan, Thomas Jenuwein, Justin Goodrich. EMBO J 2006
293
2

Cytosolic acetyl-CoA promotes histone acetylation predominantly at H3K27 in Arabidopsis.
Chen Chen, Chenlong Li, Ying Wang, Justin Renaud, Gang Tian, Shrikaar Kambhampati, Behnaz Saatian, Vi Nguyen, Abdelali Hannoufa, Frédéric Marsolais,[...]. Nat Plants 2017
42
4

GAT: a simulation framework for testing the association of genomic intervals.
Andreas Heger, Caleb Webber, Martin Goodson, Chris P Ponting, Gerton Lunter. Bioinformatics 2013
102
2

The Polycomb complex PRC2 and its mark in life.
Raphaël Margueron, Danny Reinberg. Nature 2011
2

BRAHMA-interacting proteins BRIP1 and BRIP2 are core subunits of Arabidopsis SWI/SNF complexes.
Yaoguang Yu, Zhenwei Liang, Xin Song, Wei Fu, Jianqu Xu, Yawen Lei, Liangbing Yuan, Jiuxiao Ruan, Chen Chen, Wenqun Fu,[...]. Nat Plants 2020
13
15

Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements.
Hua Wang, Chunmei Liu, Jingfei Cheng, Jian Liu, Lei Zhang, Chongsheng He, Wen-Hui Shen, Hong Jin, Lin Xu, Yijing Zhang. PLoS Genet 2016
76
2

Complementary Activities of TELOMERE REPEAT BINDING Proteins and Polycomb Group Complexes in Transcriptional Regulation of Target Genes.
Yue Zhou, Benjamin Hartwig, Geo Velikkakam James, Korbinian Schneeberger, Franziska Turck. Plant Cell 2016
42
4


Profiling histone modification patterns in plants using genomic tiling microarrays.
Anne-Valérie Gendrel, Zachary Lippman, Rob Martienssen, Vincent Colot. Nat Methods 2005
356
2

VAL- and AtBMI1-mediated H2Aub initiate the switch from embryonic to postgerminative growth in Arabidopsis.
Chao Yang, Fabian Bratzel, Nora Hohmann, Marcus Koch, Franziska Turck, Myriam Calonje. Curr Biol 2013
123
2


BEDOPS: high-performance genomic feature operations.
Shane Neph, M Scott Kuehn, Alex P Reynolds, Eric Haugen, Robert E Thurman, Audra K Johnson, Eric Rynes, Matthew T Maurano, Jeff Vierstra, Sean Thomas,[...]. Bioinformatics 2012
367
2

Interactome mapping defines BRG1, a component of the SWI/SNF chromatin remodeling complex, as a new partner of the transcriptional regulator CTCF.
Maria Michela Marino, Camilla Rega, Rosita Russo, Mariangela Valletta, Maria Teresa Gentile, Sabrina Esposito, Ilaria Baglivo, Italia De Feis, Claudia Angelini, Tioajiang Xiao,[...]. J Biol Chem 2019
17
11


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.