A citation-based method for searching scientific literature

Michael N Edmonson, Jinghui Zhang, Chunhua Yan, Richard P Finney, Daoud M Meerzaman, Kenneth H Buetow. Bioinformatics 2011
Times Cited: 78







List of co-cited articles
376 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
30

The genetic basis of early T-cell precursor acute lymphoblastic leukaemia.
Jinghui Zhang, Li Ding, Linda Holmfeldt, Gang Wu, Sue L Heatley, Debbie Payne-Turner, John Easton, Xiang Chen, Jianmin Wang, Michael Rusch,[...]. Nature 2012
25

CREST maps somatic structural variation in cancer genomes with base-pair resolution.
Jianmin Wang, Charles G Mullighan, John Easton, Stefan Roberts, Sue L Heatley, Jing Ma, Michael C Rusch, Ken Chen, Christopher C Harris, Li Ding,[...]. Nat Methods 2011
362
25

CONSERTING: integrating copy-number analysis with structural-variation detection.
Xiang Chen, Pankaj Gupta, Jianmin Wang, Joy Nakitandwe, Kathryn Roberts, James D Dalton, Matthew Parker, Samir Patel, Linda Holmfeldt, Debbie Payne,[...]. Nat Methods 2015
49
40

The Pediatric Cancer Genome Project.
James R Downing, Richard K Wilson, Jinghui Zhang, Elaine R Mardis, Ching-Hon Pui, Li Ding, Timothy J Ley, William E Evans. Nat Genet 2012
217
17

HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
17

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
16

A novel retinoblastoma therapy from genomic and epigenetic analyses.
Jinghui Zhang, Claudia A Benavente, Justina McEvoy, Jacqueline Flores-Otero, Li Ding, Xiang Chen, Anatoly Ulyanov, Gang Wu, Matthew Wilson, Jianmin Wang,[...]. Nature 2012
331
15

Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours.
Xiaotu Ma, Yu Liu, Yanling Liu, Ludmil B Alexandrov, Michael N Edmonson, Charles Gawad, Xin Zhou, Yongjin Li, Michael C Rusch, John Easton,[...]. Nature 2018
366
15

dbSNP: the NCBI database of genetic variation.
S T Sherry, M H Ward, M Kholodov, J Baker, L Phan, E M Smigielski, K Sirotkin. Nucleic Acids Res 2001
14

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
14

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
14

VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.
Daniel C Koboldt, Qunyuan Zhang, David E Larson, Dong Shen, Michael D McLellan, Ling Lin, Christopher A Miller, Elaine R Mardis, Li Ding, Richard K Wilson. Genome Res 2012
12

The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma.
Gang Wu, Alexander K Diaz, Barbara S Paugh, Sherri L Rankin, Bensheng Ju, Yongjin Li, Xiaoyan Zhu, Chunxu Qu, Xiang Chen, Junyuan Zhang,[...]. Nat Genet 2014
620
12

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples.
Kristian Cibulskis, Michael S Lawrence, Scott L Carter, Andrey Sivachenko, David Jaffe, Carrie Sougnez, Stacey Gabriel, Matthew Meyerson, Eric S Lander, Gad Getz. Nat Biotechnol 2013
12

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
12

Germline Mutations in Predisposition Genes in Pediatric Cancer.
Jinghui Zhang, Michael F Walsh, Gang Wu, Michael N Edmonson, Tanja A Gruber, John Easton, Dale Hedges, Xiaotu Ma, Xin Zhou, Donald A Yergeau,[...]. N Engl J Med 2015
588
12

An integrated map of genetic variation from 1,092 human genomes.
Goncalo R Abecasis, Adam Auton, Lisa D Brooks, Mark A DePristo, Richard M Durbin, Robert E Handsaker, Hyun Min Kang, Gabor T Marth, Gil A McVean. Nature 2012
11

Rise and fall of subclones from diagnosis to relapse in pediatric B-acute lymphoblastic leukaemia.
Xiaotu Ma, Michael Edmonson, Donald Yergeau, Donna M Muzny, Oliver A Hampton, Michael Rusch, Guangchun Song, John Easton, Richard C Harvey, David A Wheeler,[...]. Nat Commun 2015
207
11

Signatures of mutational processes in human cancer.
Ludmil B Alexandrov, Serena Nik-Zainal, David C Wedge, Samuel A J R Aparicio, Sam Behjati, Andrew V Biankin, Graham R Bignell, Niccolò Bolli, Ake Borg, Anne-Lise Børresen-Dale,[...]. Nature 2013
11

A census of human cancer genes.
P Andrew Futreal, Lachlan Coin, Mhairi Marshall, Thomas Down, Timothy Hubbard, Richard Wooster, Nazneen Rahman, Michael R Stratton. Nat Rev Cancer 2004
10

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
10

The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia.
Yu Liu, John Easton, Ying Shao, Jamie Maciaszek, Zhaoming Wang, Mark R Wilkinson, Kelly McCastlain, Michael Edmonson, Stanley B Pounds, Lei Shi,[...]. Nat Genet 2017
414
10

Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome.
Michael Rusch, Joy Nakitandwe, Sheila Shurtleff, Scott Newman, Zhaojie Zhang, Michael N Edmonson, Matthew Parker, Yuannian Jiao, Xiaotu Ma, Yanling Liu,[...]. Nat Commun 2018
84
10

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
8

Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia.
Charles G Mullighan, Xiaoping Su, Jinghui Zhang, Ina Radtke, Letha A A Phillips, Christopher B Miller, Jing Ma, Wei Liu, Cheng Cheng, Brenda A Schulman,[...]. N Engl J Med 2009
914
8

Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays.
Radoje Drmanac, Andrew B Sparks, Matthew J Callow, Aaron L Halpern, Norman L Burns, Bahram G Kermani, Paolo Carnevali, Igor Nazarenko, Geoffrey B Nilsen, George Yeung,[...]. Science 2010
774
8


Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs.
Christopher T Saunders, Wendy S W Wong, Sajani Swamy, Jennifer Becq, Lisa J Murray, R Keira Cheetham. Bioinformatics 2012
936
8

Clock-like mutational processes in human somatic cells.
Ludmil B Alexandrov, Philip H Jones, David C Wedge, Julian E Sale, Peter J Campbell, Serena Nik-Zainal, Michael R Stratton. Nat Genet 2015
479
8

CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
Liqing Tian, Yongjin Li, Michael N Edmonson, Xin Zhou, Scott Newman, Clay McLeod, Andrew Thrasher, Yu Liu, Bo Tang, Michael C Rusch,[...]. Genome Biol 2020
29
24

VarScan: variant detection in massively parallel sequencing of individual and pooled samples.
Daniel C Koboldt, Ken Chen, Todd Wylie, David E Larson, Michael D McLellan, Elaine R Mardis, George M Weinstock, Richard K Wilson, Li Ding. Bioinformatics 2009
791
7

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
7

Predicting the functional effect of amino acid substitutions and indels.
Yongwook Choi, Gregory E Sims, Sean Murphy, Jason R Miller, Agnes P Chan. PLoS One 2012
7

The genomic landscape of hypodiploid acute lymphoblastic leukemia.
Linda Holmfeldt, Lei Wei, Ernesto Diaz-Flores, Michael Walsh, Jinghui Zhang, Li Ding, Debbie Payne-Turner, Michelle Churchman, Anna Andersson, Shann-Ching Chen,[...]. Nat Genet 2013
411
7

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma.
Paul A Northcott, Catherine Lee, Thomas Zichner, Adrian M Stütz, Serap Erkek, Daisuke Kawauchi, David J H Shih, Volker Hovestadt, Marc Zapatka, Dominik Sturm,[...]. Nature 2014
350
7

limma powers differential expression analyses for RNA-sequencing and microarray studies.
Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth. Nucleic Acids Res 2015
7

A genomic random interval model for statistical analysis of genomic lesion data.
Stan Pounds, Cheng Cheng, Shaoyu Li, Zhifa Liu, Jinghui Zhang, Charles Mullighan. Bioinformatics 2013
10
60

Exploring genomic alteration in pediatric cancer using ProteinPaint.
Xin Zhou, Michael N Edmonson, Mark R Wilkinson, Aman Patel, Gang Wu, Yu Liu, Yongjin Li, Zhaojie Zhang, Michael C Rusch, Matthew Parker,[...]. Nat Genet 2016
162
7

Deciphering signatures of mutational processes operative in human cancer.
Ludmil B Alexandrov, Serena Nik-Zainal, David C Wedge, Peter J Campbell, Michael R Stratton. Cell Rep 2013
663
7

Mutational landscape, clonal evolution patterns, and role of RAS mutations in relapsed acute lymphoblastic leukemia.
Koichi Oshima, Hossein Khiabanian, Ana C da Silva-Almeida, Gannie Tzoneva, Francesco Abate, Alberto Ambesi-Impiombato, Marta Sanchez-Martin, Zachary Carpenter, Alex Penson, Arianne Perez-Garcia,[...]. Proc Natl Acad Sci U S A 2016
112
7


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
6

BLAT--the BLAST-like alignment tool.
W James Kent. Genome Res 2002
6

Treating childhood acute lymphoblastic leukemia without cranial irradiation.
Ching-Hon Pui, Dario Campana, Deqing Pei, W Paul Bowman, John T Sandlund, Sue C Kaste, Raul C Ribeiro, Jeffrey E Rubnitz, Susana C Raimondi, Mihaela Onciu,[...]. N Engl J Med 2009
777
6


Reference alignment of SNP microarray signals for copy number analysis of tumors.
Stan Pounds, Cheng Cheng, Charles Mullighan, Susana C Raimondi, Sheila Shurtleff, James R Downing. Bioinformatics 2009
50
10

Metagenes and molecular pattern discovery using matrix factorization.
Jean-Philippe Brunet, Pablo Tamayo, Todd R Golub, Jill P Mesirov. Proc Natl Acad Sci U S A 2004
749
6

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.
Pablo Cingolani, Adrian Platts, Le Lily Wang, Melissa Coon, Tung Nguyen, Luan Wang, Susan J Land, Xiangyi Lu, Douglas M Ruden. Fly (Austin) 2012
6


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.