A citation-based method for searching scientific literature

Emily Berger, Deniz Yorukoglu, Lillian Zhang, Sarah K Nyquist, Alex K Shalek, Manolis Kellis, Ibrahim Numanagić, Bonnie Berger. Nat Commun 2020
Times Cited: 4







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



Times Cited
  Times     Co-cited
Similarity


Compressive mapping for next-generation sequencing.
Deniz Yorukoglu, Yun William Yu, Jian Peng, Bonnie Berger. Nat Biotechnol 2016
15
50


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
25

AVID: A global alignment program.
Nick Bray, Inna Dubchak, Lior Pachter. Genome Res 2003
286
25



A large-scale analysis of bioinformatics code on GitHub.
Pamela H Russell, Rachel L Johnson, Shreyas Ananthan, Benjamin Harnke, Nichole E Carlson. PLoS One 2018
7
25



Rust-Bio: a fast and safe bioinformatics library.
Johannes Köster. Bioinformatics 2016
7
25

Why scientists are turning to Rust.
Jeffrey M Perkel. Nature 2020
2
50

Entropy-scaling search of massive biological data.
Y William Yu, Noah M Daniels, David Christian Danko, Bonnie Berger. Cell Syst 2015
24
25

The Bioperl toolkit: Perl modules for the life sciences.
Jason E Stajich, David Block, Kris Boulez, Steven E Brenner, Stephen A Chervitz, Chris Dagdigian, Georg Fuellen, James G R Gilbert, Ian Korf, Hilmar Lapp,[...]. Genome Res 2002
25

SeqAn an efficient, generic C++ library for sequence analysis.
Andreas Döring, David Weese, Tobias Rausch, Knut Reinert. BMC Bioinformatics 2008
159
25

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.
Faraz Hach, Iman Sarrafi, Farhad Hormozdiari, Can Alkan, Evan E Eichler, S Cenk Sahinalp. Nucleic Acids Res 2014
34
25

Biopython: freely available Python tools for computational molecular biology and bioinformatics.
Peter J A Cock, Tiago Antao, Jeffrey T Chang, Brad A Chapman, Cymon J Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski,[...]. Bioinformatics 2009
25

Reproducibility in science: important or incremental?
Robyn S Lee, William P Hanage. Lancet Microbe 2020
1
100

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
25

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.
Jacob F Degner, John C Marioni, Athma A Pai, Joseph K Pickrell, Everlyne Nkadori, Yoav Gilad, Jonathan K Pritchard. Bioinformatics 2009
320
25

Reply to 'High prevalence of clonal monoallelic expression'.
Björn Reinius, Rickard Sandberg. Nat Genet 2018
8
25

Widespread monoallelic expression on human autosomes.
Alexander Gimelbrant, John N Hutchinson, Benjamin R Thompson, Andrew Chess. Science 2007
402
25

Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance.
James J Crowley, Vasyl Zhabotynsky, Wei Sun, Shunping Huang, Isa Kemal Pakatci, Yunjung Kim, Jeremy R Wang, Andrew P Morgan, John D Calaway, David L Aylor,[...]. Nat Genet 2015
114
25

Rare and common regulatory variation in population-scale sequenced human genomes.
Stephen B Montgomery, Tuuli Lappalainen, Maria Gutierrez-Arcelus, Emmanouil T Dermitzakis. PLoS Genet 2011
71
25


Effects of sequence variation on differential allelic transcription factor occupancy and gene expression.
Timothy E Reddy, Jason Gertz, Florencia Pauli, Katerina S Kucera, Katherine E Varley, Kimberly M Newberry, Georgi K Marinov, Ali Mortazavi, Brian A Williams, Lingyun Song,[...]. Genome Res 2012
104
25

Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases.
Marco Cavalli, Nicholas Baltzer, Husen M Umer, Jan Grau, Ioana Lemnian, Gang Pan, Ola Wallerman, Rapolas Spalinskas, Pelin Sahlén, Ivo Grosse,[...]. Sci Rep 2019
12
25

Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data.
David L A Wood, Katia Nones, Anita Steptoe, Angelika Christ, Ivon Harliwong, Felicity Newell, Timothy J C Bruxner, David Miller, Nicole Cloonan, Sean M Grimmond. PLoS One 2015
13
25

cisASE: a likelihood-based method for detecting putative cis-regulated allele-specific expression in RNA sequencing data.
Zhi Liu, Tuantuan Gui, Zhen Wang, Hong Li, Yunhe Fu, Xiao Dong, Yixue Li. Bioinformatics 2016
5
25

AlleleSeq: analysis of allele-specific expression and binding in a network framework.
Joel Rozowsky, Alexej Abyzov, Jing Wang, Pedro Alves, Debasish Raha, Arif Harmanci, Jing Leng, Robert Bjornson, Yong Kong, Naoki Kitabayashi,[...]. Mol Syst Biol 2011
183
25

Identification of allele-specific alternative mRNA processing via transcriptome sequencing.
Gang Li, Jae Hoon Bahn, Jae-Hyung Lee, Guangdun Peng, Zugen Chen, Stanley F Nelson, Xinshu Xiao. Nucleic Acids Res 2012
48
25

MBASED: allele-specific expression detection in cancer tissues and cell lines.
Oleg Mayba, Houston N Gilbert, Jinfeng Liu, Peter M Haverty, Suchit Jhunjhunwala, Zhaoshi Jiang, Colin Watanabe, Zemin Zhang. Genome Biol 2014
64
25

High prevalence of clonal monoallelic expression.
Sébastien Vigneau, Svetlana Vinogradova, Virginia Savova, Alexander Gimelbrant. Nat Genet 2018
14
25

Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA.
Ei-Wen Yang, Jae Hoon Bahn, Esther Yun-Hua Hsiao, Boon Xin Tan, Yiwei Sun, Ting Fu, Bo Zhou, Eric L Van Nostrand, Gabriel A Pratt, Peter Freese,[...]. Nat Commun 2019
15
25


Leveraging allelic imbalance to refine fine-mapping for eQTL studies.
Jennifer Zou, Farhad Hormozdiari, Brandon Jew, Stephane E Castel, Tuuli Lappalainen, Jason Ernst, Jae Hoon Sul, Eleazar Eskin. PLoS Genet 2019
8
25

Tools and best practices for data processing in allelic expression analysis.
Stephane E Castel, Ami Levy-Moonshine, Pejman Mohammadi, Eric Banks, Tuuli Lappalainen. Genome Biol 2015
139
25

Allele-specific open chromatin in human iPSC neurons elucidates functional disease variants.
Siwei Zhang, Hanwen Zhang, Yifan Zhou, Min Qiao, Siming Zhao, Alena Kozlova, Jianxin Shi, Alan R Sanders, Gao Wang, Kaixuan Luo,[...]. Science 2020
19
25

The Expanding Landscape of Alternative Splicing Variation in Human Populations.
Eddie Park, Zhicheng Pan, Zijun Zhang, Lan Lin, Yi Xing. Am J Hum Genet 2018
133
25

Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq.
Björn Reinius, Jeff E Mold, Daniel Ramsköld, Qiaolin Deng, Per Johnsson, Jakob Michaëlsson, Jonas Frisén, Rickard Sandberg. Nat Genet 2016
65
25

Allele-specific DNA methylation reinforces PEAR1 enhancer activity.
Benedetta Izzi, Mariaelena Pistoni, Katrien Cludts, Pinar Akkor, Diether Lambrechts, Catherine Verfaillie, Peter Verhamme, Kathleen Freson, Marc F Hoylaerts. Blood 2016
33
25


Fine-mapping cellular QTLs with RASQUAL and ATAC-seq.
Natsuhiko Kumasaka, Andrew J Knights, Daniel J Gaffney. Nat Genet 2016
82
25


Influence of genetic background and tissue types on global DNA methylation patterns.
Howard H Yang, Nan Hu, Chaoyu Wang, Ti Ding, Barbara K Dunn, Alisa M Goldstein, Philip R Taylor, Maxwell P Lee. PLoS One 2010
21
25

Genome-wide search for exonic variants affecting translational efficiency.
Quan Li, Angeliki Makri, Yang Lu, Luc Marchand, Rosemarie Grabs, Marylene Rousseau, Houria Ounissi-Benkalha, Jerry Pelletier, Francis Robert, Eef Harmsen,[...]. Nat Commun 2013
9
25

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
25

Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer.
Najeeb M Halabi, Alejandra Martinez, Halema Al-Farsi, Eliane Mery, Laurence Puydenus, Pascal Pujol, Hanif G Khalak, Cameron McLurcan, Gwenael Ferron, Denis Querleu,[...]. PLoS Genet 2016
9
25

Allele-specific expression reveals interactions between genetic variation and environment.
David A Knowles, Joe R Davis, Hilary Edgington, Anil Raj, Marie-Julie Favé, Xiaowei Zhu, James B Potash, Myrna M Weissman, Jianxin Shi, Douglas F Levinson,[...]. Nat Methods 2017
60
25

Tumor suppressor genes and allele-specific expression: mechanisms and significance.
Evan A Clayton, Shareef Khalid, Dongjo Ban, Lu Wang, I King Jordan, John F McDonald. Oncotarget 2020
2
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.