A citation-based method for searching scientific literature

Feng Yue, Yong Cheng, Alessandra Breschi, Jeff Vierstra, Weisheng Wu, Tyrone Ryba, Richard Sandstrom, Zhihai Ma, Carrie Davis, Benjamin D Pope, Yin Shen, Dmitri D Pervouchine, Sarah Djebali, Robert E Thurman, Rajinder Kaul, Eric Rynes, Anthony Kirilusha, Georgi K Marinov, Brian A Williams, Diane Trout, Henry Amrhein, Katherine Fisher-Aylor, Igor Antoshechkin, Gilberto DeSalvo, Lei-Hoon See, Meagan Fastuca, Jorg Drenkow, Chris Zaleski, Alex Dobin, Pablo Prieto, Julien Lagarde, Giovanni Bussotti, Andrea Tanzer, Olgert Denas, Kanwei Li, M A Bender, Miaohua Zhang, Rachel Byron, Mark T Groudine, David McCleary, Long Pham, Zhen Ye, Samantha Kuan, Lee Edsall, Yi-Chieh Wu, Matthew D Rasmussen, Mukul S Bansal, Manolis Kellis, Cheryl A Keller, Christapher S Morrissey, Tejaswini Mishra, Deepti Jain, Nergiz Dogan, Robert S Harris, Philip Cayting, Trupti Kawli, Alan P Boyle, Ghia Euskirchen, Anshul Kundaje, Shin Lin, Yiing Lin, Camden Jansen, Venkat S Malladi, Melissa S Cline, Drew T Erickson, Vanessa M Kirkup, Katrina Learned, Cricket A Sloan, Kate R Rosenbloom, Beatriz Lacerda de Sousa, Kathryn Beal, Miguel Pignatelli, Paul Flicek, Jin Lian, Tamer Kahveci, Dongwon Lee, W James Kent, Miguel Ramalho Santos, Javier Herrero, Cedric Notredame, Audra Johnson, Shinny Vong, Kristen Lee, Daniel Bates, Fidencio Neri, Morgan Diegel, Theresa Canfield, Peter J Sabo, Matthew S Wilken, Thomas A Reh, Erika Giste, Anthony Shafer, Tanya Kutyavin, Eric Haugen, Douglas Dunn, Alex P Reynolds, Shane Neph, Richard Humbert, R Scott Hansen, Marella De Bruijn, Licia Selleri, Alexander Rudensky, Steven Josefowicz, Robert Samstein, Evan E Eichler, Stuart H Orkin, Dana Levasseur, Thalia Papayannopoulou, Kai-Hsin Chang, Arthur Skoultchi, Srikanta Gosh, Christine Disteche, Piper Treuting, Yanli Wang, Mitchell J Weiss, Gerd A Blobel, Xiaoyi Cao, Sheng Zhong, Ting Wang, Peter J Good, Rebecca F Lowdon, Leslie B Adams, Xiao-Qiao Zhou, Michael J Pazin, Elise A Feingold, Barbara Wold, James Taylor, Ali Mortazavi, Sherman M Weissman, John A Stamatoyannopoulos, Michael P Snyder, Roderic Guigo, Thomas R Gingeras, David M Gilbert, Ross C Hardison, Michael A Beer, Bing Ren. Nature 2014
Times Cited: 917







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



Times Cited
  Times     Co-cited
Similarity



Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics.
Linn Fagerberg, Björn M Hallström, Per Oksvold, Caroline Kampf, Dijana Djureinovic, Jacob Odeberg, Masato Habuka, Simin Tahmasebpoor, Angelika Danielsson, Karolina Edlund,[...]. Mol Cell Proteomics 2014
573
16


Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
14

Model-based analysis of ChIP-Seq (MACS).
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
13

Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
11

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
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

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
10

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
9


Principles of regulatory information conservation between mouse and human.
Yong Cheng, Zhihai Ma, Bong-Hyun Kim, Weisheng Wu, Philip Cayting, Alan P Boyle, Vasavi Sundaram, Xiaoyun Xing, Nergiz Dogan, Jingjing Li,[...]. Nature 2014
175
9

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
9

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
8

Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics.
Linn Fagerberg, Björn M Hallström, Per Oksvold, Caroline Kampf, Dijana Djureinovic, Jacob Odeberg, Masato Habuka, Simin Tahmasebpoor, Angelika Danielsson, Karolina Edlund,[...]. Mol Cell Proteomics 2014
8


Topological domains in mammalian genomes identified by analysis of chromatin interactions.
Jesse R Dixon, Siddarth Selvaraj, Feng Yue, Audrey Kim, Yan Li, Yin Shen, Ming Hu, Jun S Liu, Bing Ren. Nature 2012
7

Enhancer evolution across 20 mammalian species.
Diego Villar, Camille Berthelot, Sarah Aldridge, Tim F Rayner, Margus Lukk, Miguel Pignatelli, Thomas J Park, Robert Deaville, Jonathan T Erichsen, Anna J Jasinska,[...]. Cell 2015
342
7

A map of the cis-regulatory sequences in the mouse genome.
Yin Shen, Feng Yue, David F McCleary, Zhen Ye, Lee Edsall, Samantha Kuan, Ulrich Wagner, Jesse Dixon, Leonard Lee, Victor V Lobanenkov,[...]. Nature 2012
923
7

deepTools2: a next generation web server for deep-sequencing data analysis.
Fidel Ramírez, Devon P Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S Richter, Steffen Heyne, Friederike Dündar, Thomas Manke. Nucleic Acids Res 2016
7

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
6

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
6

Chromatin accessibility and the regulatory epigenome.
Sandy L Klemm, Zohar Shipony, William J Greenleaf. Nat Rev Genet 2019
370
6

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
6

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
6

ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide.
Jason D Buenrostro, Beijing Wu, Howard Y Chang, William J Greenleaf. Curr Protoc Mol Biol 2015
6

The human genome browser at UCSC.
W James Kent, Charles W Sugnet, Terrence S Furey, Krishna M Roskin, Tom H Pringle, Alan M Zahler, David Haussler. Genome Res 2002
6

Expanded encyclopaedias of DNA elements in the human and mouse genomes.
Jill E Moore, Michael J Purcaro, Henry E Pratt, Charles B Epstein, Noam Shoresh, Jessika Adrian, Trupti Kawli, Carrie A Davis, Alexander Dobin, Rajinder Kaul,[...]. Nature 2020
299
6

A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages.
Ying Yu, James C Fuscoe, Chen Zhao, Chao Guo, Meiwen Jia, Tao Qing, Desmond I Bannon, Lee Lancashire, Wenjun Bao, Tingting Du,[...]. Nat Commun 2014
211
6

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
5

The UCSC Genome Browser database: 2019 update.
Maximilian Haeussler, Ann S Zweig, Cath Tyner, Matthew L Speir, Kate R Rosenbloom, Brian J Raney, Christopher M Lee, Brian T Lee, Angie S Hinrichs, Jairo Navarro Gonzalez,[...]. Nucleic Acids Res 2019
378
5


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
5

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
5

GREAT improves functional interpretation of cis-regulatory regions.
Cory Y McLean, Dave Bristor, Michael Hiller, Shoa L Clarke, Bruce T Schaar, Craig B Lowe, Aaron M Wenger, Gill Bejerano. Nat Biotechnol 2010
5


Master transcription factors and mediator establish super-enhancers at key cell identity genes.
Warren A Whyte, David A Orlando, Denes Hnisz, Brian J Abraham, Charles Y Lin, Michael H Kagey, Peter B Rahl, Tong Ihn Lee, Richard A Young. Cell 2013
5

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
Helga Thorvaldsdóttir, James T Robinson, Jill P Mesirov. Brief Bioinform 2013
5

Super-enhancers in the control of cell identity and disease.
Denes Hnisz, Brian J Abraham, Tong Ihn Lee, Ashley Lau, Violaine Saint-André, Alla A Sigova, Heather A Hoke, Richard A Young. Cell 2013
5

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.
Nathaniel D Heintzman, Rhona K Stuart, Gary Hon, Yutao Fu, Christina W Ching, R David Hawkins, Leah O Barrera, Sara Van Calcar, Chunxu Qu, Keith A Ching,[...]. Nat Genet 2007
5

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
4

Histone H3K27ac separates active from poised enhancers and predicts developmental state.
Menno P Creyghton, Albert W Cheng, G Grant Welstead, Tristan Kooistra, Bryce W Carey, Eveline J Steine, Jacob Hanna, Michael A Lodato, Garrett M Frampton, Phillip A Sharp,[...]. Proc Natl Acad Sci U S A 2010
4

A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq.
Bin Li, Tao Qing, Jinhang Zhu, Zhuo Wen, Ying Yu, Ryutaro Fukumura, Yuanting Zheng, Yoichi Gondo, Leming Shi. Sci Rep 2017
70
5


A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.
Darren A Cusanovich, Andrew J Hill, Delasa Aghamirzaie, Riza M Daza, Hannah A Pliner, Joel B Berletch, Galina N Filippova, Xingfan Huang, Lena Christiansen, William S DeWitt,[...]. Cell 2018
244
4

Dynamic regulation of nucleosome positioning in the human genome.
Dustin E Schones, Kairong Cui, Suresh Cuddapah, Tae-Young Roh, Artem Barski, Zhibin Wang, Gang Wei, Keji Zhao. Cell 2008
931
4

TopHat: discovering splice junctions with RNA-Seq.
Cole Trapnell, Lior Pachter, Steven L Salzberg. Bioinformatics 2009
4

Identification of functional elements and regulatory circuits by Drosophila modENCODE.
Sushmita Roy, Jason Ernst, Peter V Kharchenko, Pouya Kheradpour, Nicolas Negre, Matthew L Eaton, Jane M Landolin, Christopher A Bristow, Lijia Ma, Michael F Lin,[...]. Science 2010
842
4

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley, Steven L Salzberg. Genome Biol 2013
4

HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
4


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.