A citation-based method for searching scientific literature

Valerio Bianchi, Arnaud Ceol, Alessandro G E Ogier, Stefano de Pretis, Eugenia Galeota, Kamal Kishore, Pranami Bora, Ottavio Croci, Stefano Campaner, Bruno Amati, Marco J Morelli, Mattia Pelizzola. Front Genet 2016
Times Cited: 20







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



Times Cited
  Times     Co-cited
Similarity



MYC: connecting selective transcriptional control to global RNA production.
Theresia R Kress, Arianna Sabò, Bruno Amati. Nat Rev Cancer 2015
228
20

Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis.
Arianna Sabò, Theresia R Kress, Mattia Pelizzola, Stefano de Pretis, Marcin M Gorski, Alessandra Tesi, Marco J Morelli, Pranami Bora, Mirko Doni, Alessandro Verrecchia,[...]. Nature 2014
263
20

Activation and repression by oncogenic MYC shape tumour-specific gene expression profiles.
Susanne Walz, Francesca Lorenzin, Jennifer Morton, Katrin E Wiese, Björn von Eyss, Steffi Herold, Lukas Rycak, Hélène Dumay-Odelot, Saadia Karim, Marek Bartkuhn,[...]. Nature 2014
255
20

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
20

Bioconductor: open software development for computational biology and bioinformatics.
Robert C Gentleman, Vincent J Carey, Douglas M Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry,[...]. Genome Biol 2004
20

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
20

methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data.
Kamal Kishore, Stefano de Pretis, Ryan Lister, Marco J Morelli, Valerio Bianchi, Bruno Amati, Joseph R Ecker, Mattia Pelizzola. BMC Bioinformatics 2015
33
20

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
Helga Thorvaldsdóttir, James T Robinson, Jill P Mesirov. Brief Bioinform 2013
15

A modified oestrogen receptor ligand-binding domain as an improved switch for the regulation of heterologous proteins.
T D Littlewood, D C Hancock, P S Danielian, M G Parker, G I Evan. Nucleic Acids Res 1995
611
15

Chipster: user-friendly analysis software for microarray and other high-throughput data.
M Aleksi Kallio, Jarno T Tuimala, Taavi Hupponen, Petri Klemelä, Massimiliano Gentile, Ilari Scheinin, Mikko Koski, Janne Käki, Eija I Korpelainen. BMC Genomics 2011
170
15

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
15

INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments.
Stefano de Pretis, Theresia Kress, Marco J Morelli, Giorgio E M Melloni, Laura Riva, Bruno Amati, Mattia Pelizzola. Bioinformatics 2015
32
15

Different promoter affinities account for specificity in MYC-dependent gene regulation.
Francesca Lorenzin, Uwe Benary, Apoorva Baluapuri, Susanne Walz, Lisa Anna Jung, Björn von Eyss, Caroline Kisker, Jana Wolf, Martin Eilers, Elmar Wolf. Elife 2016
70
15

Transcriptional activation by the human c-Myc oncoprotein in yeast requires interaction with Max.
B Amati, S Dalton, M W Brooks, T D Littlewood, G I Evan, H Land. Nature 1992
312
15

Myc and Max proteins possess distinct transcriptional activities.
L Kretzner, E M Blackwood, R N Eisenman. Nature 1992
340
15


c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells.
Zuqin Nie, Gangqing Hu, Gang Wei, Kairong Cui, Arito Yamane, Wolfgang Resch, Ruoning Wang, Douglas R Green, Lino Tessarollo, Rafael Casellas,[...]. Cell 2012
647
15

c-Myc regulates transcriptional pause release.
Peter B Rahl, Charles Y Lin, Amy C Seila, Ryan A Flynn, Scott McCuine, Christopher B Burge, Phillip A Sharp, Richard A Young. Cell 2010
841
15

Myc-binding-site recognition in the human genome is determined by chromatin context.
Ernesto Guccione, Francesca Martinato, Giacomo Finocchiaro, Lucilla Luzi, Laura Tizzoni, Valentina Dall' Olio, Giuseppe Zardo, Clara Nervi, Loris Bernard, Bruno Amati. Nat Cell Biol 2006
265
15

Identification of MYC-Dependent Transcriptional Programs in Oncogene-Addicted Liver Tumors.
Theresia R Kress, Paola Pellanda, Luca Pellegrinet, Valerio Bianchi, Paola Nicoli, Mirko Doni, Camilla Recordati, Salvatore Bianchi, Luca Rotta, Thelma Capra,[...]. Cancer Res 2016
27
15


Integrative analysis of RNA polymerase II and transcriptional dynamics upon MYC activation.
Stefano de Pretis, Theresia R Kress, Marco J Morelli, Arianna Sabò, Chiara Locarno, Alessandro Verrecchia, Mirko Doni, Stefano Campaner, Bruno Amati, Mattia Pelizzola. Genome Res 2017
25
15

Transcriptional amplification in tumor cells with elevated c-Myc.
Charles Y Lin, Jakob Lovén, Peter B Rahl, Ronald M Paranal, Christopher B Burge, James E Bradner, Tong Ihn Lee, Richard A Young. Cell 2012
853
15

Sequencing technologies - the next generation.
Michael L Metzker. Nat Rev Genet 2010
10

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
Sue Richards, Nazneen Aziz, Sherri Bale, David Bick, Soma Das, Julie Gastier-Foster, Wayne W Grody, Madhuri Hegde, Elaine Lyon, Elaine Spector,[...]. Genet Med 2015
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
10

RNA-SeQC: RNA-seq metrics for quality control and process optimization.
David S DeLuca, Joshua Z Levin, Andrey Sivachenko, Timothy Fennell, Marc-Danie Nazaire, Chris Williams, Michael Reich, Wendy Winckler, Gad Getz. Bioinformatics 2012
391
10

QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation.
Prerana Wagle, Miloš Nikolić, Peter Frommolt. BMC Genomics 2015
41
10

Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data.
Konstantin Okonechnikov, Ana Conesa, Fernando García-Alcalde. Bioinformatics 2016
407
10

Omics Pipe: a community-based framework for reproducible multi-omics data analysis.
Kathleen M Fisch, Tobias Meißner, Louis Gioia, Jean-Christophe Ducom, Tristan M Carland, Salvatore Loguercio, Andrew I Su. Bioinformatics 2015
32
10


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
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


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
10

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
10

GenePattern 2.0.
Michael Reich, Ted Liefeld, Joshua Gould, Jim Lerner, Pablo Tamayo, Jill P Mesirov. Nat Genet 2006
10

Galaxy: a platform for interactive large-scale genome analysis.
Belinda Giardine, Cathy Riemer, Ross C Hardison, Richard Burhans, Laura Elnitski, Prachi Shah, Yi Zhang, Daniel Blankenberg, Istvan Albert, James Taylor,[...]. Genome Res 2005
10

Genome Modeling System: A Knowledge Management Platform for Genomics.
Malachi Griffith, Obi L Griffith, Scott M Smith, Avinash Ramu, Matthew B Callaway, Anthony M Brummett, Michael J Kiwala, Adam C Coffman, Allison A Regier, Ben J Oberkfell,[...]. PLoS Comput Biol 2015
46
10

Sequencing depth and coverage: key considerations in genomic analyses.
David Sims, Ian Sudbery, Nicholas E Ilott, Andreas Heger, Chris P Ponting. Nat Rev Genet 2014
591
10

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nat Protoc 2009
10

Orchestrating high-throughput genomic analysis with Bioconductor.
Wolfgang Huber, Vincent J Carey, Robert Gentleman, Simon Anders, Marc Carlson, Benilton S Carvalho, Hector Corrada Bravo, Sean Davis, Laurent Gatto, Thomas Girke,[...]. Nat Methods 2015
10

BRD4 and MYC-clarifying regulatory specificity.
Arianna Sabò, Bruno Amati. Science 2018
10
20

BPTF is required for c-MYC transcriptional activity and in vivo tumorigenesis.
Laia Richart, Enrique Carrillo-de Santa Pau, Ana Río-Machín, Mónica P de Andrés, Juan C Cigudosa, Víctor J Sánchez-Arévalo Lobo, Francisco X Real. Nat Commun 2016
57
10

Global Inhibition with Specific Activation: How p53 and MYC Redistribute the Transcriptome in the DNA Double-Strand Break Response.
Joshua R Porter, Brian E Fisher, Laura Baranello, Julia C Liu, Diane M Kambach, Zuqin Nie, Woo Seuk Koh, Ji Luo, Jayne M Stommel, David Levens,[...]. Mol Cell 2017
21
10


Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation.
Kyong-Rim Kieffer-Kwon, Keisuke Nimura, Suhas S P Rao, Jianliang Xu, Seolkyoung Jung, Aleksandra Pekowska, Marei Dose, Evan Stevens, Ewy Mathe, Peng Dong,[...]. Mol Cell 2017
69
10

Genome-wide mapping of Myc binding and gene regulation in serum-stimulated fibroblasts.
D Perna, G Fagà, A Verrecchia, M M Gorski, I Barozzi, V Narang, J Khng, K C Lim, W-K Sung, R Sanges,[...]. Oncogene 2012
66
10

Interaction with WDR5 promotes target gene recognition and tumorigenesis by MYC.
Lance R Thomas, Qingguo Wang, Brian C Grieb, Jason Phan, Audra M Foshage, Qi Sun, Edward T Olejniczak, Travis Clark, Soumyadeep Dey, Shelly Lorey,[...]. Mol Cell 2015
115
10


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.