A citation-based method for searching scientific literature

Lars Feuerbach, Lina Sieverling, Katharina I Deeg, Philip Ginsbach, Barbara Hutter, Ivo Buchhalter, Paul A Northcott, Sadaf S Mughal, Priya Chudasama, Hanno Glimm, Claudia Scholl, Peter Lichter, Stefan Fröhling, Stefan M Pfister, David T W Jones, Karsten Rippe, Benedikt Brors. BMC Bioinformatics 2019
Times Cited: 9







List of co-cited articles
50 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
55

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
55

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
44

Telomerase activation by genomic rearrangements in high-risk neuroblastoma.
Martin Peifer, Falk Hertwig, Frederik Roels, Daniel Dreidax, Moritz Gartlgruber, Roopika Menon, Andrea Krämer, Justin L Roncaioli, Frederik Sand, Johannes M Heuckmann,[...]. Nature 2015
266
33

Alternative lengthening of telomeres: models, mechanisms and implications.
Anthony J Cesare, Roger R Reddel. Nat Rev Genet 2010
562
33

Altered telomeres in tumors with ATRX and DAXX mutations.
Christopher M Heaphy, Roeland F de Wilde, Yuchen Jiao, Alison P Klein, Barish H Edil, Chanjuan Shi, Chetan Bettegowda, Fausto J Rodriguez, Charles G Eberhart, Sachidanand Hebbar,[...]. Science 2011
623
33



TelNet - a database for human and yeast genes involved in telomere maintenance.
Delia M Braun, Inn Chung, Nick Kepper, Katharina I Deeg, Karsten Rippe. BMC Genet 2018
11
22

Comparative analysis of whole genome sequencing-based telomere length measurement techniques.
Michael Lee, Christine E Napier, Sile F Yang, Jonathan W Arthur, Roger R Reddel, Hilda A Pickett. Methods 2017
17
22

Integrative genomic and transcriptomic analysis of leiomyosarcoma.
Priya Chudasama, Sadaf S Mughal, Mathijs A Sanders, Daniel Hübschmann, Inn Chung, Katharina I Deeg, Siao-Han Wong, Sophie Rabe, Mario Hlevnjak, Marc Zapatka,[...]. Nat Commun 2018
81
22

Prevalence of the alternative lengthening of telomeres telomere maintenance mechanism in human cancer subtypes.
Christopher M Heaphy, Andrea P Subhawong, Seung-Mo Hong, Michael G Goggins, Elizabeth A Montgomery, Edward Gabrielson, George J Netto, Jonathan I Epstein, Tamara L Lotan, William H Westra,[...]. Am J Pathol 2011
279
22

Human telomeres contain at least three types of G-rich repeat distributed non-randomly.
R C Allshire, M Dempster, N D Hastie. Nucleic Acids Res 1989
296
22

Variant repeats are interspersed throughout the telomeres and recruit nuclear receptors in ALT cells.
Dimitri Conomos, Michael D Stutz, Mark Hills, Axel A Neumann, Tracy M Bryan, Roger R Reddel, Hilda A Pickett. J Cell Biol 2012
79
22

Frequent amplification of the telomerase reverse transcriptase gene in human tumors.
A Zhang, C Zheng, C Lindvall, M Hou, J Ekedahl, R Lewensohn, Z Yan, X Yang, M Henriksson, E Blennow,[...]. Cancer Res 2000
115
22

Systematic analysis of telomere length and somatic alterations in 31 cancer types.
Floris P Barthel, Wei Wei, Ming Tang, Emmanuel Martinez-Ledesma, Xin Hu, Samirkumar B Amin, Kadir C Akdemir, Sahil Seth, Xingzhi Song, Qianghu Wang,[...]. Nat Genet 2017
201
22

Loss of ATRX, genome instability, and an altered DNA damage response are hallmarks of the alternative lengthening of telomeres pathway.
Courtney A Lovejoy, Wendi Li, Steven Reisenweber, Supawat Thongthip, Joanne Bruno, Titia de Lange, Saurav De, John H J Petrini, Patricia A Sung, Maria Jasin,[...]. PLoS Genet 2012
342
22

Nuclear-receptor-mediated telomere insertion leads to genome instability in ALT cancers.
Paulina Marzec, Claudia Armenise, Gaëlle Pérot, Fani-Marlen Roumelioti, Eugenia Basyuk, Sarantis Gagos, Frédéric Chibon, Jérôme Déjardin. Cell 2015
56
22

Healing of broken human chromosomes by the addition of telomeric repeats.
J Flint, C F Craddock, A Villegas, D P Bentley, H J Williams, R Galanello, A Cao, W G Wood, H Ayyub, D R Higgs. Am J Hum Genet 1994
178
22

Criteria for inference of chromothripsis in cancer genomes.
Jan O Korbel, Peter J Campbell. Cell 2013
286
22

Massive genomic rearrangement acquired in a single catastrophic event during cancer development.
Philip J Stephens, Chris D Greenman, Beiyuan Fu, Fengtang Yang, Graham R Bignell, Laura J Mudie, Erin D Pleasance, King Wai Lau, David Beare, Lucy A Stebbings,[...]. Cell 2011
22

The role of microhomology in genomic structural variation.
Diego Ottaviani, Magdalena LeCain, Denise Sheer. Trends Genet 2014
92
22

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
Helga Thorvaldsdóttir, James T Robinson, Jill P Mesirov. Brief Bioinform 2013
22

Telomere dysfunction and chromothripsis.
Aurélie Ernst, David T W Jones, Kendra K Maass, Agata Rode, Katharina I Deeg, Billy Michael Chelliah Jebaraj, Andrey Korshunov, Volker Hovestadt, Michael A Tainsky, Kristian W Pajtler,[...]. Int J Cancer 2016
30
22

TERT promoter mutations in familial and sporadic melanoma.
Susanne Horn, Adina Figl, P Sivaramakrishna Rachakonda, Christine Fischer, Antje Sucker, Andreas Gast, Stephanie Kadel, Iris Moll, Eduardo Nagore, Kari Hemminki,[...]. Science 2013
22

Chromothripsis and Kataegis Induced by Telomere Crisis.
John Maciejowski, Yilong Li, Nazario Bosco, Peter J Campbell, Titia de Lange. Cell 2015
303
22

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
22


Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing.
Isidro Cortés-Ciriano, Jake June-Koo Lee, Ruibin Xi, Dhawal Jain, Youngsook L Jung, Lixing Yang, Dmitry Gordenin, Leszek J Klimczak, Cheng-Zhong Zhang, David S Pellman,[...]. Nat Genet 2020
103
22

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
22

Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes.
Jan J Molenaar, Jan Koster, Danny A Zwijnenburg, Peter van Sluis, Linda J Valentijn, Ida van der Ploeg, Mohamed Hamdi, Johan van Nes, Bart A Westerman, Jennemiek van Arkel,[...]. Nature 2012
554
22

Precision oncology based on omics data: The NCT Heidelberg experience.
Peter Horak, Barbara Klink, Christoph Heining, Stefan Gröschel, Barbara Hutter, Martina Fröhlich, Sebastian Uhrig, Daniel Hübschmann, Matthias Schlesner, Roland Eils,[...]. Int J Cancer 2017
63
22

OTP: An automatized system for managing and processing NGS data.
Eva Reisinger, Lena Genthner, Jules Kerssemakers, Philip Kensche, Stefan Borufka, Alke Jugold, Andreas Kling, Manuel Prinz, Ingrid Scholz, Gideon Zipprich,[...]. J Biotechnol 2017
14
22

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications.
Andy Rimmer, Hang Phan, Iain Mathieson, Zamin Iqbal, Stephen R F Twigg, Andrew O M Wilkie, Gil McVean, Gerton Lunter. Nat Genet 2014
496
22

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
22




ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
22

OncoKB: A Precision Oncology Knowledge Base.
Debyani Chakravarty, Jianjiong Gao, Sarah M Phillips, Ritika Kundra, Hongxin Zhang, Jiaojiao Wang, Julia E Rudolph, Rona Yaeger, Tara Soumerai, Moriah H Nissan,[...]. JCO Precis Oncol 2017
632
22

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
22


Next-generation personalised medicine for high-risk paediatric cancer patients - The INFORM pilot study.
Barbara C Worst, Cornelis M van Tilburg, Gnana Prakash Balasubramanian, Petra Fiesel, Ruth Witt, Angelika Freitag, Miream Boudalil, Christopher Previti, Stephan Wolf, Sabine Schmidt,[...]. Eur J Cancer 2016
135
22

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
22

SETDB1-dependent heterochromatin stimulates alternative lengthening of telomeres.
Mathilde Gauchier, Sophie Kan, Amandine Barral, Sandrine Sauzet, Eneritz Agirre, Erin Bonnell, Nehmé Saksouk, Teresa K Barth, Satoru Ide, Serge Urbach,[...]. Sci Adv 2019
31
22

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
22


Alternative Lengthening of Telomeres is characterized by reduced compaction of telomeric chromatin.
Harikleia Episkopou, Irena Draskovic, Amandine Van Beneden, Gaëlle Tilman, Marina Mattiussi, Matthieu Gobin, Nausica Arnoult, Arturo Londoño-Vallejo, Anabelle Decottignies. Nucleic Acids Res 2014
96
22

Genomic footprints of activated telomere maintenance mechanisms in cancer.
Lina Sieverling, Chen Hong, Sandra D Koser, Philip Ginsbach, Kortine Kleinheinz, Barbara Hutter, Delia M Braun, Isidro Cortés-Ciriano, Ruibin Xi, Rolf Kabbe,[...]. Nat Commun 2020
21
22

The Perseus computational platform for comprehensive analysis of (prote)omics data.
Stefka Tyanova, Tikira Temu, Pavel Sinitcyn, Arthur Carlson, Marco Y Hein, Tamar Geiger, Matthias Mann, Jürgen Cox. Nat Methods 2016
22


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.