A citation-based method for searching scientific literature

Jakob Hedegaard, Kasper Thorsen, Mette Katrine Lund, Anne-Mette K Hein, Stephen Jacques Hamilton-Dutoit, Søren Vang, Iver Nordentoft, Karin Birkenkamp-Demtröder, Mogens Kruhøffer, Henrik Hager, Bjarne Knudsen, Claus Lindbjerg Andersen, Karina Dalsgaard Sørensen, Jakob Skou Pedersen, Torben Falck Ørntoft, Lars Dyrskjøt. PLoS One 2014
Times Cited: 183







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



Times Cited
  Times     Co-cited
Similarity




A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples.
Anna Esteve-Codina, Oriol Arpi, Maria Martinez-García, Estela Pineda, Mar Mallo, Marta Gut, Cristina Carrato, Anna Rovira, Raquel Lopez, Avelina Tortosa,[...]. PLoS One 2017
40
35

Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples.
Stefan Graw, Richard Meier, Kay Minn, Clark Bloomer, Andrew K Godwin, Brooke Fridley, Anda Vlad, Peter Beyerlein, Jeremy Chien. Sci Rep 2015
33
36

Comparative analysis of RNA sequencing methods for degraded or low-input samples.
Xian Adiconis, Diego Borges-Rivera, Rahul Satija, David S DeLuca, Michele A Busby, Aaron M Berlin, Andrey Sivachenko, Dawn Anne Thompson, Alec Wysoker, Timothy Fennell,[...]. Nat Methods 2013
257
11

Determinants of RNA quality from FFPE samples.
Silke von Ahlfen, Andreas Missel, Klaus Bendrat, Martin Schlumpberger. PLoS One 2007
220
10

Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysis.
Michal R Schweiger, Martin Kerick, Bernd Timmermann, Marcus W Albrecht, Tatjana Borodina, Dmitri Parkhomchuk, Kurt Zatloukal, Hans Lehrach. PLoS One 2009
119
10

Effect of fixatives and tissue processing on the content and integrity of nucleic acids.
Mythily Srinivasan, Daniel Sedmak, Scott Jewell. Am J Pathol 2002
707
10

Robustness of Next Generation Sequencing on Older Formalin-Fixed Paraffin-Embedded Tissue.
Danielle Mercatante Carrick, Michele G Mehaffey, Michael C Sachs, Sean Altekruse, Corinne Camalier, Rodrigo Chuaqui, Wendy Cozen, Biswajit Das, Brenda Y Hernandez, Chih-Jian Lih,[...]. PLoS One 2015
53
18

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

Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project.
Pauline Robbe, Niko Popitsch, Samantha J L Knight, Pavlos Antoniou, Jennifer Becq, Miao He, Alexander Kanapin, Anastasia Samsonova, Dimitrios V Vavoulis, Mark T Ross,[...]. Genet Med 2018
51
19

The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing.
Marcin Cieslik, Rashmi Chugh, Yi-Mi Wu, Ming Wu, Christine Brennan, Robert Lonigro, Fengyun Su, Rui Wang, Javed Siddiqui, Rohit Mehra,[...]. Genome Res 2015
87
10

Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine.
Eliezer M Van Allen, Nikhil Wagle, Petar Stojanov, Danielle L Perrin, Kristian Cibulskis, Sara Marlow, Judit Jane-Valbuena, Dennis C Friedrich, Gregory Kryukov, Scott L Carter,[...]. Nat Med 2014
330
8

Whole exome sequencing (WES) on formalin-fixed, paraffin-embedded (FFPE) tumor tissue in gastrointestinal stromal tumors (GIST).
Annalisa Astolfi, Milena Urbini, Valentina Indio, Margherita Nannini, Chiara Giusy Genovese, Donatella Santini, Maristella Saponara, Anna Mandrioli, Giorgio Ercolani, Giovanni Brandi,[...]. BMC Genomics 2015
30
26

Comparison of clinical targeted next-generation sequence data from formalin-fixed and fresh-frozen tissue specimens.
David H Spencer, Jennifer K Sehn, Haley J Abel, Mark A Watson, John D Pfeifer, Eric J Duncavage. J Mol Diagn 2013
108
8

Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity.
Martin Kerick, Melanie Isau, Bernd Timmermann, Holger Sültmann, Ralf Herwig, Sylvia Krobitsch, Georg Schaefer, Irmgard Verdorfer, Georg Bartsch, Helmut Klocker,[...]. BMC Med Genomics 2011
118
8

Accurate RNA Sequencing From Formalin-Fixed Cancer Tissue To Represent High-Quality Transcriptome From Frozen Tissue.
Jialu Li, Chunxiao Fu, Terence P Speed, Wenyi Wang, W Fraser Symmans. JCO Precis Oncol 2018
23
34


Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.
Wei Zhao, Xiaping He, Katherine A Hoadley, Joel S Parker, David Neil Hayes, Charles M Perou. BMC Genomics 2014
153
7


The RIN: an RNA integrity number for assigning integrity values to RNA measurements.
Andreas Schroeder, Odilo Mueller, Susanne Stocker, Ruediger Salowsky, Michael Leiber, Marcus Gassmann, Samar Lightfoot, Wolfram Menzel, Martin Granzow, Thomas Ragg. BMC Mol Biol 2006
7

Nucleic acids from long-term preserved FFPE tissues are suitable for downstream analyses.
Natalie Ludyga, Barbara Grünwald, Omid Azimzadeh, Sonja Englert, Heinz Höfler, Soile Tapio, Michaela Aubele. Virchows Arch 2012
100
7

Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics.
Sarah Munchel, Yen Hoang, Yue Zhao, Joseph Cottrell, Brandy Klotzle, Andrew K Godwin, Devin Koestler, Peter Beyerlein, Jian-Bing Fan, Marina Bibikova,[...]. Oncotarget 2015
37
18

Comparison of Accuracy of Whole-Exome Sequencing with Formalin-Fixed Paraffin-Embedded and Fresh Frozen Tissue Samples.
Ensel Oh, Yoon-La Choi, Mi Jeong Kwon, Ryong Nam Kim, Yu Jin Kim, Ji-Young Song, Kyung Soo Jung, Young Kee Shin. PLoS One 2015
48
14

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
7

Comparison of triple-negative breast cancer molecular subtyping using RNA from matched fresh-frozen versus formalin-fixed paraffin-embedded tissue.
Bojana Jovanović, Quanhu Sheng, Robert S Seitz, Kasey D Lawrence, Stephan W Morris, Lance R Thomas, David R Hout, Brock L Schweitzer, Yan Guo, Jennifer A Pietenpol,[...]. BMC Cancer 2017
15
46

Gene expression, single nucleotide variant and fusion transcript discovery in archival material from breast tumors.
Nadine Norton, Zhifu Sun, Yan W Asmann, Daniel J Serie, Brian M Necela, Aditya Bhagwate, Jin Jen, Bruce W Eckloff, Krishna R Kalari, Kevin J Thompson,[...]. PLoS One 2013
34
20


Transcriptome Sequencing (RNAseq) Enables Utilization of Formalin-Fixed, Paraffin-Embedded Biopsies with Clear Cell Renal Cell Carcinoma for Exploration of Disease Biology and Biomarker Development.
Oystein Eikrem, Christian Beisland, Karin Hjelle, Arnar Flatberg, Andreas Scherer, Lea Landolt, Trude Skogstrand, Sabine Leh, Vidar Beisvag, Hans-Peter Marti. PLoS One 2016
33
18


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
6

A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples.
Sven Schuierer, Walter Carbone, Judith Knehr, Virginie Petitjean, Anita Fernandez, Marc Sultan, Guglielmo Roma. BMC Genomics 2017
35
17

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
6

Whole transcriptome RNA-Seq analysis of breast cancer recurrence risk using formalin-fixed paraffin-embedded tumor tissue.
Dominick Sinicropi, Kunbin Qu, Francois Collin, Michael Crager, Mei-Lan Liu, Robert J Pelham, Mylan Pho, Andrew Dei Rossi, Jennie Jeong, Aaron Scott,[...]. PLoS One 2012
40
15

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
5

Factors in tissue handling and processing that impact RNA obtained from formalin-fixed, paraffin-embedded tissue.
Joon-Yong Chung, Till Braunschweig, Reginald Williams, Natalie Guerrero, Karl M Hoffmann, Mijung Kwon, Young K Song, Steven K Libutti, Stephen M Hewitt. J Histochem Cytochem 2008
77
6

Deamination Effects in Formalin-Fixed, Paraffin-Embedded Tissue Samples in the Era of Precision Medicine.
Seokhwi Kim, Charny Park, Yongick Ji, Deok G Kim, Hyunsik Bae, Michael van Vrancken, Duk-Hwan Kim, Kyoung-Mee Kim. J Mol Diagn 2017
29
17

Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay.
Maureen Cronin, Mylan Pho, Debjani Dutta, James C Stephans, Steven Shak, Michael C Kiefer, Jose M Esteban, Joffre B Baker. Am J Pathol 2004
389
5

The procurement, storage, and quality assurance of frozen blood and tissue biospecimens in pathology, biorepository, and biobank settings.
Maryam Shabihkhani, Gregory M Lucey, Bowen Wei, Sergey Mareninov, Jerry J Lou, Harry V Vinters, Elyse J Singer, Timothy F Cloughesy, William H Yong. Clin Biochem 2014
102
5

A high frequency of sequence alterations is due to formalin fixation of archival specimens.
C Williams, F Pontén, C Moberg, P Söderkvist, M Uhlén, J Pontén, G Sitbon, J Lundeberg. Am J Pathol 1999
333
5

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
5



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


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
5

Mutational heterogeneity in cancer and the search for new cancer-associated genes.
Michael S Lawrence, Petar Stojanov, Paz Polak, Gregory V Kryukov, Kristian Cibulskis, Andrey Sivachenko, Scott L Carter, Chip Stewart, Craig H Mermel, Steven A Roberts,[...]. Nature 2013
5

Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.
Marco Gerlinger, Andrew J Rowan, Stuart Horswell, M Math, James Larkin, David Endesfelder, Eva Gronroos, Pierre Martinez, Nicholas Matthews, Aengus Stewart,[...]. N Engl J Med 2012
5

Performance comparison of three DNA extraction kits on human whole-exome data from formalin-fixed paraffin-embedded normal and tumor samples.
Eric Bonnet, Marie-Laure Moutet, Céline Baulard, Delphine Bacq-Daian, Florian Sandron, Lilia Mesrob, Bertrand Fin, Marc Delépine, Marie-Ange Palomares, Claire Jubin,[...]. PLoS One 2018
16
31

Assessment of the quality of DNA from various formalin-fixed paraffin-embedded (FFPE) tissues and the use of this DNA for next-generation sequencing (NGS) with no artifactual mutation.
Naoki Einaga, Akio Yoshida, Hiroko Noda, Masaaki Suemitsu, Yuki Nakayama, Akihisa Sakurada, Yoshiko Kawaji, Hiromi Yamaguchi, Yasushi Sasaki, Takashi Tokino,[...]. PLoS One 2017
41
12


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.