A citation-based method for searching scientific literature

Wagner F Molina, Gideão W W F Costa, Inailson M C Cunha, Luiz A C Bertollo, Tariq Ezaz, Thomas Liehr, Marcelo B Cioffi. Int J Mol Sci 2020
Times Cited: 3

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

Times Cited
  Times     Co-cited

Differential analysis of gene regulation at transcript resolution with RNA-seq.
Cole Trapnell, David G Hendrickson, Martin Sauvageau, Loyal Goff, John L Rinn, Lior Pachter. Nat Biotechnol 2013

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

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.
Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, Marina Haukness, Hugh E Olsen, Colleen Bosworth, Joel Armstrong, Kristof Tigyi, Nicholas Maurer, Sergey Koren,[...]. Nat Biotechnol 2020

TEclass--a tool for automated classification of unknown eukaryotic transposable elements.
György Abrusán, Norbert Grundmann, Luc DeMester, Wojciech Makalowski. Bioinformatics 2009

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.
Nicolas Servant, Nelle Varoquaux, Bryan R Lajoie, Eric Viara, Chong-Jian Chen, Jean-Philippe Vert, Edith Heard, Job Dekker, Emmanuel Barillot. Genome Biol 2015

PRINTS prepares for the new millennium.
T K Attwood, D R Flower, A P Lewis, J E Mabey, S R Morgan, P Scordis, J N Selley, W Wright. Nucleic Acids Res 1999

Temporal silencing of an androgenic gland-specific insulin-like gene affecting phenotypical gender differences and spermatogenesis.
Tomer Ventura, Rivka Manor, Eliahu D Aflalo, Simy Weil, Shaul Raviv, Lilah Glazer, Amir Sagi. Endocrinology 2009

SOAP2: an improved ultrafast tool for short read alignment.
Ruiqiang Li, Chang Yu, Yingrui Li, Tak-Wah Lam, Siu-Ming Yiu, Karsten Kristiansen, Jun Wang. Bioinformatics 2009

A sexual shift induced by silencing of a single insulin-like gene in crayfish: ovarian upregulation and testicular degeneration.
Ohad Rosen, Rivka Manor, Simy Weil, Ohad Gafni, Assaf Linial, Eliahu D Aflalo, Tomer Ventura, Amir Sagi. PLoS One 2010

Molecular cloning and expression analysis of two sex-lethal homolog genes during development in the oriental river prawn, Macrobrachium nipponense.
Y P Zhang, H Qiao, W Y Zhang, S M Sun, S F Jiang, Y S Gong, Y W Xiong, S B Jin, H T Fu. Genet Mol Res 2013

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments.
Neva C Durand, Muhammad S Shamim, Ido Machol, Suhas S P Rao, Miriam H Huntley, Eric S Lander, Erez Lieberman Aiden. Cell Syst 2016

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom.
Neva C Durand, James T Robinson, Muhammad S Shamim, Ido Machol, Jill P Mesirov, Eric S Lander, Erez Lieberman Aiden. Cell Syst 2016

De novo analysis of transcriptome dynamics in the migratory locust during the development of phase traits.
Shuang Chen, Pengcheng Yang, Feng Jiang, Yuanyuan Wei, Zongyuan Ma, Le Kang. PLoS One 2010

Human mesenchymal stem cells inhibit cancer cell proliferation by secreting DKK-1.
Y Zhu, Z Sun, Q Han, L Liao, J Wang, C Bian, J Li, X Yan, Y Liu, C Shao,[...]. Leukemia 2009

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
Felipe A Simão, Robert M Waterhouse, Panagiotis Ioannidis, Evgenia V Kriventseva, Evgeny M Zdobnov. Bioinformatics 2015

The EMBL Nucleotide Sequence Database.
Tamara Kulikova, Philippe Aldebert, Nicola Althorpe, Wendy Baker, Kirsty Bates, Paul Browne, Alexandra van den Broek, Guy Cochrane, Karyn Duggan, Ruth Eberhardt,[...]. Nucleic Acids Res 2004

The complete mitochondrial genome of Macrobrachium nipponense.
Keyi Ma, Jianbin Feng, Jingyun Lin, Jiale Li. Gene 2011

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.
Olga Dudchenko, Sanjit S Batra, Arina D Omer, Sarah K Nyquist, Marie Hoeger, Neva C Durand, Muhammad S Shamim, Ido Machol, Eric S Lander, Aviva Presser Aiden,[...]. Science 2017

The Pfam protein families database: towards a more sustainable future.
Robert D Finn, Penelope Coggill, Ruth Y Eberhardt, Sean R Eddy, Jaina Mistry, Alex L Mitchell, Simon C Potter, Marco Punta, Matloob Qureshi, Amaia Sangrador-Vegas,[...]. Nucleic Acids Res 2016

KEGG: Kyoto Encyclopedia of Genes and Genomes.
H Ogata, S Goto, K Sato, W Fujibuchi, H Bono, M Kanehisa. Nucleic Acids Res 1999

MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes.
Brandi L Cantarel, Ian Korf, Sofia M C Robb, Genis Parra, Eric Ross, Barry Moore, Carson Holt, Alejandro Sánchez Alvarado, Mark Yandell. Genome Res 2008

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.
Brigitte Boeckmann, Amos Bairoch, Rolf Apweiler, Marie-Claude Blatter, Anne Estreicher, Elisabeth Gasteiger, Maria J Martin, Karine Michoud, Claire O'Donovan, Isabelle Phan,[...]. Nucleic Acids Res 2003

HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015

Molecular cloning, expression pattern analysis, and in situ hybridization of a Transformer-2 gene in the oriental freshwater prawn, Macrobrachium nipponense (de Haan, 1849).
Yabing Wang, Shubo Jin, Hongtuo Fu, Hui Qiao, Shengming Sun, Wenyi Zhang, Sufei Jiang, Yongsheng Gong, Yiwei Xiong, Yan Wu. 3 Biotech 2019

Repbase Update, a database of eukaryotic repetitive elements.
J Jurka, V V Kapitonov, A Pavlicek, P Klonowski, O Kohany, J Walichiewicz. Cytogenet Genome Res 2005

Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
Bruce J Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K Young,[...]. PLoS One 2014

SMART: a web-based tool for the study of genetically mobile domains.
J Schultz, R R Copley, T Doerks, C P Ponting, P Bork. Nucleic Acids Res 2000

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
Stéphane Guindon, Jean-François Dufayard, Vincent Lefort, Maria Anisimova, Wim Hordijk, Olivier Gascuel. Syst Biol 2010

LoRDEC: accurate and efficient long read error correction.
Leena Salmela, Eric Rivals. Bioinformatics 2014

Recent improvements of the ProDom database of protein domain families.
F Corpet, J Gouzy, D Kahn. Nucleic Acids Res 1999

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity.
Yupeng Wang, Haibao Tang, Jeremy D Debarry, Xu Tan, Jingping Li, Xiyin Wang, Tae-ho Lee, Huizhe Jin, Barry Marler, Hui Guo,[...]. Nucleic Acids Res 2012

Analysis of testis metabolome and transcriptome from the oriental river prawn (Macrobrachium nipponense) in response to different temperatures and illumination times.
Shubo Jin, Yuning Hu, Hongtuo Fu, Shengming Sun, Sufei Jiang, Yiwei Xiong, Hui Qiao, Wenyi Zhang, Yongsheng Gong, Yan Wu. Comp Biochem Physiol Part D Genomics Proteomics 2020

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times.
Sudhir Kumar, Glen Stecher, Michael Suleski, S Blair Hedges. Mol Biol Evol 2017

Expression of an Androgenic Gland-Specific Insulin-Like Peptide during the Course of Prawn Sexual and Morphotypic Differentiation.
Tomer Ventura, Rivka Manor, Eliahu D Aflalo, Simy Weil, Isam Khalaila, Ohad Rosen, Amir Sagi. ISRN Endocrinol 2011

Demographic and genetic consequences of disturbed sex determination.
Claus Wedekind. Philos Trans R Soc Lond B Biol Sci 2017

GeneWise and Genomewise.
Ewan Birney, Michele Clamp, Richard Durbin. Genome Res 2004

A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
Suhas S P Rao, Miriam H Huntley, Neva C Durand, Elena K Stamenova, Ivan D Bochkov, James T Robinson, Adrian L Sanborn, Ido Machol, Arina D Omer, Eric S Lander,[...]. Cell 2014

Using RepeatMasker to identify repetitive elements in genomic sequences.
Maja Tarailo-Graovac, Nansheng Chen. Curr Protoc Bioinformatics 2009

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.