Manuel A Garrido-Ramos. Cytogenet Genome Res 2015
Times Cited: 85
Times Cited: 85
Times Cited
Times Co-cited
Similarity
RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads.
Petr Novák, Pavel Neumann, Jiří Pech, Jaroslav Steinhaisl, Jiří Macas. Bioinformatics 2013
Petr Novák, Pavel Neumann, Jiří Pech, Jaroslav Steinhaisl, Jiří Macas. Bioinformatics 2013
64
TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads.
Petr Novák, Laura Ávila Robledillo, Andrea Koblížková, Iva Vrbová, Pavel Neumann, Jirí Macas. Nucleic Acids Res 2017
Petr Novák, Laura Ávila Robledillo, Andrea Koblížková, Iva Vrbová, Pavel Neumann, Jirí Macas. Nucleic Acids Res 2017
42
Repetitive sequences in plant nuclear DNA: types, distribution, evolution and function.
Shweta Mehrotra, Vinod Goyal. Genomics Proteomics Bioinformatics 2014
Shweta Mehrotra, Vinod Goyal. Genomics Proteomics Bioinformatics 2014
41
High-throughput analysis of the satellitome illuminates satellite DNA evolution.
Francisco J Ruiz-Ruano, María Dolores López-León, Josefa Cabrero, Juan Pedro M Camacho. Sci Rep 2016
Francisco J Ruiz-Ruano, María Dolores López-León, Josefa Cabrero, Juan Pedro M Camacho. Sci Rep 2016
36
Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data.
Petr Novák, Pavel Neumann, Jirí Macas. BMC Bioinformatics 2010
Petr Novák, Pavel Neumann, Jirí Macas. BMC Bioinformatics 2010
34
In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae.
Jiří Macas, Petr Novák, Jaume Pellicer, Jana Čížková, Andrea Koblížková, Pavel Neumann, Iva Fuková, Jaroslav Doležel, Laura J Kelly, Ilia J Leitch. PLoS One 2015
Jiří Macas, Petr Novák, Jaume Pellicer, Jana Čížková, Andrea Koblížková, Pavel Neumann, Iva Fuková, Jaroslav Doležel, Laura J Kelly, Ilia J Leitch. PLoS One 2015
27
25
Repetitive DNA in eukaryotic genomes.
Maria Assunta Biscotti, Ettore Olmo, J S Pat Heslop-Harrison. Chromosome Res 2015
Maria Assunta Biscotti, Ettore Olmo, J S Pat Heslop-Harrison. Chromosome Res 2015
25
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution.
Daniël P Melters, Keith R Bradnam, Hugh A Young, Natalie Telis, Michael R May, J Graham Ruby, Robert Sebra, Paul Peluso, John Eid, David Rank,[...]. Genome Biol 2013
Daniël P Melters, Keith R Bradnam, Hugh A Young, Natalie Telis, Michael R May, J Graham Ruby, Robert Sebra, Paul Peluso, John Eid, David Rank,[...]. Genome Biol 2013
24
Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin.
Miroslav Plohl, Andrea Luchetti, Nevenka Mestrović, Barbara Mantovani. Gene 2008
Miroslav Plohl, Andrea Luchetti, Nevenka Mestrović, Barbara Mantovani. Gene 2008
23
The evolutionary dynamics of repetitive DNA in eukaryotes.
B Charlesworth, P Sniegowski, W Stephan. Nature 1994
B Charlesworth, P Sniegowski, W Stephan. Nature 1994
21
Structural and functional liaisons between transposable elements and satellite DNAs.
Nevenka Meštrović, Brankica Mravinac, Martina Pavlek, Tanja Vojvoda-Zeljko, Eva Šatović, Miroslav Plohl. Chromosome Res 2015
Nevenka Meštrović, Brankica Mravinac, Martina Pavlek, Tanja Vojvoda-Zeljko, Eva Šatović, Miroslav Plohl. Chromosome Res 2015
26
PlantSat: a specialized database for plant satellite repeats.
Jirí Macas, Tibor Mészáros, Marcela Nouzová. Bioinformatics 2002
Jirí Macas, Tibor Mészáros, Marcela Nouzová. Bioinformatics 2002
20
Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
18
Nucleotide sequences of HS-alpha satellite DNA from kangaroo rat Dipodomys ordii and characterization of similar sequences in other rodents.
K Fry, W Salser. Cell 1977
K Fry, W Salser. Cell 1977
18
Organisation of the plant genome in chromosomes.
J S Pat Heslop-Harrison, Trude Schwarzacher. Plant J 2011
J S Pat Heslop-Harrison, Trude Schwarzacher. Plant J 2011
17
Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification.
Pavel Neumann, Petr Novák, Nina Hoštáková, Jiří Macas. Mob DNA 2019
Pavel Neumann, Petr Novák, Nina Hoštáková, Jiří Macas. Mob DNA 2019
17
Organization and evolution of subtelomeric satellite repeats in the potato genome.
Giovana A Torres, Zhiyun Gong, Marina Iovene, Cory D Hirsch, C Robin Buell, Glenn J Bryan, Petr Novák, Jiří Macas, Jiming Jiang. G3 (Bethesda) 2011
Giovana A Torres, Zhiyun Gong, Marina Iovene, Cory D Hirsch, C Robin Buell, Glenn J Bryan, Petr Novák, Jiří Macas, Jiming Jiang. G3 (Bethesda) 2011
26
The holocentric species Luzula elegans shows interplay between centromere and large-scale genome organization.
Stefan Heckmann, Jiri Macas, Katrin Kumke, Jörg Fuchs, Veit Schubert, Lu Ma, Petr Novák, Pavel Neumann, Stefan Taudien, Matthias Platzer,[...]. Plant J 2013
Stefan Heckmann, Jiri Macas, Katrin Kumke, Jörg Fuchs, Veit Schubert, Lu Ma, Petr Novák, Pavel Neumann, Stefan Taudien, Matthias Platzer,[...]. Plant J 2013
23
Centromere identity from the DNA point of view.
Miroslav Plohl, Nevenka Meštrović, Brankica Mravinac. Chromosoma 2014
Miroslav Plohl, Nevenka Meštrović, Brankica Mravinac. Chromosoma 2014
15
The B73 maize genome: complexity, diversity, and dynamics.
Patrick S Schnable, Doreen Ware, Robert S Fulton, Joshua C Stein, Fusheng Wei, Shiran Pasternak, Chengzhi Liang, Jianwei Zhang, Lucinda Fulton, Tina A Graves,[...]. Science 2009
Patrick S Schnable, Doreen Ware, Robert S Fulton, Joshua C Stein, Fusheng Wei, Shiran Pasternak, Chengzhi Liang, Jianwei Zhang, Lucinda Fulton, Tina A Graves,[...]. Science 2009
15
A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis.
E L Sonnhammer, R Durbin. Gene 1995
E L Sonnhammer, R Durbin. Gene 1995
15
Next generation sequencing-based analysis of repetitive DNA in the model dioecious [corrected] plant Silene latifolia.
Jiří Macas, Eduard Kejnovský, Pavel Neumann, Petr Novák, Andrea Koblížková, Boris Vyskot. PLoS One 2011
Jiří Macas, Eduard Kejnovský, Pavel Neumann, Petr Novák, Andrea Koblížková, Boris Vyskot. PLoS One 2011
17
Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
15
Differential amplification of satellite PaB6 in chromosomally hypervariable Prospero autumnale complex (Hyacinthaceae).
Khatere Emadzade, Tae-Soo Jang, Jiří Macas, Ales Kovařík, Petr Novák, John Parker, Hanna Weiss-Schneeweiss. Ann Bot 2014
Khatere Emadzade, Tae-Soo Jang, Jiří Macas, Ales Kovařík, Petr Novák, John Parker, Hanna Weiss-Schneeweiss. Ann Bot 2014
32
Plant centromeric retrotransposons: a structural and cytogenetic perspective.
Pavel Neumann, Alice Navrátilová, Andrea Koblížková, Eduard Kejnovský, Eva Hřibová, Roman Hobza, Alex Widmer, Jaroslav Doležel, Jiří Macas. Mob DNA 2011
Pavel Neumann, Alice Navrátilová, Andrea Koblížková, Eduard Kejnovský, Eva Hřibová, Roman Hobza, Alex Widmer, Jaroslav Doležel, Jiří Macas. Mob DNA 2011
14
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Robert C Edgar. Nucleic Acids Res 2004
Robert C Edgar. Nucleic Acids Res 2004
14
Cloning and characterization of ribosomal RNA genes from wheat and barley.
W L Gerlach, J R Bedbrook. Nucleic Acids Res 1979
W L Gerlach, J R Bedbrook. Nucleic Acids Res 1979
14
The repetitive DNA content of eukaryotic genomes.
I López-Flores, M A Garrido-Ramos. Genome Dyn 2012
I López-Flores, M A Garrido-Ramos. Genome Dyn 2012
14
Hypervariable 3' UTR region of plant LTR-retrotransposons as a source of novel satellite repeats.
Jirí Macas, Andrea Koblízková, Alice Navrátilová, Pavel Neumann. Gene 2009
Jirí Macas, Andrea Koblízková, Alice Navrátilová, Pavel Neumann. Gene 2009
21
The contributions of transposable elements to the structure, function, and evolution of plant genomes.
Jeffrey L Bennetzen, Hao Wang. Annu Rev Plant Biol 2014
Jeffrey L Bennetzen, Hao Wang. Annu Rev Plant Biol 2014
14
Satellite DNA evolution: old ideas, new approaches.
Sarah Sander Lower, Michael P McGurk, Andrew G Clark, Daniel A Barbash. Curr Opin Genet Dev 2018
Sarah Sander Lower, Michael P McGurk, Andrew G Clark, Daniel A Barbash. Curr Opin Genet Dev 2018
16
Satellite DNA in Vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing.
Laura Ávila Robledillo, Andrea Koblížková, Petr Novák, Katharina Böttinger, Iva Vrbová, Pavel Neumann, Ingo Schubert, Jiří Macas. Sci Rep 2018
Laura Ávila Robledillo, Andrea Koblížková, Petr Novák, Katharina Böttinger, Iva Vrbová, Pavel Neumann, Ingo Schubert, Jiří Macas. Sci Rep 2018
34
Characterization of repeat arrays in ultra-long nanopore reads reveals frequent origin of satellite DNA from retrotransposon-derived tandem repeats.
Tihana Vondrak, Laura Ávila Robledillo, Petr Novák, Andrea Koblížková, Pavel Neumann, Jiří Macas. Plant J 2020
Tihana Vondrak, Laura Ávila Robledillo, Petr Novák, Andrea Koblížková, Pavel Neumann, Jiří Macas. Plant J 2020
29
Organization and evolution of highly repeated satellite DNA sequences in plant chromosomes.
S Sharma, S N Raina. Cytogenet Genome Res 2005
S Sharma, S N Raina. Cytogenet Genome Res 2005
15
Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula.
Jirí Macas, Pavel Neumann, Alice Navrátilová. BMC Genomics 2007
Jirí Macas, Pavel Neumann, Alice Navrátilová. BMC Genomics 2007
12
Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.
Matthew Kearse, Richard Moir, Amy Wilson, Steven Stones-Havas, Matthew Cheung, Shane Sturrock, Simon Buxton, Alex Cooper, Sidney Markowitz, Chris Duran,[...]. Bioinformatics 2012
Matthew Kearse, Richard Moir, Amy Wilson, Steven Stones-Havas, Matthew Cheung, Shane Sturrock, Simon Buxton, Alex Cooper, Sidney Markowitz, Chris Duran,[...]. Bioinformatics 2012
12
Diverse retrotransposon families and an AT-rich satellite DNA revealed in giant genomes of Fritillaria lilies.
Katerina Ambrozová, Terezie Mandáková, Petr Bures, Pavel Neumann, Ilia J Leitch, Andrea Koblízková, Jirí Macas, Martin A Lysak. Ann Bot 2011
Katerina Ambrozová, Terezie Mandáková, Petr Bures, Pavel Neumann, Ilia J Leitch, Andrea Koblízková, Jirí Macas, Martin A Lysak. Ann Bot 2011
20
Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2.
Petr Novák, Pavel Neumann, Jiří Macas. Nat Protoc 2020
Petr Novák, Pavel Neumann, Jiří Macas. Nat Protoc 2020
20
The centromere paradox: stable inheritance with rapidly evolving DNA.
S Henikoff, K Ahmad, H S Malik. Science 2001
S Henikoff, K Ahmad, H S Malik. Science 2001
11
Repeatless and repeat-based centromeres in potato: implications for centromere evolution.
Zhiyun Gong, Yufeng Wu, Andrea Koblízková, Giovana A Torres, Kai Wang, Marina Iovene, Pavel Neumann, Wenli Zhang, Petr Novák, C Robin Buell,[...]. Plant Cell 2012
Zhiyun Gong, Yufeng Wu, Andrea Koblízková, Giovana A Torres, Kai Wang, Marina Iovene, Pavel Neumann, Wenli Zhang, Petr Novák, C Robin Buell,[...]. Plant Cell 2012
11
Equilibrium sedimentation in density gradients of DNA preparations from animal tissues.
S KIT. J Mol Biol 1961
S KIT. J Mol Biol 1961
11
Long-term conservation vs high sequence divergence: the case of an extraordinarily old satellite DNA in bivalve mollusks.
M Plohl, V Petrović, A Luchetti, A Ricci, E Satović, M Passamonti, B Mantovani. Heredity (Edinb) 2010
M Plohl, V Petrović, A Luchetti, A Ricci, E Satović, M Passamonti, B Mantovani. Heredity (Edinb) 2010
21
Stretching the rules: monocentric chromosomes with multiple centromere domains.
Pavel Neumann, Alice Navrátilová, Elizabeth Schroeder-Reiter, Andrea Koblížková, Veronika Steinbauerová, Eva Chocholová, Petr Novák, Gerhard Wanner, Jiří Macas. PLoS Genet 2012
Pavel Neumann, Alice Navrátilová, Elizabeth Schroeder-Reiter, Andrea Koblížková, Veronika Steinbauerová, Eva Chocholová, Petr Novák, Gerhard Wanner, Jiří Macas. PLoS Genet 2012
11
Satellite DNA-mediated effects on genome regulation.
Z Pezer, J Brajković, I Feliciello, D Ugarkovć. Genome Dyn 2012
Z Pezer, J Brajković, I Feliciello, D Ugarkovć. Genome Dyn 2012
18
Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice.
Benoit Piegu, Romain Guyot, Nathalie Picault, Anne Roulin, Abhijit Sanyal, Hyeran Kim, Kristi Collura, Darshan S Brar, Scott Jackson, Rod A Wing,[...]. Genome Res 2006
Benoit Piegu, Romain Guyot, Nathalie Picault, Anne Roulin, Abhijit Sanyal, Hyeran Kim, Kristi Collura, Darshan S Brar, Scott Jackson, Rod A Wing,[...]. Genome Res 2006
11
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.