Ab initio gene identification in metagenomic sequences

por Zhu, Wenhan, Lomsadze, Alexandre, Borodovsky, Mark
Publicado 2010

Identification of protein coding regions in RNA transcripts

por Tang, Shiyuyun, Lomsadze, Alexandre, Borodovsky, Mark
Publicado 2015

GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins

por Brůna, Tomáš, Lomsadze, Alexandre, Borodovsky, Mark
Publicado 2020

StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes

por Gemayel, Karl, Lomsadze, Alexandre, Borodovsky, Mark
Publicado 2021

GeneMark-ETP: Automatic Gene Finding in Eukaryotic Genomes in Consistency with Extrinsic Data

por Bruna, Tomas, Lomsadze, Alexandre, Borodovsky, Mark
Publicado 2023

Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

por Lomsadze, Alexandre, Burns, Paul D., Borodovsky, Mark
Publicado 2014

Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes

por Lomsadze, Alexandre, Gemayel, Karl, Tang, Shiyuyun, Borodovsky, Mark
Publicado 2018

GeneMark-HM: improving gene prediction in DNA sequences of human microbiome

por Lomsadze, Alexandre, Bonny, Christophe, Strozzi, Francesco, Borodovsky, Mark
Publicado 2021

Gene identification in novel eukaryotic genomes by self-training algorithm

por Lomsadze, Alexandre, Ter-Hovhannisyan, Vardges, Chernoff, Yury O., Borodovsky, Mark
Publicado 2005

Improving gene annotation of complete viral genomes

por Mills, Ryan, Rozanov, Michael, Lomsadze, Alexandre, Tatusova, Tatiana, Borodovsky, Mark
Publicado 2003

Bioinformatics Pipeline for Human Papillomavirus Short Read Genomic Sequences Classification Using Support Vector Machine

por Lomsadze, Alexandre, Li, Tengguo, Rajeevan, Mangalathu S., Unger, Elizabeth R., Borodovsky, Mark
Publicado 2020

BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database

por Brůna, Tomáš, Hoff, Katharina J, Lomsadze, Alexandre, Stanke, Mario, Borodovsky, Mark
Publicado 2021

BRAKER3: Fully Automated Genome Annotation Using RNA-Seq and Protein Evidence with GeneMark-ETP, AUGUSTUS and TSEBRA

por Gabriel, Lars, Brůna, Tomáš, Hoff, Katharina J., Ebel, Matthis, Lomsadze, Alexandre, Borodovsky, Mark, Stanke, Mario
Publicado 2023

NCBI prokaryotic genome annotation pipeline

por Tatusova, Tatiana, DiCuccio, Michael, Badretdin, Azat, Chetvernin, Vyacheslav, Nawrocki, Eric P., Zaslavsky, Leonid, Lomsadze, Alexandre, Pruitt, Kim D., Borodovsky, Mark, Ostell, James
Publicado 2016

Development of a workflow for identification of nuclear genotyping markers for Cyclospora cayetanensis

por Houghton, Katelyn A., Lomsadze, Alexandre, Park, Subin, Nascimento, Fernanda S., Barratt, Joel, Arrowood, Michael J., VanRoey, Erik, Talundzic, Eldin, Borodovsky, Mark, Qvarnstrom, Yvonne
Publicado 2020

The Genome Sequence of the North-European Cucumber (Cucumis sativus L.) Unravels Evolutionary Adaptation Mechanisms in Plants

por Wóycicki, Rafał, Witkowicz, Justyna, Gawroński, Piotr, Dąbrowska, Joanna, Lomsadze, Alexandre, Pawełkowicz, Magdalena, Siedlecka, Ewa, Yagi, Kohei, Pląder, Wojciech, Seroczyńska, Anna, Śmiech, Mieczysław, Gutman, Wojciech, Niemirowicz-Szczytt, Katarzyna, Bartoszewski, Grzegorz, Tagashira, Norikazu, Hoshi, Yoshikazu, Borodovsky, Mark, Karpiński, Stanisław, Malepszy, Stefan, Przybecki, Zbigniew
Publicado 2011

The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry)

por Buti, Matteo, Moretto, Marco, Barghini, Elena, Mascagni, Flavia, Natali, Lucia, Brilli, Matteo, Lomsadze, Alexandre, Sonego, Paolo, Giongo, Lara, Alonge, Michael, Velasco, Riccardo, Varotto, Claudio, Šurbanovski, Nada, Borodovsky, Mark, Ward, Judson A, Engelen, Kristof, Cavallini, Andrea, Cestaro, Alessandro, Sargent, Daniel James
Publicado 2017

The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation

por Blanc, Guillaume, Agarkova, Irina, Grimwood, Jane, Kuo, Alan, Brueggeman, Andrew, Dunigan, David D, Gurnon, James, Ladunga, Istvan, Lindquist, Erika, Lucas, Susan, Pangilinan, Jasmyn, Pröschold, Thomas, Salamov, Asaf, Schmutz, Jeremy, Weeks, Donald, Yamada, Takashi, Lomsadze, Alexandre, Borodovsky, Mark, Claverie, Jean-Michel, Grigoriev, Igor V, Van Etten, James L
Publicado 2012

A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. “Hillquist”)

por Brůna, Tomáš, Aryal, Rishi, Dudchenko, Olga, Sargent, Daniel James, Mead, Daniel, Buti, Matteo, Cavallini, Andrea, Hytönen, Timo, Andrés, Javier, Pham, Melanie, Weisz, David, Mascagni, Flavia, Usai, Gabriele, Natali, Lucia, Bassil, Nahla, Fernandez, Gina E, Lomsadze, Alexandre, Armour, Mitchell, Olukolu, Bode, Poorten, Thomas, Britton, Caitlin, Davik, Jahn, Ashrafi, Hamid, Aiden, Erez Lieberman, Borodovsky, Mark, Worthington, Margaret
Publicado 2022

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

por Wu, G. Albert, Prochnik, Simon, Jenkins, Jerry, Salse, Jerome, Hellsten, Uffe, Murat, Florent, Perrier, Xavier, Ruiz, Manuel, Scalabrin, Simone, Terol, Javier, Takita, Marco Aurélio, Labadie, Karine, Poulain, Julie, Couloux, Arnaud, Jabbari, Kamel, Cattonaro, Federica, Del Fabbro, Cristian, Pinosio, Sara, Zuccolo, Andrea, Chapman, Jarrod, Grimwood, Jane, Tadeo, Francisco R., Estornell, Leandro H., Muñoz-Sanz, Juan V., Ibanez, Victoria, Herrero-Ortega, Amparo, Aleza, Pablo, Pérez-Pérez, Julián, Ramón, Daniel, Brunel, Dominique, Luro, François, Chen, Chunxian, Farmerie, William G., Desany, Brian, Kodira, Chinnappa, Mohiuddin, Mohammed, Harkins, Tim, Fredrikson, Karin, Burns, Paul, Lomsadze, Alexandre, Borodovsky, Mark, Reforgiato, Giuseppe, Freitas-Astúa, Juliana, Quetier, Francis, Navarro, Luis, Roose, Mikeal, Wincker, Patrick, Schmutz, Jeremy, Morgante, Michele, Machado, Marcos Antonio, Talon, Manuel, Jaillon, Olivier, Ollitrault, Patrick, Gmitter, Frederick, Rokhsar, Daniel
Publicado 2014