Search Results - "Borodovsky, Mark"

Identification of protein coding regions in RNA transcripts by Tang, Shiyuyun, Lomsadze, Alexandre, Borodovsky, Mark

“…Massive parallel sequencing of RNA transcripts by next-generation technology (RNA-Seq) generates critically important data for eukaryotic gene discovery. Gene…”
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Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes by Lomsadze, Alexandre, Gemayel, Karl, Tang, Shiyuyun, Borodovsky, Mark

“…In a conventional view of the prokaryotic genome organization, promoters precede operons and ribosome binding sites (RBSs) with Shine-Dalgarno consensus…”
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TSEBRA: transcript selector for BRAKER by Gabriel, Lars, Hoff, Katharina J, Brůna, TomáÅ, Borodovsky, Mark, Stanke, Mario

“…Abstract Background BRAKER is a suite of automatic pipelines, BRAKER1 and BRAKER2, for the accurate annotation of protein-coding genes in eukaryotic genomes…”
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Eukaryotic gene prediction using GeneMark.hmm-E and GeneMark-ES by Borodovsky, Mark, Lomsadze, Alex

“…This unit describes how to use the gene-finding programs GeneMark.hmm-E and GeneMark-ES for finding protein-coding genes in the genomic DNA of eukaryotic…”
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Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication by 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

“…Genome sequences of nine species of citrus, including oranges, pummelos and mandarins, reveal pathways of domestication and provide resources for breeding…”
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Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus) by Stajich, Jason E., Wilke, Sarah K., Ahrén, Dag, Au, Chun Hang, Birren, Bruce W., Borodovsky, Mark, Burns, Claire, Canbäck, Björn, Casselton, Lorna A., Cheng, C.K., Deng, Jixin, Dietrich, Fred S., Fargo, David C., Farman, Mark L., Gathman, Allen C., Goldberg, Jonathan, Guigó, Roderic, Hoegger, Patrick J., Hooker, James B., Huggins, Ashleigh, James, Timothy Y., Kamada, Takashi, Kilaru, Sreedhar, Kodira, Chinnapa, Kües, Ursula, Kupfer, Doris, Kwan, H.S., Lomsadze, Alexandre, Li, Weixi, Lilly, Walt W., Ma, Li-Jun, Mackey, Aaron J., Manning, Gerard, Martin, Francis, Muraguchi, Hajime, Natvig, Donald O., Palmerini, Heather, Ramesh, Marilee A., Rehmeyer, Cathy J., Roe, Bruce A., Shenoy, Narmada, Stanke, Mario, Ter-Hovhannisyan, Vardges, Tunlid, Anders, Velagapudi, Rajesh, Vision, Todd J., Zeng, Qiandong, Zolan, Miriam E., Pukkila, Patricia J., Bennett, Joan Wennstrom

“…The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life…”
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genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation by 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

“…BACKGROUND: Little is known about the mechanisms of adaptation of life to the extreme environmental conditions encountered in polar regions. Here we present…”
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StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes by Gemayel, Karl, Lomsadze, Alexandre, Borodovsky, Mark

“…State-of-the-art algorithms of ab initio gene prediction for prokaryotic genomes were shown to be sufficiently accurate. A pair of algorithms would agree on…”
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Protein secondary structure prediction for a single-sequence using hidden semi-Markov models by Aydin, Zafer, Altunbasak, Yucel, Borodovsky, Mark

“…The accuracy of protein secondary structure prediction has been improving steadily towards the 88% estimated theoretical limit. There are two types of…”
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The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants by 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

“…Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas and secondary domestication regions includes highly divergent…”
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Bioinformatics Pipeline for Human Papillomavirus Short Read Genomic Sequences Classification Using Support Vector Machine by Lomsadze, Alexandre, Li, Tengguo, Rajeevan, Mangalathu S, Unger, Elizabeth R, Borodovsky, Mark

“…We recently developed a test based on the Agilent SureSelect target enrichment system capturing genomic fragments from 191 human papillomaviruses (HPV) types…”
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A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. “Hillquist”) by 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

“…Abstract Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for…”
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Development of a workflow for identification of nuclear genotyping markers for Cyclospora cayetanensis by Houghton, Katelyn A, Lomsadze, Alexandre, Park, Subin, Nascimento, Fernanda S, Barratt, Joel, Arrowood, Michael J, VanRoey, Erik, Talundzic, Eldin, Borodovsky, Mark, Qvarnstrom, Yvonne

“…Cyclospora cayetanensis is an intestinal parasite responsible for the diarrheal illness, cyclosporiasis. Molecular genotyping, using targeted amplicon…”
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Bacillus anthracis genome organization in light of whole transcriptome sequencing by Martin, Jeffrey, Zhu, Wenhan, Passalacqua, Karla D, Bergman, Nicholas, Borodovsky, Mark

“…Emerging knowledge of whole prokaryotic transcriptomes could validate a number of theoretical concepts introduced in the early days of genomics. What are the…”
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Exonization of the LTR transposable elements in human genome by Piriyapongsa, Jittima, Polavarapu, Nalini, Borodovsky, Mark, McDonald, John

“…Retrotransposons have been shown to contribute to evolution of both structure and regulation of protein coding genes. It has been postulated that the primary…”
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cag, a Pathogenicity Island of Helicobacter pylori, Encodes Type I-Specific and Disease-Associated Virulence Factors by Censini, Stefano, Lange, Christina, Xiang, Zhaoying, Crabtree, Jean E., Ghiara, Paolo, Borodovsky, Mark, Rappuoli, Rino, Covacci, Antonello

“…cagA, a gene that codes for an immunodominant antigen, is present only in Helicobacter pylori strains that are associated with severe forms of gastroduodenal…”
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Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi by Xu, Junhuan, Linning, Rob, Fellers, John, Dickinson, Matthew, Zhu, Wenhan, Antonov, Ivan, Joly, David L, Donaldson, Michael E, Eilam, Tamar, Anikster, Yehoshua, Banks, Travis, Munro, Sarah, Mayo, Michael, Wynhoven, Brian, Ali, Johar, Moore, Richard, McCallum, Brent, Borodovsky, Mark, Saville, Barry, Bakkeren, Guus

“…Rust fungi are biotrophic basidiomycete plant pathogens that cause major diseases on plants and trees world-wide, affecting agriculture and forestry. Their…”
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Identification of Proteins Associated with Murine Cytomegalovirus Virions by Kattenhorn, Lisa M, Mills, Ryan, Wagner, Markus, Lomsadze, Alexandre, Makeev, Vsevolod, Borodovsky, Mark, Ploegh, Hidde L, Kessler, Benedikt M

“…Article Usage Stats Services JVI Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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Disproportionate presence of adenosine in mitochondrial and chloroplast DNA of Chlamydomonas reinhardtii by El-Sayed, Waleed M.M., Gombolay, Alli L., Xu, Penghao, Yang, Taehwan, Jeon, Youngkyu, Balachander, Sathya, Newnam, Gary, Tao, Sijia, Bowen, Nicole E., Brůna, Tomáš, Borodovsky, Mark, Schinazi, Raymond F., Kim, Baek, Chen, Yongsheng, Storici, Francesca

“…Ribonucleoside monophosphates (rNMPs) represent the most common non-standard nucleotides found in the genome of cells. The distribution of rNMPs in DNA has…”
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Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii by Bult, Carol J., White, Owen, Olsen, Gary J., Zhou, Lixin, Fleischmann, Robert D., Sutton, Granger G., Blake, Judith A., FitzGerald, Lisa M., Clayton, Rebecca A., Gocayne, Jeannine D., Kerlavage, Anthony R., Dougherty, Brian A., Tomb, Jean-Francois, Adams, Mark D., Reich, Claudia I., Overbeek, Ross, Kirkness, Ewen F., Weinstock, Keith G., Merrick, Joseph M., Glodek, Anna, Scott, John L., Neil S. M. Geoghagen, Weidman, Janice F., Fuhrmann, Joyce L., Nguyen, Dave, Utterback, Teresa R., Kelley, Jenny M., Peterson, Jeremy D., Sadow, Paul W., Hanna, Michael C., Cotton, Matthew D., Roberts, Kevin M., Hurst, Margaret A., Kaine, Brian P., Borodovsky, Mark, Klenk, Hans-Peter, Fraser, Claire M., Smith, Hamilton O., Woese, Carl R., Venter, J. Craig

“…The complete 1.66-megabase pair genome sequence of an autotrophic archaeon, Methanococcus jannaschii, and its 58- and 16-kilobase pair extrachromosomal…”
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