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Accurate isoform discovery with IsoQuant using long reads
Prjibelski, Andrey D., Mikheenko, Alla, Joglekar, Anoushka, Smetanin, Alexander, Jarroux, Julien, Lapidus, Alla L., Tilgner, Hagen U.
Published in Nature biotechnology (01.07.2023)
Published in Nature biotechnology (01.07.2023)
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rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data
Bushmanova, Elena, Antipov, Dmitry, Lapidus, Alla, Prjibelski, Andrey D
Published in Gigascience (01.09.2019)
Published in Gigascience (01.09.2019)
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plasmidSPAdes: assembling plasmids from whole genome sequencing data
Antipov, Dmitry, Hartwick, Nolan, Shen, Max, Raiko, Mikhail, Lapidus, Alla, Pevzner, Pavel A.
Published in Bioinformatics (Oxford, England) (15.11.2016)
Published in Bioinformatics (Oxford, England) (15.11.2016)
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Plasmid detection and assembly in genomic and metagenomic data sets
Antipov, Dmitry, Raiko, Mikhail, Lapidus, Alla, Pevzner, Pavel A.
Published in Genome research (01.06.2019)
Published in Genome research (01.06.2019)
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MGnify: the microbiome analysis resource in 2020
Mitchell, Alex L, Almeida, Alexandre, Beracochea, Martin, Boland, Miguel, Burgin, Josephine, Cochrane, Guy, Crusoe, Michael R, Kale, Varsha, Potter, Simon C, Richardson, Lorna J, Sakharova, Ekaterina, Scheremetjew, Maxim, Korobeynikov, Anton, Shlemov, Alex, Kunyavskaya, Olga, Lapidus, Alla, Finn, Robert D
Published in Nucleic acids research (08.01.2020)
Published in Nucleic acids research (08.01.2020)
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Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T B K, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs J G, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Murat Eren, A, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, Woyke, Tanja
Published in Nature biotechnology (01.08.2017)
Published in Nature biotechnology (01.08.2017)
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rnaQUAST: a quality assessment tool for de novo transcriptome assemblies
Bushmanova, Elena, Antipov, Dmitry, Lapidus, Alla, Suvorov, Vladimir, Prjibelski, Andrey D.
Published in Bioinformatics (Oxford, England) (15.07.2016)
Published in Bioinformatics (Oxford, England) (15.07.2016)
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Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus
de Vries, Ronald P., Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Amillis, Sotiris, Uchima, Cristiane Akemi, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna A., Caldana, Camila, Cánovas, David, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, dos Santos, Renato Augusto Corrêa, Damásio, André Ricardo de Lima, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María Laura, Henrissat, Bernard, Hildén, Kristiina S., Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen L., Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio F., MacCabe, Andrew, Mäkelä, Miia R., Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos P., Mulé, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean Paul, Overkamp, Karin M., Park, Hee-Soo, Perrone, Giancarlo, Piumi, Francois, Punt, Peter J., Ram, Arthur F. J., Ramón, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego Mauricio, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio M., Sun, Hui, Susca, Antonia, Todd, Richard B., Tsang, Adrian, Unkles, Shiela E., van de Wiele, Nathalie, van Rossen-Uffink, Diana, Oliveira, Juliana Velasco de Castro, Vesth, Tammi C., Visser, Jaap, Yu, Jae-Hyuk, Zhou, Miaomiao, Andersen, Mikael R.
Published in Genome Biology (14.02.2017)
Published in Genome Biology (14.02.2017)
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Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles
Castanera, Raúl, López-Varas, Leticia, Borgognone, Alessandra, LaButti, Kurt, Lapidus, Alla, Schmutz, Jeremy, Grimwood, Jane, Pérez, Gúmer, Pisabarro, Antonio G., Grigoriev, Igor V., Stajich, Jason E., Ramírez, Lucía
Published in PLoS genetics (13.06.2016)
Published in PLoS genetics (13.06.2016)
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Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation
Salinero, Kennan, Keller, Keith, Feil, William S, Feil, Helene, Trong, Stephan, Di Bartolo, Genevieve, Lapidus, Alla
Published in BMC genomics (03.08.2009)
Published in BMC genomics (03.08.2009)
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Comparative genomics of biotechnologically important yeasts
Riley, Robert, Haridas, Sajeet, Wolfe, Kenneth H., Lopes, Mariana R., Hittinger, Chris Todd, Göker, Markus, Salamov, Asaf A., Wisecaver, Jennifer H., Long, Tanya M., Calvey, Christopher H., Aerts, Andrea L., Barry, Kerrie W., Choi, Cindy, Clum, Alicia, Coughlan, Aisling Y., Deshpande, Shweta, Douglass, Alexander P., Hanson, Sara J., Klenk, Hans-Peter, LaButti, Kurt M., Lapidus, Alla, Lindquist, Erika A., Lipzen, Anna M., Meier-Kolthoff, Jan P., Ohm, Robin A., Otillar, Robert P., Pangilinan, Jasmyn L., Peng, Yi, Rokas, Antonis, Rosa, Carlos A., Scheuner, Carmen, Sibirny, Andriy A., Slot, Jason C., Stielow, J. Benjamin, Sun, Hui, Kurtzman, Cletus P., Blackwell, Meredith, Grigoriev, Igor V., Jeffries, Thomas W.
Published in Proceedings of the National Academy of Sciences - PNAS (30.08.2016)
Published in Proceedings of the National Academy of Sciences - PNAS (30.08.2016)
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The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry
de Wit, Pierre J. G. M., van der Burgt, Ate, Ökmen, Bilal, Stergiopoulos, Ioannis, Abd-Elsalam, Kamel A., Aerts, Andrea L., Bahkali, Ali H., Beenen, Henriek G., Chettri, Pranav, Cox, Murray P., Datema, Erwin, de Vries, Ronald P., Dhillon, Braham, Ganley, Austen R., Griffiths, Scott A., Guo, Yanan, Hamelin, Richard C., Henrissat, Bernard, Kabir, M. Shahjahan, Jashni, Mansoor Karimi, Kema, Gert, Klaubauf, Sylvia, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Mehrabi, Rahim, Ohm, Robin A., Owen, Timothy J., Salamov, Asaf, Schwelm, Arne, Schijlen, Elio, Sun, Hui, van den Burg, Harrold A., van Ham, Roeland C. H. J., Zhang, Shuguang, Goodwin, Stephen B., Grigoriev, Igor V., Collemare, Jérôme, Bradshaw, Rosie E.
Published in PLoS genetics (01.11.2012)
Published in PLoS genetics (01.11.2012)
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The genome of Syntrophomonas wolfei: new insights into syntrophic metabolism and biohydrogen production
Sieber, Jessica R., Sims, David R., Han, Cliff, Kim, Edwin, Lykidis, Athanasios, Lapidus, Alla L., McDonnald, Erin, Rohlin, Lars, Culley, David E., Gunsalus, Robert, McInerney, Michael J.
Published in Environmental microbiology (01.08.2010)
Published in Environmental microbiology (01.08.2010)
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The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation
Mavromatis, Konstantinos, Land, Miriam L., Brettin, Thomas S., Quest, Daniel J., Copeland, Alex, Clum, Alicia, Goodwin, Lynne, Woyke, Tanja, Lapidus, Alla, Klenk, Hans Peter, Cottingham, Robert W., Kyrpides, Nikos C.
Published in PloS one (12.12.2012)
Published in PloS one (12.12.2012)
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A genomic perspective on the potential of Actinobacillus succinogenes for industrial succinate production
McKinlay, James B, Laivenieks, Maris, Schindler, Bryan D, McKinlay, Anastasia A, Siddaramappa, Shivakumara, Challacombe, Jean F, Lowry, Stephen R, Clum, Alicia, Lapidus, Alla L, Burkhart, Kirk B, Harkins, Victoria, Vieille, Claire
Published in BMC genomics (30.11.2010)
Published in BMC genomics (30.11.2010)
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The Complete Genome Sequence of Cupriavidus metallidurans Strain CH34, a Master Survivalist in Harsh and Anthropogenic Environments
Janssen, Paul J., Van Houdt, Rob, Moors, Hugo, Monsieurs, Pieter, Morin, Nicolas, Michaux, Arlette, Benotmane, Mohammed A., Leys, Natalie, Vallaeys, Tatiana, Lapidus, Alla, Monchy, Sébastien, Médigue, Claudine, Taghavi, Safiyh, McCorkle, Sean, Dunn, John, van der Lelie, Daniël, Mergeay, Max
Published in PloS one (05.05.2010)
Published in PloS one (05.05.2010)
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