Search Results - "Salamov, A A"

Comparative genomics of xylose-fermenting fungi for enhanced biofuel production by Wohlbach, Dana J, Kuo, Alan, Sato, Trey K, Potts, Katlyn M, Salamov, Asaf A, LaButti, Kurt M, Sun, Hui, Clum, Alicia, Pangilinan, Jasmyn L, Lindquist, Erika A, Lucas, Susan, Lapidus, Alla, Jin, Mingjie, Gunawan, Christa, Balan, Venkatesh, Dale, Bruce E, Jeffries, Thomas W, Zinkel, Robert, Barry, Kerrie W, Grigoriev, Igor V, Gasch, Audrey P

“…Cellulosic biomass is an abundant and underused substrate for biofuel production. The inability of many microbes to metabolize the pentose sugars abundant…”
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Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi by Riley, Robert, Salamov, Asaf A., Brown, Daren W., Nagy, Laszlo G., Floudas, Dimitrios, Held, Benjamin W., Levasseur, Anthony, Lombard, Vincent, Morin, Emmanuelle, Otillar, Robert, Lindquist, Erika A., Sun, Hui, LaButti, Kurt M., Schmutz, Jeremy, Jabbour, Dina, Luoi, Hong, Baker, Scott E., Pisabarro, Antonio G., Walton, Jonathan D., Blanchette, Robert A., Henrissat, Bernard, Martin, Francis, Cullen, Dan, Hibbett, David S., Grigoriev, Igor V.

“…Basidiomycota (basidiomycetes) make up 32% of the described fungi and include most wood-decaying species, as well as pathogens and mutualistic symbionts…”
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Ab initio gene finding in Drosophila genomic DNA by Salamov, A A, Solovyev, V V

“…Ab initio gene identification in the genomic sequence of Drosophila melanogaster was obtained using (human gene predictor) and Fgenesh programs that have…”
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Comparative Metagenomics of Microbial Communities by Tringe, Susannah Green, von Mering, Christian, Kobayashi, Arthur, Salamov, Asaf A, Chen, Kevin, Chang, Hwai W, Podar, Mircea, Short, Jay M, Mathur, Eric J, Detter, John C, Bork, Peer, Hugenholtz, Philip, Rubin, Edward M

“…The species complexity of microbial communities and challenges in culturing representative isolates make it difficult to obtain assembled genomes. Here we…”
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Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits by Dort, E. N., Layne, E., Feau, N., Butyaev, A., Henrissat, B., Martin, F. M., Haridas, S., Salamov, A., Grigoriev, I. V., Blanchette, M., Hamelin, R. C.

“…Invasive plant pathogenic fungi have a global impact, with devastating economic and environmental effects on crops and forests. Biosurveillance, a critical…”
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The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi by Aguilar-Pontes, M.V., Brandl, J., McDonnell, E., Strasser, K., Nguyen, T.T.M., Riley, R., Mondo, S., Salamov, A., Nybo, J.L., Vesth, T.C., Grigoriev, I.V., Andersen, M.R., Tsang, A., de Vries, R.P.

“…The fungal kingdom is too large to be discovered exclusively by classical genetics. The access to omics data opens a new opportunity to study the diversity…”
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Identification of promoter regions and regulatory sites by Solovyev, Victor V, Shahmuradov, Ilham A, Salamov, Asaf A

“…Promoter sequences are the main regulatory elements of gene expression. Their recognition by computer algorithms is fundamental for understanding gene…”
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Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities by Hugenholtz, Philip, Martín, Héctor García, Ivanova, Natalia, Kunin, Victor, Warnecke, Falk, Barry, Kerrie W, McHardy, Alice C, Yeates, Christine, He, Shaomei, Salamov, Asaf A, Szeto, Ernest, Dalin, Eileen, Putnam, Nik H, Shapiro, Harris J, Pangilinan, Jasmyn L, Rigoutsos, Isidore, Kyrpides, Nikos C, Blackall, Linda Louise, McMahon, Katherine D

“…Enhanced biological phosphorus removal (EBPR) is one of the best-studied microbially mediated industrial processes because of its ecological and economic…”
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Physical and Mechanical Properties of Polybutylene Terephthalate Stabilized with Various Antioxidants by Borukaev, T. A., Lukyaeva, Z. M., Salamov, A. Kh

“…Polybutylene terephthalate samples stabilized with various chain antioxidants were obtained, and their basic physical–mechanical properties were studied. It…”
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A parts list for fungal cellulosomes revealed by comparative genomics by Haitjema, Charles H., Gilmore, Sean P., Henske, John K., Solomon, Kevin V., de Groot, Randall, Kuo, Alan, Mondo, Stephen J., Salamov, Asaf A., LaButti, Kurt, Zhao, Zhiying, Chiniquy, Jennifer, Barry, Kerrie, Brewer, Heather M., Purvine, Samuel O., Wright, Aaron T., Hainaut, Matthieu, Boxma, Brigitte, van Alen, Theo, Hackstein, Johannes H. P., Henrissat, Bernard, Baker, Scott E., Grigoriev, Igor V., O'Malley, Michelle A.

“…Cellulosomes are large, multiprotein complexes that tether plant biomass-degrading enzymes together for improved hydrolysis 1 . These complexes were first…”
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Comparative genomics of biotechnologically important yeasts by 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.

“…Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and…”
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Assessing protein coding region integrity in cDNA sequencing projects by Salamov, A.A, Nishikawa, T, Swindells, M.B

“…In cDNA sequencing projects, it is vital to know whether the protein coding region of a sequence is complete, or whether errors have occurred during library…”
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Sorghum bicolor genome and the diversification of grasses by Paterson, Andrew H, Bowers, John E, Bruggmann, Remy, Dubchak, Inna, Grimwood, Jane, Gundlach, Heidrun, Haberer, Georg, Hellsten, Uffe, Mitros, Therese, Poliakov, Alexander, Schmutz, Jeremy, Spannagl, Manuel, Tang, Haibao, Wang, Xiyin, Wicker, Thomas, Ware, Doreen

“…Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the 730-megabase Sorghum…”
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Genomic and proteomic biases inform metabolic engineering strategies for anaerobic fungi by Wilken, St. Elmo, Seppälä, Susanna, Lankiewicz, Thomas S., Saxena, Mohan, Henske, John K., Salamov, Asaf A., Grigoriev, Igor V., O’Malley, Michelle A.

“…Anaerobic fungi (Neocallimastigomycota) are emerging non-model hosts for biotechnology due to their wealth of biomass-degrading enzymes, yet tools to engineer…”
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Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis by Fernandez-Fueyo, Elena, Ruiz-Dueñas, Francisco J., Ferreira, Patricia, Floudas, Dimitrios, Hibbett, David S., Canessa, Paulo, Larrondo, Luis F., James, Tim Y., Seelenfreund, Daniela, Lobos, Sergio, Polanco, Rubén, Tello, Mario, Honda, Yoichi, Watanabe, Takahito, Watanabe, Takashi, San, Ryu Jae, Kubicek, Christian P., Schmoll, Monika, Gaskell, Jill, Hammel, Kenneth E., St. John, Franz J., Wymelenberg, Amber Vanden, Sabat, Grzegorz, BonDurant, Sandra Splinter, Syed, Khajamohiddin, Yadav, Jagjit S., Doddapaneni, Harshavardhan, Subramanian, Venkataramanan, Lavín, José L., Oguiza, José A., Perez, Gumer, Pisabarro, Antonio G., Ramirez, Lucia, Santoyo, Francisco, Master, Emma, Coutinho, Pedro M., Henrissat, Bernard, Lombard, Vincent, Magnuson, Jon Karl, Kües, Ursula, Hori, Chiaki, Igarashi, Kiyohiko, Samejima, Masahiro, Held, Benjamin W., Barry, Kerrie W., LaButti, Kurt M., Lapidus, Alla, Lindquist, Erika A., Lucas, Susan M., Riley, Robert, Salamov, Asaf A., Hoffmeister, Dirk, Schwenk, Daniel, Hadar, Yitzhak, Yarden, Oded, de Vries, Ronald P., Wiebenga, Ad, Stenlid, Jan, Eastwood, Daniel, Grigoriev, Igor V., Berka, Randy M., Blanchette, Robert A., Kersten, Phil, Martinez, Angel T., Vicuna, Rafael, Cullen, Dan

“…Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referred to as white rot fungi. Phanerochaete chrysosporium…”
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Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames by Solovyev, Victor V., Salamov, Asaf A., Lawrence, Charles B.

“…A new method which predicts internal exon sequences In human DNA has been developed. The method Is based on a splice site prediction algorithm that uses the…”
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Prediction of Protein Secondary Structure by Combining Nearest-neighbor Algorithms and Multiple Sequence Alignments by Salamov, Asaf A., Solovyev, Victor V.

“…Recently Yi & Lander used a neural network and nearest and nearest-neighbor method with a scoring system that combined a sequence-similarity matrix with the…”
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Comparative genomics of xylose-fermenting fungi for enhanced biofuel production by D. J.,Wohlbach, A.,Kuo, T. K.,Sato, K. M.,Potts, A. A.,Salamov, K. M.,LaButti, H.,Sun, A.,Clum, J. L.,Pangilinan, E. A.,Lindquist, S.,Lucas, A.,Lapidus, M.,Jin, C.,Gunawan, V.,Balan, B. E.,Dale, T. W.,Jeffries, R.,Zinkel, K. W.,Barry, I. V.,Grigoriev, A. P.,Gasch

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The Arabidopsis lyrata genome sequence and the basis of rapid genome size change by Hu, Tina T, Pattyn, Pedro, Bakker, Erica G, Cao, Jun, Cheng, Jan-Fang, Clark, Richard M, Fahlgren, Noah, Fawcett, Jeffrey A, Grimwood, Jane, Gundlach, Heidrun, Haberer, Georg, Hollister, Jesse D, Ossowski, Stephan, Ottilar, Robert P, Salamov, Asaf A, Schneeberger, Korbinian, Spannagl, Manuel, Wang, Xi, Yang, Liang, Nasrallah, Mikhail E, Bergelson, Joy, Carrington, James C, Gaut, Brandon S, Schmutz, Jeremy, Mayer, Klaus F X, Van de Peer, Yves, Grigoriev, Igor V, Nordborg, Magnus, Weigel, Detlef, Guo, Ya-Long

“…Detlef Weigel and colleagues report the genome sequence of Arabidopsis lyrata . In comparison with the much smaller genome of A. thaliana , from which A…”
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Protein secondary structure prediction using local alignments by Salamov, Asaf A, Solovyev, Victor V

“…The accuracy of secondary structure prediction methods has been improved significantly by the use of aligned protein sequences. The PHD method and the NNSSP…”
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