Search Results - "Syed, Mustafa H."

CAZymes Analysis Toolkit (CAT): Web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database by Park, Byung H, Karpinets, Tatiana V, Syed, Mustafa H, Leuze, Michael R, Uberbacher, Edward C

“…The Carbohydrate-Active Enzyme (CAZy) database provides a rich set of manually annotated enzymes that degrade, modify, or create glycosidic bonds. Despite rich…”
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Applications of Machine Learning in miRNA Discovery and Target Prediction by Parveen, Alisha, Mustafa, Syed H., Yadav, Pankaj, Kumar, Abhishek

“…MicroRNA (miRNA) is a small non-coding molecule that is involved in gene regulation and RNA silencing by complementary on their targets. Experimental methods…”
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Industrial robustness: understanding the mechanism of tolerance for the Populus hydrolysate-tolerant mutant strain of Clostridium thermocellum by Linville, Jessica L, Rodriguez, Jr, Miguel, Land, Miriam, Syed, Mustafa H, Engle, Nancy L, Tschaplinski, Timothy J, Mielenz, Jonathan R, Cox, Chris D

“…An industrially robust microorganism that can efficiently degrade and convert lignocellulosic biomass into ethanol and next-generation fuels is required to…”
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Metabolic environments and genomic features associated with pathogenic and mutualistic interactions between bacteria and plants by Karpinets, Tatiana V, Park, Byung H, Syed, Mustafa H, Klotz, Martin G, Uberbacher, Edward C

“…Genomic characteristics discriminating parasitic and mutualistic relationship of bacterial symbionts with plants are poorly understood. This study…”
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KBase: The United States Department of Energy Systems Biology Knowledgebase by Arkin, Adam P, Cottingham, Robert W, Henry, Christopher S, Harris, Nomi L, Stevens, Rick L, Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W, Henderson, Matthew L, Riehl, William J, Murphy-Olson, Dan, Chan, Stephen Y, Kamimura, Roy T, Kumari, Sunita, Drake, Meghan M, Brettin, Thomas S, Glass, Elizabeth M, Chivian, Dylan, Gunter, Dan, Weston, David J, Allen, Benjamin H, Baumohl, Jason, Best, Aaron A, Bowen, Ben, Brenner, Steven E, Bun, Christopher C, Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J, Davison, Brian H, DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N, Fang, Gang, Faria, José P, Frybarger, Paul M, Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L, He, Fei, Jain, Rashmi, Joachimiak, Marcin P, Keegan, Kevin P, Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L, Meyer, Folker, Mills, Marissa, Novichkov, Pavel S, Oh, Taeyun, Olsen, Gary J, Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S, Price, Gavin A, Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C, Schatz, Michael C, Seaver, Samuel M D, Shukla, Maulik, Sutormin, Roman A, Syed, Mustafa H, Thomason, James, Tintle, Nathan L, Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, Yu, Dantong

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LacI Transcriptional Regulatory Networks in Clostridium thermocellum DSM1313 by Wilson, Charlotte M, Klingeman, Dawn M, Schlachter, Caleb, Syed, Mustafa H, Wu, Chia-Wei, Guss, Adam M, Brown, Steven D

“…Organisms regulate gene expression in response to the environment to coordinate metabolic reactions. expresses enzymes for both lignocellulose solubilization…”
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Erratum: Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients by Zehir, Ahmet, Benayed, Ryma, Shah, Ronak H, Syed, Aijazuddin, Middha, Sumit, Kim, Hyunjae R, Srinivasan, Preethi, Gao, Jianjiong, Chakravarty, Debyani, Devlin, Sean M, Hellmann, Matthew D, Barron, David A, Schram, Alison M, Hameed, Meera, Dogan, Snjezana, Ross, Dara S, Hechtman, Jaclyn F, DeLair, Deborah F, Yao, JinJuan, Mandelker, Diana L, Cheng, Donavan T, Chandramohan, Raghu, Mohanty, Abhinita S, Ptashkin, Ryan N, Jayakumaran, Gowtham, Prasad, Meera, Syed, Mustafa H, Rema, Anoop Balakrishnan, Liu, Zhen Y, Nafa, Khedoudja, Borsu, Laetitia, Sadowska, Justyna, Casanova, Jacklyn, Bacares, Ruben, Kiecka, Iwona J, Razumova, Anna, Son, Julie B, Stewart, Lisa, Baldi, Tessara, Mullaney, Kerry A, Al-Ahmadie, Hikmat, Vakiani, Efsevia, Abeshouse, Adam A, Penson, Alexander V, Jonsson, Philip, Camacho, Niedzica, Chang, Matthew T, Won, Helen H, Gross, Benjamin E, Kundra, Ritika, Heins, Zachary J, Chen, Hsiao-Wei, Phillips, Sarah, Zhang, Hongxin, Wang, Jiaojiao, Ochoa, Angelica, Wills, Jonathan, Eubank, Michael, Thomas, Stacy B, Gardos, Stuart M, Reales, Dalicia N, Galle, Jesse, Durany, Robert, Cambria, Roy, Abida, Wassim, Cercek, Andrea, Feldman, Darren R, Gounder, Mrinal M, Hakimi, A Ari, Harding, James J, Iyer, Gopa, Janjigian, Yelena Y, Jordan, Emmet J, Kelly, Ciara M, Lowery, Maeve A, Morris, Luc G T, Omuro, Antonio M, Raj, Nitya, Razavi, Pedram, Shoushtari, Alexander N, Shukla, Neerav, Soumerai, Tara E, Varghese, Anna M, Yaeger, Rona, Coleman, Jonathan, Bochner, Bernard, Riely, Gregory J, Saltz, Leonard B, Scher, Howard I, Sabbatini, Paul J, Robson, Mark E, Klimstra, David S, Taylor, Barry S, Baselga, Jose, Schultz, Nikolaus, Hyman, David M, Arcila, Maria E, Solit, David B, Ladanyi, Marc, Berger, Michael F

“…Nat. Med. 23, 703–713 (2017); published online 08 May 2017; corrected after print 14 June 2017 In the version of this article initially published online, the…”
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Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA by Leuze, Michael R., Karpinets, Tatiana V., Syed, Mustafa H., Beliaev, Alexander S., Uberbacher, Edward C.

“…Bacterial gene regulation involves transcription factors (TF) that bind to DNA recognition sequences in operon promoters. These recognition sequences, many of…”
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Baseline VDJ clonotype detection using a targeted sequencing NGS assay: allowing for subsequent MRD assessment by Hultcrantz, Malin, Rustad, Even Holth, Yellapantula, Venkata, Arcila, Maria, Ho, Caleb, Syed, Mustafa H., Papaemmanuil, Elli, Zhang, Yanming, Maura, Francesco, Landgren, Ola

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Clonally-Related CD5+ CLL/SLL and CD10+ high grade B-cell lymphoma suggests common neoplastic progenitor with branched disease evolution, with therapeutic implications by Kumar, Priyadarshini, Uppal, Manik, Xiao, Wenbin, Dogan, Ahmet, Roshal, Mikhail, Gao, Qi, Aypar, Umut, Zhang, Yanming, Arcila, Maria E., Moung, Christine, Yao, Jinjuan, Nafa, Khedoudja, Yu, Wayne, Syed, Mustafa H., Park, Jae, Kumar, Anita, Ho, Caleb

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Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions by Karpinets, Tatiana V, Romine, Margaret F, Schmoyer, Denise D, Kora, Guruprasad H, Syed, Mustafa H, Leuze, Michael R, Serres, Margrethe H, Park, Byung H, Samatova, Nagiza F, Uberbacher, Edward C

“…Shewanellae are facultative gamma-proteobacteria whose remarkable respiratory versatility has resulted in interest in their utility for bioremediation of heavy…”
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PUMA2—grid-based high-throughput analysis of genomes and metabolic pathways by Maltsev, Natalia, Glass, Elizabeth, Sulakhe, Dinanath, Rodriguez, Alexis, Syed, Mustafa H., Bompada, Tanuja, Zhang, Yi, D'Souza, Mark

“…The PUMA2 system (available at http://compbio.mcs.anl.gov/puma2) is an interactive, integrated bioinformatics environment for high-throughput genetic sequence…”
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BESC knowledgebase public portal by SYED, Mustafa H, KARPINETS, Tatiana V, PARANG, Morey, LEUZE, Michael R, PARK, Byung H, HYATT, Doug, BROWN, Steven D, MOULTON, Steve, GALLOWAY, Michael D, UBERBACHER, Edward C

“…The BioEnergy Science Center (BESC) is undertaking large experimental campaigns to understand the biosynthesis and biodegradation of biomass and to develop…”
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Sentra: a database of signal transduction proteins for comparative genome analysis by D'Souza, Mark, Glass, Elizabeth M, Syed, Mustafa H, Zhang, Yi, Rodriguez, Alexis, Maltsev, Natalia, Galperin, Michael Y

“…Sentra (http://compbio.mcs.anl.gov/sentra), a database of signal transduction proteins encoded in completely sequenced prokaryotic genomes, has been updated to…”
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Sentra: a database of signal transduction proteins for comparative genome analysis by D'Souza, Mark, Glass, Elizabeth M, Syed, Mustafa H, Zhang, Yi, Rodriguez, Alexis, Maltsev, Natalia, Galperin, Michael Y

“…Sentra (http://compbio.mcs.anl.gov/sentra), a database of signal transduction proteins encoded in completely sequenced prokaryotic genomes, has been updated to…”
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Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass by Wilson, Charlotte M, Rodriguez, Miguel Jr, Johnson, Courtney M, Martin, Stanton L, Chu, Tzu Ming, Wolfinger, Russ D, Hauser, Loren J, Land, Miriam L, Klingeman, Dawn M, Syed, Mustafa H, Ragauskas, Arthur J, Tschaplinski, Timothy J, Mielenz, Jonathan R, Brown, Steven D

“…BACKGROUND: The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production…”
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Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients by Zehir, Ahmet, Benayed, Ryma, Shah, Ronak H, Syed, Aijazuddin, Middha, Sumit, Kim, Hyunjae R, Srinivasan, Preethi, Gao, Jianjiong, Chakravarty, Debyani, Devlin, Sean M, Hellmann, Matthew D, Barron, David A, Schram, Alison M, Hameed, Meera, Dogan, Snjezana, Ross, Dara S, Hechtman, Jaclyn F, DeLair, Deborah F, Yao, JinJuan, Mandelker, Diana L, Cheng, Donavan T, Chandramohan, Raghu, Mohanty, Abhinita S, Ptashkin, Ryan N, Jayakumaran, Gowtham, Prasad, Meera, Syed, Mustafa H, Rema, Anoop Balakrishnan, Liu, Zhen Y, Nafa, Khedoudja, Borsu, Laetitia, Sadowska, Justyna, Casanova, Jacklyn, Bacares, Ruben, Kiecka, Iwona J, Razumova, Anna, Son, Julie B, Stewart, Lisa, Baldi, Tessara, Mullaney, Kerry A, Al-Ahmadie, Hikmat, Vakiani, Efsevia, Abeshouse, Adam A, Penson, Alexander V, Jonsson, Philip, Camacho, Niedzica, Chang, Matthew T, Won, Helen H, Gross, Benjamin E, Kundra, Ritika, Heins, Zachary J, Chen, Hsiao-Wei, Phillips, Sarah, Zhang, Hongxin, Wang, Jiaojiao, Ochoa, Angelica, Wills, Jonathan, Eubank, Michael, Thomas, Stacy B, Gardos, Stuart M, Reales, Dalicia N, Galle, Jesse, Durany, Robert, Cambria, Roy, Abida, Wassim, Cercek, Andrea, Feldman, Darren R, Gounder, Mrinal M, Hakimi, A Ari, Harding, James J, Iyer, Gopa, Janjigian, Yelena Y, Jordan, Emmet J, Kelly, Ciara M, Lowery, Maeve A, Morris, Luc G T, Omuro, Antonio M, Raj, Nitya, Razavi, Pedram, Shoushtari, Alexander N, Shukla, Neerav, Soumerai, Tara E, Varghese, Anna M, Yaeger, Rona, Coleman, Jonathan, Bochner, Bernard, Riely, Gregory J, Saltz, Leonard B, Scher, Howard I, Sabbatini, Paul J, Robson, Mark E, Klimstra, David S, Taylor, Barry S, Baselga, Jose, Schultz, Nikolaus, Hyman, David M, Arcila, Maria E, Solit, David B, Ladanyi, Marc, Berger, Michael F

“…MSK-IMPACT is a clinical sequencing platform able to detect genomic mutations, copy number alterations and structural variants in a panel of cancer-related…”
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Shewregdb: database and visualization environment for experimental and predicted regulatory information in Shewanella oneidensis mr-1 by Syed, Mustafa H, Karpinets, Tatiana V, Leuze, Michael R, Kora, Guruprasad H, Romine, Margaret R, Uberbacher, Edward C

“…Shewanella oneidensis MR-1 is an important model organism for environmental research as it has an exceptional metabolic and respiratory versatility regulated…”
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The BioPAX community standard for pathway by Syed, Mustafa H

“…Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange…”
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Clinical utility of clonality testing by next generation sequencing in the monitoring of B-cell and T-cell malignancies by Syed, Mustafa H., Ho, Caleb, Petrova-Drus, Kseniya, Yao, JinJuan, Yu, Wayne, Zehir, Ahmet, Nafa, Khedoudja, Arcila, Maria E.

“…Abstract only 72 Background: Clonality testing is an integral part of the initial assessment of B and T cell malignancies. The further use of conventional…”
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