Search Results - "Genome research"

Maftools: efficient and comprehensive analysis of somatic variants in cancer by Mayakonda, Anand, Lin, De-Chen, Assenov, Yassen, Plass, Christoph, Koeffler, H Phillip

“…Numerous large-scale genomic studies of matched tumor-normal samples have established the somatic landscapes of most cancer types. However, the downstream…”
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The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity by Zhou, Zhemin, Alikhan, Nabil-Fareed, Mohamed, Khaled, Fan, Yulei, Achtman, Mark

“…EnteroBase is an integrated software environment that supports the identification of global population structures within several bacterial genera that include…”
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Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation by Koren, Sergey, Walenz, Brian P, Berlin, Konstantin, Miller, Jason R, Bergman, Nicholas H, Phillippy, Adam M

“…Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. However,…”
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metaSPAdes: a new versatile metagenomic assembler by Nurk, Sergey, Meleshko, Dmitry, Korobeynikov, Anton, Pevzner, Pavel A

“…While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus…”
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Fast and accurate de novo genome assembly from long uncorrected reads by Vaser, Robert, Sović, Ivan, Nagarajan, Niranjan, Šikić, Mile

“…The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies typically requires resource-intensive error-correction and…”
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HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads by Nurk, Sergey, Walenz, Brian P, Rhie, Arang, Vollger, Mitchell R, Logsdon, Glennis A, Grothe, Robert, Miga, Karen H, Eichler, Evan E, Phillippy, Adam M, Koren, Sergey

“…Complete and accurate genome assemblies form the basis of most downstream genomic analyses and are of critical importance. Recent genome assembly projects have…”
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Benchmark and integration of resources for the estimation of human transcription factor activities by Garcia-Alonso, Luz, Holland, Christian H, Ibrahim, Mahmoud M, Turei, Denes, Saez-Rodriguez, Julio

“…The prediction of transcription factor (TF) activities from the gene expression of their targets (i.e., TF regulon) is becoming a widely used approach to…”
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GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens by Zhou, Zhemin, Alikhan, Nabil-Fareed, Sergeant, Martin J, Luhmann, Nina, Vaz, Cátia, Francisco, Alexandre P, Carriço, João André, Achtman, Mark

“…Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of…”
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UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy by Smith, Tom, Heger, Andreas, Sudbery, Ian

“…Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes that are increasingly used in high-throughput sequencing experiments. Through a UMI,…”
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CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes by Parks, Donovan H, Imelfort, Michael, Skennerton, Connor T, Hugenholtz, Philip, Tyson, Gene W

“…Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial…”
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Accurate and efficient detection of gene fusions from RNA sequencing data by Uhrig, Sebastian, Ellermann, Julia, Walther, Tatjana, Burkhardt, Pauline, Fröhlich, Martina, Hutter, Barbara, Toprak, Umut H, Neumann, Olaf, Stenzinger, Albrecht, Scholl, Claudia, Fröhling, Stefan, Brors, Benedikt

“…The identification of gene fusions from RNA sequencing data is a routine task in cancer research and precision oncology. However, despite the availability of…”
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Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid by Miller, Steve, Naccache, Samia N, Samayoa, Erik, Messacar, Kevin, Arevalo, Shaun, Federman, Scot, Stryke, Doug, Pham, Elizabeth, Fung, Becky, Bolosky, William J, Ingebrigtsen, Danielle, Lorizio, Walter, Paff, Sandra M, Leake, John A, Pesano, Rick, DeBiasi, Roberta, Dominguez, Samuel, Chiu, Charles Y

“…Metagenomic next-generation sequencing (mNGS) for pan-pathogen detection has been successfully tested in proof-of-concept case studies in patients with acute…”
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Centrifuge: rapid and sensitive classification of metagenomic sequences by Kim, Daehwan, Song, Li, Breitwieser, Florian P, Salzberg, Steven L

“…Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species on desktop…”
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Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly by Schneider, Valerie A, Graves-Lindsay, Tina, Howe, Kerstin, Bouk, Nathan, Chen, Hsiu-Chuan, Kitts, Paul A, Murphy, Terence D, Pruitt, Kim D, Thibaud-Nissen, Françoise, Albracht, Derek, Fulton, Robert S, Kremitzki, Milinn, Magrini, Vincent, Markovic, Chris, McGrath, Sean, Steinberg, Karyn Meltz, Auger, Kate, Chow, William, Collins, Joanna, Harden, Glenn, Hubbard, Timothy, Pelan, Sarah, Simpson, Jared T, Threadgold, Glen, Torrance, James, Wood, Jonathan M, Clarke, Laura, Koren, Sergey, Boitano, Matthew, Peluso, Paul, Li, Heng, Chin, Chen-Shan, Phillippy, Adam M, Durbin, Richard, Wilson, Richard K, Flicek, Paul, Eichler, Evan E, Church, Deanna M

“…The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing…”
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Diverse alternative back-splicing and alternative splicing landscape of circular RNAs by Zhang, Xiao-Ou, Dong, Rui, Zhang, Yang, Zhang, Jia-Lin, Luo, Zheng, Zhang, Jun, Chen, Ling-Ling, Yang, Li

“…Circular RNAs (circRNAs) derived from back-spliced exons have been widely identified as being co-expressed with their linear counterparts. A single gene locus…”
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Accurate and complete genomes from metagenomes by Chen, Lin-Xing, Anantharaman, Karthik, Shaiber, Alon, Eren, A Murat, Banfield, Jillian F

“…Genomes are an integral component of the biological information about an organism; thus, the more complete the genome, the more informative it is…”
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Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA by Vaisvila, Romualdas, Ponnaluri, V.K. Chaithanya, Sun, Zhiyi, Langhorst, Bradley W., Saleh, Lana, Guan, Shengxi, Dai, Nan, Campbell, Matthew A., Sexton, Brittany S., Marks, Katherine, Samaranayake, Mala, Samuelson, James C., Church, Heidi E., Tamanaha, Esta, Corrêa, Ivan R., Pradhan, Sriharsa, Dimalanta, Eileen T., Evans, Thomas C., Williams, Louise, Davis, Theodore B.

“…Bisulfite sequencing detects 5mC and 5hmC at single-base resolution. However, bisulfite treatment damages DNA, which results in fragmentation, DNA loss, and…”
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Direct determination of diploid genome sequences by Weisenfeld, Neil I, Kumar, Vijay, Shah, Preyas, Church, Deanna M, Jaffe, David B

“…Determining the genome sequence of an organism is challenging, yet fundamental to understanding its biology. Over the past decade, thousands of human genomes…”
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Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks by Kelley, David R, Snoek, Jasper, Rinn, John L

“…The complex language of eukaryotic gene expression remains incompletely understood. Despite the importance suggested by many noncoding variants statistically…”
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Microbial strain-level population structure and genetic diversity from metagenomes by Truong, Duy Tin, Tett, Adrian, Pasolli, Edoardo, Huttenhower, Curtis, Segata, Nicola

“…Among the human health conditions linked to microbial communities, phenotypes are often associated with only a subset of strains within causal microbial…”
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