Results 31 to 40 of about 1,004,545 (280)
Long-read single-molecule maps of the functional methylome [PDF]
Genome Research, 2019 We report on the development of a methylation analysis workflow for optical detection of fluorescent methylation profiles along chromosomal DNA molecules. In combination with Bionano Genomics genome mapping technology, these profiles provide a hybrid genetic/epigenetic genome-wide map composed of DNA molecules spanning hundreds of kilobase pairs.Hila Sharim, Assaf Grunwald, Tslil Gabrieli, Yael Michaeli, Sapir Margalit, Dmitry Torchinsky, Rani Arielly, Gil Nifker, Matyas Juhasz, Felix Gularek, Miguel Almalvez, Brandon Dufault, Sreetama Sen Chandra, Alexander Liu, Surajit Bhattacharya, Yi-Wen Chen, Eric Vilain, Kathryn R. Wagner, Jonathan Pevsner, Jeff Reifenberger, Ernest T. Lam, Alex R. Hastie, Han Cao, Hayk Barseghyan, Elmar Weinhold, Yuval Ebenstein +25 moreopenaire +5 more sourcesChromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding [PDF]
, 2016 We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish ...A Bairoch, A Christoffels, A Gurevich, A Kozomara, A McKenna, A Mitchell, A Morgulis, A Morgulis, A Pradhan, A Reiner, A Rodriguez-Mari, A Stamatakis, A Yates, AI Makunin, AJ Enright, AL Price, AL Price, Alan Christoffels, Aleksey Komissarov, Alexey Tupikin, Amy Hin Yan Tong, Andrey A. Yurchenko, AR Quinlan, B Langmead, B Star, C Berthelot, C Camacho, C Holt, C Wang, Chen-Shan Chin, CS Chin, D Brawand, D Ellinghaus, DA Benson, Darrell Green, DC Hardie, Dean R. Jerry, DH Alexander, Doreen Lau, DR Kelley, DRS-K, C. Jerry, E Casacuberta, E. TG Staristina, EW Myers, F Abascal, F Chen, F Yang, FC Jones, FJ Krsticevic, Fritz J. Sedlazeck, G Abrusan, G Benson, G Lin, G Marcais, G Parra, G Parra, G Tamazian, GH Yue, GH Yue, Gopikrishna Gopalapillai, Gregory W. Vurture, GS Slater, GT Valente, H Li, H Saiga, Heiner Kuhl, HH Kazazian Jr., I Braasch, Inna S. Kuznetsova, IS Kuznetsova, J Castresana, J Eid, J Huerta-Cepas, J Jurka, J Lin, James P. Drake, JG Ruby, JN Volff, JN Volff, Jolly M. Saju, Jonas Korlach, JS Chew, Junhui Jiang, K Howe, K Katoh, K Prufer, Kathiresan Purushothaman, KD Pruitt, KJ Hoff, KP Koepfli, KW Tzung, Lawrence S. Hon, László Orbán, M Blanchette, M Kanehisa, M Kasahara, M Kolmogorov, M Krzywinski, M Martin, M Schartl, M Tarailoâ-Graovac, M Tine, MA Larkin, Mario Jonas, Marsel Kabilov, Matthew Boitano, MB Stocks, MG Grabherr, Michael C. Schatz, MJ Chaisson, MR Friedlander, N Siegel, Natascha M. Thevasagayam, NM Thevasagayam, O Jaillon, O Otero, P Cingolani, P Ravi, P Schattner, P Shannon, P Xu, Paul M. Richardson, PE Warburton, Peter Van Heusden, R Kajitani, R Lorenz, R Luo, R Moore, R Pethiyagoda, R Poulter, R She, R Sreenivasan, Ramkumar Lachumanan, RD Ward, RD Ward, Richard Hall, RJ Roberts, S Chen, S Guindon, S Hoegg, S Hoegg, S Koren, S Vij, S Zhou, Sai Rama Sridatta Prakki, Sarah Mwangi, SF Altschul, Shubha Vij, Si Lok, Si Yan Ngoh, Siddharth Singh, Simon Moxon, SM Kielbasa, Sridhar Sivasubbu, Stanley Kimbung Mbandi, Stephen J. O'Brien, Stephen W. Turner, T Anantharaman, Tamás Dalmay, Tansyn H. Noble, TD Wu, TF DeLuca, TH O'Hare, TLO Davis, TS Anantharaman, Tyler Garvin, U Consortium, U Grimholt, V Douard, V Ravi, Vinaya Kumar Katneni, Vinod Scaria, Vladimir Trifonov, W Xue, WC Liew, Woei Chang Liew, WS Davidson, X Huang, X Zheng, XG Wang, XG Wang, Xueyan Shen, Y Guiguen, Y Han, Y Hashiguchi, Y Moriya, Y Sato, Y Sato, Y Sato, Z Lai, Ø Hammer +190 morecore +5 more sourcesJabba: hybrid error correction for long sequencing reads [PDF]
, 2016 Background: Third generation sequencing platforms produce longer reads with higher error rates than second generation technologies. While the improved read length can provide useful information for downstream analysis, underlying algorithms are ...Audenaert, P., Demeester, Piet, Fostier, Jan, Heydari, Mahdi, Miclotte, Giles, Rombauts, Stephane, Van de Peer, Yves +6 morecore +3 more sourcesSOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner [PDF]
, 2013 To tackle the exponentially increasing throughput of Next-Generation
Sequencing (NGS), most of the existing short-read aligners can be configured to
favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging
the computational power of Chang Yu, Chi-Man Liu, David W Cheung, Edward Wu, Haoxiang Lin, Hing-Fung Ting, Jianqiao Zhu, Lap-Kei Lee, Ruibang Luo, Ruiqiang Li, Shaoliang Peng, Siu-Ming Yiu, Tak-Wah Lam, Thomas Wong, Wenjuan Zhu, Xiaoqian Zhu, Yingrui Li +16 morecore +8 more sourcesStructural variant calling: the long and the short of it
Genome Biology, 2019 Recent research into structural variants (SVs) has established their importance to medicine and molecular biology, elucidating their role in various diseases, regulation of gene expression, ethnic diversity, and large-scale chromosome evolution—giving ...Medhat Mahmoud, Nastassia Gobet, Diana Ivette Cruz-Dávalos, Ninon Mounier, Christophe Dessimoz, Fritz J. Sedlazeck +5 moredoaj +1 more sourceS-conLSH: alignment-free gapped mapping of noisy long reads [PDF]
BMC Bioinformatics, 2019 Abstract Background The advancement of SMRT technology has unfolded new opportunities of genome analysis with its longer read length and low GC bias. Alignment of the reads to their appropriate positions in the respective reference genome is the first but costliest step of any analysis pipeline Chakraborty, Angana, Morgenstern, Burkhard, Bandyopadhyay, Sanghamitra, Chakraborty, Angana; Department of Computer Science, West Bengal Education Service, Kolkata, India, Morgenstern, Burkhard; Department of Bioinformatics (IMG), University of Göttingen, Göttingen, Germany, Bandyopadhyay, Sanghamitra; Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India +5 moreopenaire +5 more sourcesA whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome [PDF]
, 2015 Citation: Chapman, J. A., Mascher, M., Buluç, A., Barry, K., Georganas, E., Session, A., . . . Rokhsar, D. S. (2015). A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biology, 16(1). doi:10.1186/s13059-A Graner, A Kovach, A Zimin, Adam Session, AR Hastie, AR Quinlan, Aydın Buluç, B Nystedt, C Alkan, C Feuillet, C Feuillet, C Saintenac, CR Cavanagh, CW Nossa, D Arend, Daniel S Rokhsar, E Paux, EK Khlestkina, EP Wilhelm, Evangelos Georganas, EW Myers, F Choulet, G Zhang, Gary J Muehlbauer, H Li, H Li, HQ Ling, I Birol, International Barley Genome Sequencing Consortium, International Rice Genome Sequencing P, International Wheat Genome Sequencing Consortium, J Dolezel, J Jia, J Jurka, J Oeveren van, JA Chapman, JA Poland, Jarrod A Chapman, JC Venter, Jeremy Schmutz, Jerry Jenkins, Jesse A Poland, JJ Smith, JL Weber, K Arumuganathan, K Devos, K Mochida, Katherine A Yelick, KD Pruitt, Kerrie Barry, KR Bradnam, KS Caldwell, L Ramsay, Leonid Oliker, LG Neves, LJ Williams, M Mascher, M Mascher, M Mascher, M Mascher, M Muñoz-Amatriaín, M-C Luo, Martin Mascher, ME Sorrells, MJ Truco, MW Hahn, N Poursarebani, Nils Stein, P Green, PS Schnable, R Brenchley, R Flavell, Robbie Waugh, SF Altschul, SF Altschul, Sunish Sehgal, T Belova, The Mouse Genome Sequencing Consortium, Uwe Scholz, Veronika Strnadova, X Wang, X Xu, Y Wu, Z Zhang +83 morecore +5 more sourcesSequencing and de novo assembly of 150 genomes from Denmark as a population reference [PDF]
, 2017 Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits.A Helgason, A Kong, A Telenti, AD Børglum, Ali Syed, Anders D. Børglum, Anders E. Halager, Anders Krogh, Bent Petersen, BJ Stucky, Chen Ye, Christian N. S. Pedersen, Christian Theil Have, Christina M. Hultman, David Westergaard, DF Gudbjartsson, Esben Flindt, Francesco Lescai, G Lunter, GA Van der Auwera, GD Poznik, GM Cooper, H Cao, H Eiberg, H Kupfermann, H Li, H Li, H Li, Hans Eiberg, Hongzhi Cao, J Huddleston, Jacob Malte Jensen, Jakob Grove, Jette Bork-Jensen, Jihua Sun, Johan van Beusekom, Jonas Andreas Sibbesen, Jose M. G. Izarzugaza, JS Seo, JT Simpson, Jun Wang, Junhua Rao, K Katoh, K Tamura, Karsten Kristiansen, Kirstine Belling, KM Steinberg, L Paternoster, Lars Bolund, Lasse Maretty, Laurits Skov, LC Francioli, M Lek, M Nothnagel, M Oven, M Pendleton, MA Eberle, Maria Luisa Matey-Hernandez, Marie Grosjean, MC Frith, Mikkel Heide Schierup, MR Hoehe, Ning Li, Ole Lund, Ole Mors, Oluf Pedersen, P Rice, Palle Villesen, Patrick Sullivan, Peter Løngren, PH Sudmant, PL Auer, R Hubley, R Luo, Rachita Yadav, Ramneek Gupta, Ruiqi Xu, Rune M. Friborg, S Besenbacher, S Deorowicz, S Gnerre, S Liu, S Ripke, SF Altschul, Shengting Li, Shujia Huang, Simon Rasmussen, Siyang Liu, SM Kiełbasa, Stephanie Le Hellard, Søren Besenbacher, Søren Brunak, T Espeseth, T Magocˇ, Thomas D. Als, Thomas Espeseth, Thomas Mailund, Thomas Sicheritz-Pontén, Thorkild I. A. Sørensen, Torben Hansen, VA Schneider, Weijian Ye, WP Kloosterman, WS Wong, Xiaosen Guo, Xun Xu, Yuqi Chang +106 morecore +3 more sources
