Topic 07 -- Abstracts with Biological Entities (English) - 75 Topics / Sub-Topic Model 37 - 15 Topics

cite ad title authors publish year publish time dataset abstract mentions covid pmcid pubmed id doi cord uid topic weight Similarity scispacy Similarity specter
1 Morfopoulou_2015 Bayesian mixture analysis for metagenomic community profiling Morfopoulou, Sofia; Plagnol, Vincent 2015 2015-09-15 COMM-USE N PMC4565032 26002885.0 10.1093/bioinformatics/btv317 z29xsj1o 0.808235 Chang_2011, Cheng_2013, Deng_2015, Lee_C_2017 Morfopoulou_2014, Baldwin_2014
2 Morfopoulou_2014 Bayesian mixture analysis for metagenomic community profiling. Sofia Morfopoulou; Vincent Plagnol 2014 2014-07-25 BioRxiv N 10.1101/007476 058r9486 0.791874 Chang_2011, Lee_C_2017 Morfopoulou_2015, Miller_2013, Baldwin_2014
3 Minot_2014 SIANN: Strain Identification by Alignment to Near Neighbors Samuel Minot; Stephen D Turner; Krista L Ternus; Dana R Kadavy 2014 2014-01-10 BioRxiv N 10.1101/001727 vho70jcx 0.751943 Chang_2011, Lee_C_2017, Deng_2015 Shifman_2019, Tausch_2018, ZHANG_2018, Morfopoulou_2014
4 Gardner_2005 Draft versus finished sequence data for DNA and protein diagnostic signature development Gardner, Shea N.; Lam, Marisa W.; Smith, Jason R.; Torres, Clinton L.; Slezak, Tom R. 2005 2005-10-20 PMC N PMC1266063 16243783.0 10.1093/nar/gki896 t40ybhgb 0.674635 Chang_2011, Deng_2015, Cheng_2013, Lee_C_2017 Gardner_2004, Wang_2010, Viehweger_2019
5 Shcherbina_2016 Evaluating performance of metagenomic characterization algorithms using in silico datasets generated with FASTQSim Anna Shcherbina; Darrell O. Ricke; Nelson Chiu 2016 2016-03-31 BioRxiv N 10.1101/046532 csokkcqq 0.663328 Cheng_2013, Lee_C_2017, O'Leary_2016 Baldwin_2014, Twin_2013, Zinter_2018
6 Deng_2015 An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data Deng, Xutao; Naccache, Samia N.; Ng, Terry; Federman, Scot; Li, Linlin; Chiu, Charles Y.; Delwart, Eric L. 2015 2015-04-20 COMM-USE N PMC4402509 25586223.0 10.1093/nar/gkv002 gr108zuo 0.625216 Cheng_2013, Chang_2011, Whiteford_2005, Lee_C_2017 Wang_2010, Lin_Y_2017, Wang_2013, Viehweger_2019
7 Chen_2019 A binning tool to reconstruct viral haplotypes from assembled contigs Jiao Chen; Jiayu Shang; Jianrong Wang; Yanni Sun 2019 2019-07-16 BioRxiv N 10.1101/704288 2basllfv 0.605222 Chang_2011, Deng_2015, Lee_C_2017, Harel_2019 Chen_2019, Dacheux_2014
8 Chen_2019 A binning tool to reconstruct viral haplotypes from assembled contigs Chen, Jiao; Shang, Jiayu; Wang, Jianrong; Sun, Yanni 2019 2019-11-04 COMM-USE N PMC6829986 31684876.0 10.1186/s12859-019-3138-1 6tss9ydx 0.604478 Chang_2011, Deng_2015, Lee_C_2017, Chen_2019, Cheng_2013 Chen_2019, Wang_2010
9 Ludwig_2019 ZODIAC: database-independent molecular formula annotation using Gibbs sampling reveals unknown small molecules Marcus Ludwig; Louis-Félix Nothias; Kai Dührkop; Irina Koester; Markus Fleischauer; Martin A. Hoffmann; Daniel Petras; Fernando Vargas; Mustafa Morsy; Lihini Aluwihare; Pieter C. Dorrestein; Sebastian Böcker 2019 2019-11-16 BioRxiv N 10.1101/842740 03uonbrv 0.586841 Deng_2015, Chang_2011
10 Shang_2020 CHEER: hierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning Jiayu Shang; Yanni Sun 2020 2020-03-27 BioRxiv N 10.1101/2020.03.26.009001 pd0cmefo 0.572328 Chang_2011, Lee_C_2017, Cheng_2013 Zhang_2017
11 Castro_2019 The effect of variant interference on de novo assembly for viral deep sequencing Christina J. Castro; Rachel L. Marine; Edward Ramos; Terry Fei Fan Ng 2019 2019-10-22 BioRxiv N 10.1101/815480 d5ghy39g 0.572212 Deng_2015, Whiteford_2005, Harel_2019
12 Mordecai_2015 Diversity in a honey bee pathogen: first report of a third master variant of the Deformed Wing Virus quasispecies Mordecai, Gideon J; Wilfert, Lena; Martin, Stephen J; Jones, Ian M; Schroeder, Declan C 2015 2015-11-17 NONCOMM N PMC5029213 26574686.0 10.1038/ismej.2015.178 k2n6ropo 0.570782 Grewelle_2020
13 Warren_2007 Assembling millions of short DNA sequences using SSAKE Warren, René L.; Sutton, Granger G.; Jones, Steven J. M.; Holt, Robert A. 2007 2007-02-15 NONCOMM N PMC7109930 17158514.0 10.1093/bioinformatics/btl629 ojy6s49w 0.559605 Deng_2015, Whiteford_2005, Cheng_2013, Chang_2011 Viehweger_2019, Viehweger_2018, Harel_2019
14 Lin_Y_2017 De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline Lin, You-Yu; Hsieh, Chia-Hung; Chen, Jiun-Hong; Lu, Xuemei; Kao, Jia-Horng; Chen, Pei-Jer; Chen, Ding-Shinn; Wang, Hurng-Yi 2017 2017-04-26 COMM-USE N PMC5406902 28446139.0 10.1186/s12859-017-1630-z rbwgi0ql 0.545049 Cheng_2013, Deng_2015, Chang_2011, Lee_C_2017, Whiteford_2005 Wang_2013, Deng_2015, Shepard_2016
15 Routh_2013 Discovery of functional genomic motifs in viruses with ViReMa–a Virus Recombination Mapper–for analysis of next-generation sequencing data Routh, Andrew; Johnson, John E. 2013 2013-10-09 COMM-USE N PMC3902915 24137010.0 10.1093/nar/gkt916 55ge7kmr 0.512639 Whiteford_2005, Chang_2011, Deng_2015, Warren_2007 Routh_2012
16 Slezak_2020 Chapter 20 Design of genomic signatures for pathogen identification and characterization Slezak, Tom; Hart, Bradley; Jaing, Crystal 2020 2020-12-31 PMC N PMC7153316 10.1016/b978-0-12-815379-6.00020-9 cydvmm4r 0.468355 Chang_2011, Francis_2016, Brister_2015, Priest_2012 Slezak_2011
17 Chen-Harris_2013 Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs Chen-Harris, Haiyin; Borucki, Monica K; Torres, Clinton; Slezak, Tom R; Allen, Jonathan E 2013 2013-02-12 COMM-USE N PMC3599684 23402258.0 10.1186/1471-2164-14-96 604gho1u 0.453349 Harel_2019, Chang_2011, Deng_2015, Whiteford_2005, Schlub_2018 Harel_2019, Lewandowska_2017, Lu_I_2020, Isakov_2015
18 Harel_2019 Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations Harel, Noam; Meir, Moran; Gophna, Uri; Stern, Adi 2019 2019-12-16 PMC N PMC7107797 31665473.0 10.1093/nar/gkz907 rloey02j 0.446006 Deng_2015, Chang_2011, Whiteford_2005, Phillippy_2009 Viehweger_2019, Viehweger_2018, Yang_2018
19 Lee_C_2017 A Pairwise Alignment Algorithm for Long Sequences of High Similarity Lee, Chien-Tai; Peng, Sheng-Lung 2017 2017-10-13 PMC N PMC7123042 10.1007/978-981-10-5508-9_27 t1e0tr4w 0.431427 Chang_2011
20 Li_K_2010 ANDES: Statistical tools for the ANalyses of DEep Sequencing Li, Kelvin; Venter, Eli; Yooseph, Shibu; Stockwell, Timothy B; Eckerle, Lance D; Denison, Mark R; Spiro, David J; Methé, Barbara A 2010 2010-07-15 COMM-USE N PMC2921379 20633290.0 10.1186/1756-0500-3-199 2n5vetzw 0.413669 Chang_2011, Cheng_2013 Harel_2019, Twin_2013, Lewandowska_2017, Baldwin_2014
21 Li_Y_2016 VIP: an integrated pipeline for metagenomics of virus identification and discovery Li, Yang; Wang, Hao; Nie, Kai; Zhang, Chen; Zhang, Yi; Wang, Ji; Niu, Peihua; Ma, Xuejun 2016 2016-03-30 None N PMC4824449 27026381.0 10.1038/srep23774 vn6x3fb0 0.399048 Deng_2015, Cheng_2013, Brister_2015, Smith_2013 Dacheux_2014, Alquezar-Planas_2013, Shifman_2019
22 Gardner_2004 Sequencing Needs for Viral Diagnostics Gardner, Shea N.; Lam, Marisa W.; Mulakken, Nisha J.; Torres, Clinton L.; Smith, Jason R.; Slezak, Tom R. 2004 2004-12-01 None N PMC535215 15583268.0 10.1128/jcm.42.12.5472-5476.2004 sd81bz0m 0.396680 Chang_2011 Wang_2010
23 Shepard_2016 Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler Shepard, Samuel S.; Meno, Sarah; Bahl, Justin; Wilson, Malania M.; Barnes, John; Neuhaus, Elizabeth 2016 2016-09-05 COMM-USE N PMC5011931 27595578.0 10.1186/s12864-016-3030-6 xyru2q9o 0.396481 Cheng_2013, Deng_2015, Lee_C_2017, Chang_2011
24 Tithi_2017 Fast Virome Explorer: A Pipeline for Virus and Phage Identification and Abundance Profiling in Metagenomics Data Saima Sultana Tithi; Roderick V. Jensen; Liqing Zhang 2017 2017-10-02 BioRxiv N 10.1101/196998 uw76y16g 0.389644 Tithi_2018, Djikeng_2009, Brister_2015, Lee_C_2017 Tithi_2018, Li_C_2020, Dacheux_2014
25 Tapinos_2019 The Utility of Data Transformation for Alignment, De Novo Assembly and Classification of Short Read Virus Sequences Tapinos, Avraam; Constantinides, Bede; Phan, My V. T.; Kouchaki, Samaneh; Cotten, Matthew; Robertson, David L. 2019 2019-04-26 COMM-USE N PMC6563281 31035503.0 10.3390/v11050394 y5xsf3ij 0.385608 Chang_2011, Deng_2015 Zhang_2017, Wang_2010
26 Tithi_2018 FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data Tithi, Saima Sultana; Aylward, Frank O.; Jensen, Roderick V.; Zhang, Liqing 2018 2018-01-12 COMM-USE N PMC5768174 29340239.0 10.7717/peerj.4227 sjl8x1jt 0.375283 Deng_2015, Cheng_2013, Chang_2011 Tithi_2017, Li_C_2020, Dacheux_2014
27 Sabath_2012 Evolution of Viral Proteins Originated De Novo by Overprinting Sabath, Niv; Wagner, Andreas; Karlin, David 2012 2012-07-19 None N PMC3494269 22821011.0 10.1093/molbev/mss179 629fwmgk 0.375123 Francis_2016
28 Sahli_2012 Arapan-S: a fast and highly accurate whole-genome assembly software for viruses and small genomes Sahli, Mohammed; Shibuya, Tetsuo 2012 2012-05-16 COMM-USE N PMC3441218 22591859.0 10.1186/1756-0500-5-243 nz4qpumr 0.375110 Lee_C_2017, Chang_2011, Cheng_2013, Deng_2015 Wang_2010
29 Dufraigne_2005 Detection and characterization of horizontal transfers in prokaryotes using genomic signature Dufraigne, Christine; Fertil, Bernard; Lespinats, Sylvain; Giron, Alain; Deschavanne, Patrick 2005 2005-01-13 PMC N PMC546175 15653627.0 10.1093/nar/gni004 yba7mdtb 0.373231 Chang_2011, Francis_2016, Gardner_2004 Lima_2015
30 Whiteford_2005 An analysis of the feasibility of short read sequencing Whiteford, Nava; Haslam, Niall; Weber, Gerald; Prügel-Bennett, Adam; Essex, Jonathan W.; Roach, Peter L.; Bradley, Mark; Neylon, Cameron 2005 2005-11-07 PMC N PMC1278949 16275781.0 10.1093/nar/gni170 g2f151oc 0.373094 Deng_2015, Phillippy_2009, Warren_2007, Chang_2011 Harel_2019, Viehweger_2019, Viehweger_2018
31 Chen_2019 TAR-VIR: a pipeline for TARgeted VIRal strain reconstruction from metagenomic data Chen, Jiao; Huang, Jiating; Sun, Yanni 2019 2019-06-04 None N PMC6549370 31164077.0 10.1186/s12859-019-2878-2 6frnbfh4 0.360986 Cheng_2013, Lee_C_2017, Deng_2015, Chang_2011
32 Sampath_2012 Comprehensive Biothreat Cluster Identification by PCR/Electrospray-Ionization Mass Spectrometry Sampath, Rangarajan; Mulholland, Niveen; Blyn, Lawrence B.; Massire, Christian; Whitehouse, Chris A.; Waybright, Nicole; Harter, Courtney; Bogan, Joseph; Miranda, Mary Sue; Smith, David; Baldwin, Carson; Wolcott, Mark; Norwood, David; Kreft, Rachael; Frinder, Mark; Lovari, Robert; Yasuda, Irene; Matthews, Heather; Toleno, Donna; Housley, Roberta; Duncan, David; Li, Feng; Warren, Robin; Eshoo, Mark W.; Hall, Thomas A.; Hofstadler, Steven A.; Ecker, David J. 2012 2012-06-29 COMM-USE N PMC3387173 22768032.0 10.1371/journal.pone.0036528 w75flrwv 0.344293 Gardner_2004, Chang_2011, Priest_2012, Gamermann_2014
33 Isakov_2015 Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum Isakov, Ofer; Bordería, Antonio V.; Golan, David; Hamenahem, Amir; Celniker, Gershon; Yoffe, Liron; Blanc, Hervé; Vignuzzi, Marco; Shomron, Noam 2015 2015-07-01 NONCOMM N PMC4481840 25701575.0 10.1093/bioinformatics/btv101 h7zxyzca 0.343028 Chang_2011, Brister_2015, Lee_C_2017, Cheng_2013
34 Moshiri_2020 ViralMSA: Massively scalable reference-guided multiple sequence alignment of viral genomes Niema Moshiri 2020 2020-04-21 BioRxiv N 10.1101/2020.04.20.052068 l9a7upui 0.320646 Cheng_2013, Chang_2011, Lee_C_2017
35 Smits_2014 Assembly of viral genomes from metagenomes Smits, Saskia L.; Bodewes, Rogier; Ruiz-Gonzalez, Aritz; Baumgärtner, Wolfgang; Koopmans, Marion P.; Osterhaus, Albert D. M. E.; Schürch, Anita C. 2014 2014-12-18 COMM-USE N PMC4270193 25566226.0 10.3389/fmicb.2014.00714 jw4n2j6y 0.313882 Cheng_2013 Cook_2013
36 SCHAT_2008 16 AVIAN IMMUNOSUPPRESSIVE DISEASES AND IMMUNE EVASION SCHAT, KAREL A.; SKINNER, MICHAEL A. 2008 2008-12-31 PMC N PMC7150292 10.1016/b978-012370634-8.50019-6 9qsce2jg 0.308035
37 Naccache_2014 A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples Naccache, Samia N.; Federman, Scot; Veeraraghavan, Narayanan; Zaharia, Matei; Lee, Deanna; Samayoa, Erik; Bouquet, Jerome; Greninger, Alexander L.; Luk, Ka-Cheung; Enge, Barryett; Wadford, Debra A.; Messenger, Sharon L.; Genrich, Gillian L.; Pellegrino, Kristen; Grard, Gilda; Leroy, Eric; Schneider, Bradley S.; Fair, Joseph N.; Martínez, Miguel A.; Isa, Pavel; Crump, John A.; DeRisi, Joseph L.; Sittler, Taylor; Hackett, John; Miller, Steve; Chiu, Charles Y. 2014 2014-06-04 None N PMC4079973 24899342.0 10.1101/gr.171934.113 tg52towp 0.305614 Deng_2015, Djikeng_2009, Cheng_2013, Manning_2020, Brister_2015 Tausch_2018, Li_C_2020, Lewandowski_2019