Topic 10 -- 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 Slootstra_1996 Structural aspects of antibody-antigen interaction revealed through small random peptide libraries Slootstra, Jerry W.; Puijk, Wouter C.; Ligtvoet, Gerard J.; Langeveld, Jan P. M.; Meloen, Rob H. 1996 1996-01-01 PMC N PMC7088776 9237197.0 10.1007/bf01721323 oabo8wgp 0.773585 Phillippy_2009, Chang_2011
2 Hashimoto_2005 Comparative analysis of selected genes from Diachasmimorpha longicaudata entomopoxvirus and other poxviruses Hashimoto, Y.; Lawrence, P.O. 2005 2005-02-28 PMC N PMC7094658 15749105.0 10.1016/j.jinsphys.2004.10.010 f5hfssk5 0.749631
3 Basler_2005 A Novel Paramyxovirus? Basler, Christopher F.; García-Sastre, Adolfo; Palese, Peter 2005 2005-01-23 PMC N PMC3294354 15705331.0 10.3201/eid1101.040653 hhebiwca 0.690621 Lian_2014
4 Cox_E_2015 Identification of SUMO E3 Ligase-Specific Substrates Using the HuProt Human Proteome Microarray Cox, Eric; Uzoma, Ijeoma; Guzzo, Catherine; Jeong, Jun Seop; Matunis, Michael; Blackshaw, Seth; Zhu, Heng 2015 2015-01-01 PMC N PMC5882486 25820740.0 10.1007/978-1-4939-2550-6_32 g15gtag8 0.594341
5 Kang_2017 Prophage genomics reveals patterns in phage genome organization and replication Han Suh Kang; Katelyn McNair; Daniel A. Cuevas; Barbara A. Bailey; Anca M. Segall; Robert A. Edwards 2017 2017-03-07 BioRxiv N 10.1101/114819 0abutzb3 0.555593
6 Guo_F_2006 ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes Guo, Feng-Biao; Zhang, Chun-Ting 2006 2006-01-10 COMM-USE N PMC1352377 16401352.0 10.1186/1471-2105-7-9 h640qddv 0.529598 Lee_C_2017, Cheng_2013, Chang_2011, Gardner_2004, Francis_2016 Wang_2010
7 Kanduc_2008 Massive peptide sharing between viral and human proteomes Kanduc, Darja; Stufano, Angela; Lucchese, Guglielmo; Kusalik, Anthony 2008 2008-10-31 PMC N PMC7115663 18582510.0 10.1016/j.peptides.2008.05.022 knhkdlq7 0.498388
8 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 0.495115 Francis_2016
9 Li_S_2014 System analysis of synonymous codon usage biases in archaeal virus genomes Li, Sen; Yang, Jie 2014 2014-08-21 PMC N PMC7094158 24685889.0 10.1016/j.jtbi.2014.03.022 kg53pbyw 0.463565 Francis_2016
10 Kuchibhatla_2014 Powerful Sequence Similarity Search Methods and In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently “Orphan” Viral Proteins Kuchibhatla, Durga B.; Sherman, Westley A.; Chung, Betty Y. W.; Cook, Shelley; Schneider, Georg; Eisenhaber, Birgit; Karlin, David G. 2014 2014-01-23 COMM-USE N PMC3911697 24155369.0 10.1128/jvi.02595-13 fvj3cpie 0.432961 Gardner_2004, Lee_C_2017, Smits_2014, Odom_2009 Zhang_2017
11 Ackermann_1998 Tailed Bacteriophages: The Order Caudovirales Ackermann, Hans-W. 1998 1998-12-31 PMC N 9891587.0 10.1016/s0065-3527(08)60785-x v5avfe7l 0.424431 Mushegian_2018
12 Finkel_2018 Viral Short ORFs and Their Possible Functions Finkel, Yaara; Stern‐Ginossar, Noam; Schwartz, Michal 2018 2018-01-19 PMC N PMC7167739 29150926.0 10.1002/pmic.201700255 l9gb6znr 0.421892 Schlub_2018, Francis_2016
13 Ho_C_2013 Romance of the three domains: how cladistics transformed the classification of cellular organisms Ho, Chi-Chun; Lau, Susanna K. P.; Woo, Patrick C. Y. 2013 2013-07-19 PMC N PMC4875529 23873078.0 10.1007/s13238-013-3050-9 wbrzoyvr 0.404142
14 Soffer_2013 Potential role of viruses in white plague coral disease Soffer, Nitzan; Brandt, Marilyn E; Correa, Adrienne MS; Smith, Tyler B; Thurber, Rebecca Vega 2013 2013-08-15 PMC N PMC3906806 23949663.0 10.1038/ismej.2013.137 pgqsezq2 0.378214
15 Coutinho_2015 Homology-Independent Metrics for Comparative Genomics Coutinho, Tarcisio José Domingos; Franco, Glória Regina; Lobo, Francisco Pereira 2015 2015-05-04 COMM-USE N PMC4446528 26029354.0 10.1016/j.csbj.2015.04.005 flznxurb 0.376606 Chang_2011, Francis_2016, Lee_C_2017 Francis_2016, Zhang_2017
16 Schlub_2018 A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences Schlub, Timothy E; Buchmann, Jan P; Holmes, Edward C 2018 2018-08-07 NONCOMM N PMC6188560 30099499.0 10.1093/molbev/msy155 yiqdsf9z 0.367297 Chang_2011, Francis_2016, Lee_C_2017 Wang_2010
17 Han_L_2015 Inferring Infection Patterns Based on a Connectivity Map of Host Transcriptional Responses Han, Lu; He, Haochen; Li, Fei; Cui, Xiuliang; Xie, Dafei; Liu, Yang; Zheng, Xiaofei; Bai, Hui; Wang, Shengqi; Bo, Xiaochen 2015 2015-10-28 COMM-USE N PMC4623713 26508266.0 10.1038/srep15820 jgwvjkbj 0.367166 Gamermann_2014, Chang_2011
18 Hewson_2011 Description of viral assemblages associated with the Gorgonia ventalina holobiont Hewson, I.; Brown, J. M.; Burge, C. A.; Couch, C. S.; LaBarre, B. A.; Mouchka, M. E.; Naito, M.; Harvell, C. D. 2011 2011-12-29 PMC N PMC7087884 10.1007/s00338-011-0864-x cy049zbi 0.348806
19 Wang_2010 VIGOR, an annotation program for small viral genomes Wang, Shiliang; Sundaram, Jaideep P; Spiro, David 2010 2010-09-07 COMM-USE N PMC2942859 20822531.0 10.1186/1471-2105-11-451 0lbxvudt 0.341127 Cheng_2013, Lee_C_2017, Brister_2015
20 Firth_2014 Mapping overlapping functional elements embedded within the protein-coding regions of RNA viruses Firth, Andrew E. 2014 2014-11-10 None N PMC4227794 25326325.0 10.1093/nar/gku981 oicbf5l1 0.340036 Chang_2011
21 Francis_2016 Similar ratios of introns to intergenic sequence across animal genomes Warren R. Francis; Gert Wörheide 2016 2016-08-09 BioRxiv N 10.1101/068627 tiyjmih7 0.338136 Chang_2011
22 Schlüter_2008 Mass spectrometry for monitoring protease reactions Schlüter, H.; Hildebrand, D.; Gallin, C.; Schulz, A.; Thiemann, J.; Trusch, M. 2008 2008-06-27 PMC N PMC7080141 18584157.0 10.1007/s00216-008-2213-7 ozljm6kl 0.330869 Lee_C_2017
23 Zeigler_Allen_2017 The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses Zeigler Allen, Lisa; McCrow, John P.; Ininbergs, Karolina; Dupont, Christopher L.; Badger, Jonathan H.; Hoffman, Jeffery M.; Ekman, Martin; Allen, Andrew E.; Bergman, Birgitta; Venter, J. Craig 2017 2017-02-14 COMM-USE N PMC5309335 28217745.0 10.1128/msystems.00125-16 r6y06zwj 0.326400 Roux_2019
24 Odom_2009 Poxvirus protein evolution: Family wide assessment of possible horizontal gene transfer events Odom, Mary R.; Curtis Hendrickson, R.; Lefkowitz, Elliot J. 2009 2009-09-30 None N PMC2779260 19464330.0 10.1016/j.virusres.2009.05.006 r397r5zv 0.316228 Mushegian_2018
25 Kames_2020 Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design Jacob Kames; David Dillon Holcomb; Ofer Kimchi; Michael DiCuccio; Nobuko Hamasaki-Katagiri; Tony Wang; Anton A Komar; Aikaterini Alexaki; Chava Kimchi-Sarfaty 2020 2020-03-31 BioRxiv Y 10.1101/2020.03.30.016832 2fn25l6m 0.306600 Lee_C_2017