Topic 07 -- Abstracts with Biological Entities (English) - 75 Topics / Sub-Topic Model 31 - 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 Zhang_2011 MULTIPRED2: A computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles Zhang, Guang Lan; DeLuca, David S.; Keskin, Derin B.; Chitkushev, Lou; Zlateva, Tanya; Lund, Ole; Reinherz, Ellis L.; Brusic, Vladimir 2011 2011-11-30 None N PMC3090484 21130094.0 10.1016/j.jim.2010.11.009 bom4rhsh 0.965843 Sidney_2008, O’Connor_2007, Lavi_1988 Wang_2012, Niu_L_2013, Hou_Y_2012
2 Niu_L_2013 Structural basis for the differential classification of HLA-A*6802 and HLA-A*6801 into the A2 and A3 supertypes Niu, Ling; Cheng, Hao; Zhang, Shihong; Tan, Shuguang; Zhang, Yudan; Qi, Jianxun; Liu, Jun; Gao, George F. 2013 2013-10-31 None N PMC7112617 23566939.0 10.1016/j.molimm.2013.03.015 sknah4dx 0.962403 Sidney_2008, Hausmann_1997 Wang_2012, Zhu_S_2019, Lv_Y_2009
3 Molero-Abraham_2014 Customized Predictions of Peptide–MHC Binding and T-Cell Epitopes Using EPIMHC Molero-Abraham, Magdalena; Lafuente, Esther M.; Reche, Pedro 2014 2014-05-06 PMC N PMC7122735 25048133.0 10.1007/978-1-4939-1115-8_18 pejm0c3a 0.932302 Hausmann_1997, Eisenlohr_1992, Lavi_1988 Wang_2012, Kim_S_2012, Calderon-Gonzalez_2015
4 Zhu_S_2019 Divergent Peptide Presentations of HLA-A(*)30 Alleles Revealed by Structures With Pathogen Peptides Zhu, Shiyan; Liu, Kefang; Chai, Yan; Wu, Yanan; Lu, Dan; Xiao, Wenling; Cheng, Hao; Zhao, Yingze; Ding, Chunming; Lyu, Jianxin; Lou, Yongliang; Gao, George F.; Liu, William J. 2019 2019-07-23 COMM-USE N PMC6664060 31396224.0 10.3389/fimmu.2019.01709 va15szxu 0.910479 Wang_2012
5 Ji_W_2019 Salt bridge-forming residues positioned over viral peptides presented by MHC class I impacts T-cell recognition in a binding-dependent manner Ji, Wei; Niu, Ling; Peng, Weiyu; Zhang, Yongli; Cheng, Hao; Gao, Feng; Shi, Yi; Qi, Jianxun; Gao, George F.; Liu, William J. 2019 2019-08-31 PMC N PMC7112684 31226552.0 10.1016/j.molimm.2019.06.005 z5vmhopa 0.898904 Lavi_1988, Hausmann_1997 Kim_S_2012
6 Srinivasan_2004 Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens Srinivasan, K.N.; Zhang, G.L.; Khan, A.M.; August, J.T.; Brusic, V. 2004 2004-08-04 PMC N PMC7110022 15262812.0 10.1093/bioinformatics/bth943 vmc0rrrk 0.893018 Eisenlohr_1992 Wang_2012, Kim_S_2012, TANG_2015
7 Basu_2020 Strategies for vaccine design for corona virus using Immunoinformatics techniques Anamika Basu; Anasua Sarkar; Ujjwal Maulik 2020 2020-03-02 BioRxiv N 10.1101/2020.02.27.967422 618glydc 0.811471
8 Sidney_2008 HLA class I supertypes: a revised and updated classification Sidney, John; Peters, Bjoern; Frahm, Nicole; Brander, Christian; Sette, Alessandro 2008 2008-01-22 COMM-USE N PMC2245908 18211710.0 10.1186/1471-2172-9-1 mp4dydqd 0.794980 Wang_2012, Li_X_2011
9 Zhang_2013 A combination of epitope prediction and molecular docking allows for good identification of MHC class I restricted T-cell epitopes Zhang, Xue Wu 2013 2013-08-31 PMC N PMC7106517 23666426.0 10.1016/j.compbiolchem.2013.03.003 9lqh0evn 0.760054 Khan_2006 Hou_Y_2012, Wang_2012
10 Wang_2018 Prediction and identification of human leukocyte antigen-A2-restricted cytotoxic T lymphocyte epitope peptides from the human papillomavirus 58 E7 protein Wang, He; Chen, Lilai; Ma, Weihong; Zeng, Yue; Qin, Lu; Chen, Mengjie; Li, Li 2018 2018-06-01 PMC N PMC6036542 30008894.0 10.3892/ol.2018.8875 qujgbe8z 0.729407 Wang_2012, Ding_2013, Sun_L_2014
11 Li_L_2020 Epitope-based peptide vaccine design and target site characterization against novel coronavirus disease caused by SARS-CoV-2 Lin Li; Ting Sun; Yufei He; Wendong Li; Yubo Fan; Jing Zhang 2020 2020-02-27 BioRxiv Y 10.1101/2020.02.25.965434 e9vq3fe3 0.722449 Kim_T_2005
12 Liu_G_2008 Construction and functional test of a chicken MHC-I (BF2*15)/peptide tetramer Liu, Guangliang; Wang, Qun; Tong, Tiegang; Xiao, Yihong; Bai, Yu; Liu, Shengwang; Wu, Donglai 2008 2008-03-15 PMC N PMC7126500 18077001.0 10.1016/j.vetimm.2007.10.019 3tl7f6tt 0.712064 Kim_S_2012, Wang_2012, Russell_2018
13 Li_X_2011 Two Distinct Conformations of a Rinderpest Virus Epitope Presented by Bovine Major Histocompatibility Complex Class I N*01801: a Host Strategy To Present Featured Peptides Li, Xin; Liu, Jun; Qi, Jianxun; Gao, Feng; Li, Qirun; Li, Xiaoying; Zhang, Nianzhi; Xia, Chun; Gao, George F. 2011 2011-03-30 None N PMC3126294 21450819.0 10.1128/jvi.00030-11 p3ytja2h 0.696337 Hausmann_1997, Eisenlohr_1992 Wang_2012, Kim_S_2012
14 Campbell_2020 Prediction of SARS-CoV-2 epitopes across 9360 HLA class I alleles Katie M. Campbell; Gabriela Steiner; Daniel K. Wells; Antoni Ribas; Anusha Kalbasi 2020 2020-04-01 BioRxiv Y 10.1101/2020.03.30.016931 bj454swk 0.692209 Eisenlohr_1992, Sidney_2008 Li_L_2020
15 Axelsson-Robertson_2010 Human Leukocyte Antigens A*3001 and A*3002 Show Distinct Peptide-Binding Patterns of the Mycobacterium tuberculosis Protein TB10.4: Consequences for Immune Recognition Axelsson-Robertson, Rebecca; Ahmed, Raija K.; Weichold, Frank F.; Ehlers, Marthie M.; Kock, Marleen M.; Sizemore, Donata; Sadoff, Jerry; Maeurer, Markus 2010 2010-11-17 None N PMC3019778 21084459.0 10.1128/cvi.00302-10 tx6es6u5 0.691218 Hansen_2018, Eisenlohr_1992, Kim_T_2005, Hausmann_1997 Wang_2012, Zhu_S_2019
16 Srivastava_2018 Structural basis of development of multi-epitope vaccine against Middle East respiratory syndrome using in silico approach Srivastava, Sukrit; Kamthania, Mohit; Singh, Soni; Saxena, Ajay K; Sharma, Nishi 2018 2018-11-21 NONCOMM N PMC6254671 30538505.0 10.2147/idr.s175114 33h22ikl 0.667110 Kolls_2012, Kim_T_2005
17 Wang_2012 Weak binder for MHC molecule is a potent Mycobacterium tuberculosis-specific CTL epitope in the context of HLA-A24 allele Wang, Yan; Sun, Meiyi; He, Min; Cui, Honglian; Zhang, Junxian; Shi, Limin; Wang, Wei; Xu, Wenjiong; Gao, Bin; Ding, Jie 2012 2012-10-31 PMC N PMC7127545 22819798.0 10.1016/j.micpath.2012.07.002 wuty839o 0.660842 Hansen_2018, Eisenlohr_1992, Zhao_2011, Lavi_1988, Kim_T_2005 Kim_S_2012, Sun_L_2014
18 Baruah_2020 Immunoinformatics‐aided identification of T cell and B cell epitopes in the surface glycoprotein of 2019‐nCoV Baruah, Vargab; Bose, Sujoy 2020 2020-03-03 PMC Y PMC7166505 32022276.0 10.1002/jmv.25698 5dle3e3c 0.650255 Kim_T_2005, Eisenlohr_1992, Kolls_2012, Hausmann_1997, Hansen_2018 Li_L_2020, Sun_L_2014
19 Badrinath_2014 A Micropolymorphism Altering the Residue Triad 97/114/156 Determines the Relative Levels of Tapasin Independence and Distinct Peptide Profiles for HLA-A(*)24 Allotypes Badrinath, Soumya; Kunze-Schumacher, Heike; Blasczyk, Rainer; Huyton, Trevor; Bade-Doeding, Christina 2014 2014-12-04 COMM-USE N PMC4353853 25802875.0 10.1155/2014/298145 3hs4f022 0.606609 Hausmann_1997 Zhu_S_2019
20 Chang_2012 Conditional ligands for Asian HLA variants facilitate the definition of CD8(+) T-cell responses in acute and chronic viral diseases Chang, Cynthia X L; Tan, Anthony T; Or, Ming Yan; Toh, Kai Yee; Lim, Pei Yiing; Chia, Adeline S E; Froesig, Thomas M; Nadua, Karen D; Oh, Hsueh-Ling J; Leong, Hoe Nam; Hadrup, Sine R; Gehring, Adam J; Tan, Yee-Joo; Bertoletti, Antonio; Grotenbreg, Gijsbert M 2012 2012-12-26 None N PMC3655610 23280567.0 10.1002/eji.201243088 5fgbxwm3 0.599972 Wang_2012, Sun_L_2014
21 Panahi_2018 A comprehensive in silico analysis for identification of therapeutic epitopes in HPV16, 18, 31 and 45 oncoproteins Panahi, Heidar Ali; Bolhassani, Azam; Javadi, Gholamreza; Noormohammadi, Zahra 2018 2018-10-24 COMM-USE N PMC6200245 30356257.0 10.1371/journal.pone.0205933 vu9b5a14 0.590057 Kolls_2012
22 Ou_D_1992 Characterization of the specificity and genetic restriction of human CD4+ cytotoxic T cell clones reactive to capsid antigen of rubella virus Ou, Dawei; Chong, Pele; McVeish, Paul; Jefferies, Wilfred A.; Gillam, Shirley 1992 1992-12-31 PMC N PMC7131658 1280381.0 10.1016/0042-6822(92)90243-i e6fujokw 0.581847 Hansen_2018, Kim_T_2005
23 Sun_L_2014 A new unconventional HLA-A2-restricted epitope from HBV core protein elicits antiviral cytotoxic T lymphocytes Sun, Lu; Zhang, Yu; Zhao, Bao; Deng, Mengmeng; Liu, Jun; Li, Xin; Hou, Junwei; Gui, Mingming; Zhang, Shuijun; Li, Xiaodong; Gao, George F.; Meng, Songdong 2014 2014-03-22 PMC N PMC3978166 24659387.0 10.1007/s13238-014-0041-4 pxzbirqd 0.579096 Kim_T_2005
24 Duru_2019 Tuning antiviral CD8 T-cell response via proline-altered peptide ligand vaccination Adil Doganay Duru; Renhua Sun; Eva B. Allerbring; Jesseka Chadderton; Nadir Kadri; Xiao Han; Hannes Uchtenhagen; Chaithanya Madhurantakam; Sara Pellegrino; Tatyana Sandalova; Per-Åke Nygren; Stephen J. Turner; Adnane Achour 2019 2019-12-02 BioRxiv N 10.1101/862144 cne5whf5 0.575501 Hansen_2018, Kolls_2012, Hwang_2015, Hausmann_1997, Selin_2004 Kim_S_2012, Butler_2008, Kim_S_2005
25 Ma_Y_2016 Structure and Function of HLA-A*02-Restricted Hantaan Virus Cytotoxic T-Cell Epitope That Mediates Effective Protective Responses in HLA-A2.1/K(b) Transgenic Mice Ma, Ying; Cheng, Linfeng; Yuan, Bin; Zhang, Yusi; Zhang, Chunmei; Zhang, Yun; Tang, Kang; Zhuang, Ran; Chen, Lihua; Yang, Kun; Zhang, Fanglin; Jin, Boquan 2016 2016-08-08 COMM-USE N PMC4976285 27551282.0 10.3389/fimmu.2016.00298 2gmerfkv 0.570378 Kim_T_2005, Hansen_2018, Hwang_2015 Wang_2012, Zhao_2010
26 Meng_2011 Identification of an HLA-DPB1*0501 Restricted Melan-A/MART-1 Epitope Recognized by CD4(+) T Lymphocytes: Prevalence for Immunotherapy in Asian Populations Meng, Zhaoting; Wang, Yadong; Zhang, Guanzhong; Ke, Yuehua; Yan, Yanfeng; Wu, Liangliang; Huang, Qianrong; Zeng, Gang; Wang, Yu; Ying, Han; Jiao, Shunchang 2011 2011-09-01 PMC N PMC4426979 21760531.0 10.1097/cji.0b013e318226bd45 kavg2xuj 0.567422 Hansen_2018, Lavi_1988, Kim_T_2005, Zhao_2011, Kolls_2012 Wang_2012, Cong_2012
27 Khan_2006 A systematic bioinformatics approach for selection of epitope-based vaccine targets Khan, Asif M.; Miotto, Olivo; Heiny, A.T.; Salmon, Jerome; Srinivasan, K.N.; Nascimento, Eduardo; Marques, Ernesto T.; Brusic, Vladimir; Tan, Tin Wee; August, J. Thomas 2006 2006-12-01 PMC N PMC2041846 17434154.0 10.1016/j.cellimm.2007.02.005 p37j3olh 0.508704 Kolls_2012
28 Eisenlohr_1992 A transient transfection system for identifying biosynthesized proteins processed and presented to class I MHC restricted T lymphocytes Eisenlohr, Laurence C.; Yewdell, Jonathan W.; Bennink, Jack R. 1992 1992-09-18 PMC N PMC7131252 1401939.0 10.1016/0022-1759(92)90220-n d3cgb80n 0.471524 Hansen_2018, Hwang_2015, Kolls_2012, Zhao_2011 Kim_S_2012, Mascolo_2007, Takagi_2013, Wang_2012
29 Hou_Y_2012 Prediction and Identification of T Cell Epitopes in the H5N1 Influenza Virus Nucleoprotein in Chicken Hou, Yanxia; Guo, Yingying; Wu, Chunyan; Shen, Nan; Jiang, Yongping; Wang, Jingfei 2012 2012-06-20 COMM-USE N PMC3379973 22745738.0 10.1371/journal.pone.0039344 g5sum116 0.461175 Kim_T_2005
30 Matsui_2014 Introduction of a point mutation into an HLA class I single-chain trimer induces enhancement of CTL priming and antitumor immunity Matsui, Masanori; Kawano, Masaaki; Matsushita, Sho; Akatsuka, Toshitaka 2014 2014-07-02 NONCOMM N PMC4362367 26015969.0 10.1038/mtm.2014.27 gbf3ivzc 0.455580 Hansen_2018, Eisenlohr_1992, Kim_T_2005, Hausmann_1997, Hwang_2015 Kim_S_2012, Wang_2012
31 Maeurer_2005 TCR Analyses: T-cell receptor CDR3 analysis: Molecular fingerprinting of the T-cell receptor repertoire Maeurer, Markus J. 2005 2005-01-01 PMC N PMC7120667 10.1007/1-4020-3623-x_14 d7v4mg12 0.446039 Hansen_2018, Kolls_2012, Hausmann_1997, Hwang_2015, Koch_2012 Wang_2012, Kim_S_2012, Sigal_2016, Moseman_2013
32 Holmes_2013 Polymorphisms and Tissue Expression of the Feline Leukocyte Antigen Class I Loci FLAI-E, -H and -K Holmes, Jennifer C.; Holmer, Savannah G.; Ross, Peter; Buntzman, Adam S.; Frelinger, Jeffrey A.; Hess, Paul R. 2013 2013-06-30 PMC N PMC3777221 23812210.0 10.1007/s00251-013-0711-z 90ycfz3h 0.427768 Russell_2018
33 Tang_2017 Novel Identified HLA-A*0201-Restricted Hantaan Virus Glycoprotein Cytotoxic T-Cell Epitopes Could Effectively Induce Protective Responses in HLA-A2.1/K(b) Transgenic Mice May Associate with the Severity of Hemorrhagic Fever with Renal Syndrome Tang, Kang; Cheng, Linfeng; Zhang, Chunmei; Zhang, Yusi; Zheng, Xuyang; Zhang, Yun; Zhuang, Ran; Jin, Boquan; Zhang, Fanglin; Ma, Ying 2017 2017-12-12 COMM-USE N PMC5732971 29312318.0 10.3389/fimmu.2017.01797 ivoyw3fn 0.424045 Kim_T_2005 Wang_2012, Cong_2012, Zhao_2010
34 Frankild_2008 Amino Acid Similarity Accounts for T Cell Cross-Reactivity and for “Holes” in the T Cell Repertoire Frankild, Sune; de Boer, Rob J.; Lund, Ole; Nielsen, Morten; Kesmir, Can 2008 2008-03-19 COMM-USE N PMC2263130 18350167.0 10.1371/journal.pone.0001831 x80cs5bc 0.423543 Kolls_2012, Hausmann_1997, Hansen_2018 Butler_2008, Kim_S_2005, Wang_2012
35 Calderon-Gonzalez_2015 Identification and characterisation of T-cell epitopes for incorporation into dendritic cell-delivered Listeria vaccines Calderon-Gonzalez, Ricardo; Tobes, Raquel; Pareja, Eduardo; Frande-Cabanes, Elisabet; Petrovsky, Nikolai; Alvarez-Dominguez, Carmen 2015 2015-09-30 PMC N PMC7127673 26031451.0 10.1016/j.jim.2015.05.009 658lmb7d 0.412735 Kolls_2012 Kim_S_2012, Takagi_2013, Matsuo_2012
36 Sylvester‐Hvid_2008 SARS CTL Vaccine Candidates — HLA Supertype, Genome‐Wide Scanning and Biochemical Validation Sylvester‐Hvid, C.; Nielsen, M.; Lamberth, K.; Røder, G.; Justesen, S.; Lundegaard, C.; Worning, P.; Thomadsen, H.; Lund, O.; Brunak, S.; Buus, S. 2008 2008-06-28 PMC N PMC7169620 10.1111/j.0300-9475.2004.01423bd.x yi25yh8f 0.406019 Khan_2006
37 Hausmann_1997 Activation of autoreactive T cells by peptides from human pathogens Hausmann, Stefan; Wucherpfennig, Kai W 1997 1997-12-31 PMC N PMC7134830 9492986.0 10.1016/s0952-7915(97)80186-0 olt49mp1 0.405194 Hansen_2018, Hwang_2015, Koch_2012, Zhao_2011 Sigal_2016, van_Haren_2013
38 Butler_2008 Prevention of Cytotoxic T Cell Escape Using a Heteroclitic Subdominant Viral T Cell Determinant Butler, Noah S.; Theodossis, Alex; Webb, Andrew I.; Nastovska, Roza; Ramarathinam, Sri Harsha; Dunstone, Michelle A.; Rossjohn, Jamie; Purcell, Anthony W.; Perlman, Stanley 2008 2008-10-24 COMM-USE N PMC2563037 18949029.0 10.1371/journal.ppat.1000186 h8upyzb1 0.402184 Hansen_2018, Kolls_2012, Hwang_2015, Hausmann_1997, Selin_2004
39 Adhikari_2017 Overlapping CD8+ and CD4+ T-cell epitopes identification for the progression of epitope-based peptide vaccine from nucleocapsid and glycoprotein of emerging Rift Valley fever virus using immunoinformatics approach Adhikari, Utpal Kumar; Rahman, M. Mizanur 2017 2017-12-31 PMC N PMC7106247 29107145.0 10.1016/j.meegid.2017.10.022 vr5o5kze 0.396003 Hansen_2018, Kim_T_2005, Platt_2013
40 Chen_2012 In vitro and in vivo identification of a novel cytotoxic T lymphocyte epitope from Rv3425 of Mycobacterium tuberculosis Chen, Fei; Zhai, Ming‐xia; Zhu, Yu‐huang; Qi, Yuan‐ming; Zhai, Wen‐jie; Gao, Yan‐feng 2012 2012-07-26 PMC N PMC7168511 22537173.0 10.1111/j.1348-0421.2012.00470.x ikclflcl 0.391505 Hansen_2018, Hwang_2015, Kolls_2012, Zhao_2011, Eisenlohr_1992
41 O’Connor_2007 Comprehensive characterization of MHC class II haplotypes in Mauritian cynomolgus macaques O’Connor, Shelby L.; Blasky, Alex J.; Pendley, Chad J.; Becker, Ericka A.; Wiseman, Roger W.; Karl, Julie A.; Hughes, Austin L.; O’Connor, David H. 2007 2007-03-24 PMC N PMC2836927 17384942.0 10.1007/s00251-007-0209-7 qahik4g7 0.386049 Lavi_1988
42 TANG_2015 Identification of human leukemia antigen A*0201-restricted epitopes derived from epidermal growth factor pathway substrate number 8 TANG, BAISHAN; ZHOU, WEIJUN; DU, JINGWEN; HE, YANJIE; LI, YUHUA 2015 2015-04-23 COMM-USE N PMC4463842 25936538.0 10.3892/mmr.2015.3673 fvoke2yc 0.385926 Hansen_2018, Hwang_2015, Kolls_2012, Zhao_2011, Koch_2012 Wang_2012, Betting_2009
43 de_Silva_1991 Multiple sclerosis patients have reduced HLA class II-restricted cytotoxic responses specific for both measles and herpes virus de Silva, Shari M.; McFarland, Henry F. 1991 1991-12-31 PMC N PMC7119527 1659588.0 10.1016/0165-5728(91)90176-8 12eqrhql 0.348664 Hwang_2015, Kim_T_2005, Hansen_2018, Kolls_2012 Wang_2012
44 Weber_2009 T cell epitope: Friend or Foe? Immunogenicity of biologics in context Weber, Constanze A.; Mehta, Preema J.; Ardito, Matt; Moise, Lenny; Martin, Bill; De Groot, Anne S. 2009 2009-09-30 PMC N PMC7103283 19619593.0 10.1016/j.addr.2009.07.001 5267m0ey 0.336073 Kolls_2012 Graham_2003
45 Gough_2007 The HLA Region and Autoimmune Disease: Associations and Mechanisms of Action Gough, S.C.L; Simmonds, M.J 2007 2007-11-23 COMM-USE N PMC2647156 19412418.0 10.2174/138920207783591690 bpjkwcfb 0.312774 Lavi_1988, Kolls_2012 Wang_2012, ’t_Hart_2001