cran: SMM | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1006457

Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes
Cited by: 118
Author(s): Weilong Zhao, Xinwei Sher
Software Mentions: 10
Published: almost 6 years ago

10.1186/1471-2172-9-8

Evaluation of MHC class I peptide binding prediction servers: Applications for vaccine research
Cited by: 219
Author(s): Honghuang Lin, Surajit Ray, Songsak Tongchusak, Ellis L. Reinherz, Vladimir Brusic
Software Mentions: 5
Published: over 16 years ago

10.1186/s12885-019-5402-1

The neoepitope landscape of breast cancer: implications for immunotherapy
Cited by: 64
Author(s): Pooja Narang, Meixuan Chen, Amit Sharma, Karen S. Anderson, Melissa A. Wilson
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2105-6-132

Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method
Cited by: 457
Author(s): Bjoern Peters, Alessandro Sette
Software Mentions: 4
Published: over 19 years ago

10.3389/fimmu.2021.598778

A Proteome-Wide Immunoinformatics Tool to Accelerate T-Cell Epitope Discovery and Vaccine Design in the Context of Emerging Infectious Diseases: An Ethnicity-Oriented Approach
Cited by: 14
Author(s): Patricio Oyarzún, Manju Kashyap, Victor Fica, Alexis Salas-Burgos, Faviel F. Gonzalez-Galarza, Antony McCabe, Andrew R. Jones, Derek Middleton, Boštjan Kobe
Software Mentions: 4
Published: over 3 years ago

10.1111/mec.16029

The impact of indoor residual spraying on Plasmodium falciparum microsatellite variation in an area of high seasonal malaria transmission in Ghana, West Africa
Cited by: 5
Author(s): Dionne C. Argyropoulos, Shazia Ruybal‐Pesántez, Samantha Deed, Abraham Oduro, Samuel Dadzie, Maxwell A. Appawu, Victor Asoala, Mercedes Pascual, Kwadwo A. Koram, Karen P. Day, Kathryn E. Tiedje
Software Mentions: 4
Published: about 3 years ago

10.7554/eLife.07661

An open-source computational and data resource to analyze digital maps of immunopeptidomes
Cited by: 92
Author(s): Étienne Caron, Lucia Espona Pernas, Daniel J. Kowalewski, Heiko Schuster, Nicola Ternette, Adán Alpízar, Ralf B. Schittenhelm, Sri H. Ramarathinam, Cecilia S. Lindestam Arlehamn, Ching Chiek Koh, Ludovic Gillet, Armin Rabsteyn, Pedro J. Navarro, Sangtae Kim, Henry H N Lam, Theo Sturm, Miguel Marcilla, Alessandro Sette, D. S. Campbell, Eric W. Deutsch, Robert L. Moritz, Anthony W. Purcell, Hans‐Georg Rammensee, Stefan Stevanović, Ruedi Aebersold
Software Mentions: 3
Published: about 9 years ago

10.1093/gigascience/gix017

PSSMHCpan: a novel PSSM-based software for predicting class I peptide-HLA binding affinity
Cited by: 49
Author(s): Geng Li, Dongli Li, Zhang Li, Si Qiu, Wenhui Li, Cheng‐Chi Chao, Naibo Yang, Handong Li, Zhen Cheng, Xin Song, Lei Cheng, Xiuqing Zhang, Jian Wang, Huanming Yang, Kun Ma, Yong Hou, Bo Li
Software Mentions: 3
Published: over 7 years ago

10.3390/vaccines2030515

Peptide Vaccine: Progress and Challenges
Cited by: 479
Author(s): Weidang Li, Medha Joshi, Smita Singhania, Kyle H. Ramsey, Ashlesh K. Murthy
Software Mentions: 3
Published: about 10 years ago

10.1155/2014/402492

Prediction of Epitope-Based Peptides for the Utility of Vaccine Development from Fusion and Glycoprotein of Nipah Virus UsingIn SilicoApproach
Cited by: 38
Author(s): M. Sadman Sakib, Md. Rezaul Islam, A. K. M. Mahbub Hasan, A.H.M. Nurun Nabi
Software Mentions: 3
Published: about 10 years ago

10.1093/sysbio/syz005

Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits
Cited by: 54
Author(s): Sergei Tarasov
Software Mentions: 3
Published: over 5 years ago

10.3390/v7031313

Selection Pressure in CD8+ T-cell Epitopes in the pol Gene of HIV-1 Infected Individuals in Colombia. A Bioinformatic Approach
Cited by: 6
Author(s): Liliana Acevedo-Sáenz, Rodrigo Ochoa, Marı́a Teresa Rugeles, Patricia Olaya-García, Paula A. Velilla, Francisco J. Díaz
Software Mentions: 3
Published: over 9 years ago

10.1073/pnas.2013554117

HLA tapasin independence: broader peptide repertoire and HIV control
Cited by: 46
Author(s): Arman Bashirova, Mathias Viard, Vivek Naranbhai, Alba Grifoni, Wilfredo F. García-Beltrán, Marjan Akdag, Yuko Yuki, Xiaojiang Gao, Colm Ó'hUigín, Malini Raghavan, Steven M. Wolinsky, Jay H. Bream, Priya Duggal, Jeremy Martinson, Nelson L. Michael, Gregory D. Kirk, Susan Buchbinder, David W. Haas, James J. Goedert, Steven G. Deeks, Jacques Fellay, Bruce D. Walker, Philip Goulder, Peter Cresswell, Tim Elliott, Alessandro Sette, Jonathan M. Carlson, Mary Carrington
Software Mentions: 3
Published: almost 4 years ago

10.1155/2020/2861240

Recurrent Neoantigens in Colorectal Cancer as Potential Immunotherapy Targets
Cited by: 8
Author(s): Chao Chen, Songming Liu, Ruokai Qu, Bo Li
Software Mentions: 2
Published: about 4 years ago

10.18632/aging.203053

Identification of novel hepatitis B virus therapeutic vaccine candidates derived from polymerase protein
Cited by: 4
Author(s): Juzeng Zheng, Ziqiang Xia, Yilun Xu, Zhanfan Ou, Xiuqing Lin, Sisi Jin, Yang Liu, Jinming Wu
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2105-8-238

Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method
Cited by: 477
Author(s): Morten Nielsen, Claus Lundegaard, Ole Lund
Software Mentions: 2
Published: about 17 years ago

10.1186/s12920-020-0694-1

neoANT-HILL: an integrated tool for identification of potential neoantigens
Cited by: 5
Author(s): Ana Carolina Coelho, André Fonseca, Daniel Freitas Freire Martins, Paulo Lins, Lucas Marques da Cunha, Sandro J. de Souza
Software Mentions: 2
Published: over 4 years ago

10.1155/2021/6693909

Bioinformatic HLA Studies in the Context of SARS-CoV-2 Pandemic and Review on Association of HLA Alleles with Preexisting Medical Conditions
Cited by: 5
Author(s): Mina Mobini Kesheh, Jalil Azami, Parastoo Hosseini, Rezvan Kakavand‐Ghalehnoei, Hossein Keyvani
Software Mentions: 2
Published: over 3 years ago

10.1007/s41116-018-0015-3

Solar UV and X-ray spectral diagnostics
Cited by: 150
Author(s): G. Del Zanna, H. E. Mason
Software Mentions: 2
Published: about 6 years ago

10.3390/microorganisms7080226

Peptide-Based Subunit Vaccine Design of T- and B-Cells Multi-Epitopes against Zika Virus Using Immunoinformatics Approaches
Cited by: 24
Author(s): Vivitri Dewi Prasasty, Karel Grazzolie, Rosmalena Rosmalena, Fatmawaty Yazid, Fransiskus Xaverius Ivan, Ernawati Sinaga
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pcbi.1000107

Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan
Cited by: 240
Author(s): Morten Nielsen, Claus Lundegaard, Thomas Blicher, Bjoern Peters, Alessandro Sette, Sune Justesen, Søren Buus, Ole Lund
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pcbi.1007757

Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system
Cited by: 53
Author(s): Sinu Paul, Nathan P. Croft, Anthony W. Purcell, David C. Tscharke, Alessandro Sette, Morten Nielsen, Bjoern Peters
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pntd.0005930

Substantial population structure of Plasmodium vivax in Thailand facilitates identification of the sources of residual transmission
Cited by: 12
Author(s): Veerayuth Kittichai, Cristian Koepfli, Wang Nguitragool, Jetsumon Sattabongkot, Liwang Cui
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0090532

Quantitation of Glucocorticoid Receptor DNA-Binding Dynamics by Single-Molecule Microscopy and FRAP
Cited by: 53
Author(s): Femke Groeneweg, Martin E. van Royen, Susanne F. Fenz, Veer I. P. Keizer, Bart Geverts, Jurriën Prins, E. Ronald de Kloet, Adriaan B. Houtsmuller, Thomas Schmidt, Marcel J. M. Schaaf
Software Mentions: 2
Published: over 10 years ago

10.1155/2013/467852

Evaluating the Immunogenicity of Protein Drugs by ApplyingIn VitroMHC Binding Data and the Immune Epitope Database and Analysis Resource
Cited by: 48
Author(s): Sinu Paul, Ravi V. Kolla, John Sidney, Daniela Weiskopf, Ward Fleri, Young S. Kim, Bjoern Peters, Alessandro Sette
Software Mentions: 2
Published: over 11 years ago

10.3389/fgene.2019.01191

Peptide-Major Histocompatibility Complex Class I Binding Prediction Based on Deep Learning With Novel Feature
Cited by: 18
Author(s): Tianyi Zhao, Cheng Liang, Tianyi Zang, Yang Hu
Software Mentions: 2
Published: almost 5 years ago

10.1186/s13073-016-0263-6

Designing string-of-beads vaccines with optimal spacers
Cited by: 38
Author(s): Benjamin Schubert, Oliver Kohlbacher
Software Mentions: 2
Published: over 8 years ago

10.1186/s13073-019-0666-2

Best practices for bioinformatic characterization of neoantigens for clinical utility
Cited by: 126
Author(s): Megan M. Richters, Huiming Xia, Katie M. Campbell, William E. Gillanders, Malachi Griffith
Software Mentions: 2
Published: about 5 years ago

10.1172/jci.insight.98575

Comprehensive immunoproteogenomic analyses of malignant pleural mesothelioma
Cited by: 36
Author(s): Hyun-Sung Lee, Hee-Jin Jang, Jong Min Choi, Jun Zhang, Veronica Lenge De Rosen, Thomas M. Wheeler, Ju-Seog Lee, Thuydung Tu, Peter T. Jindra, Ronald H. Kerman, Sung Yun Jung, Farrah Kheradmand, David J. Sugarbaker, Bryan M. Burt
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-77466-4

Identification and validation of 174 COVID-19 vaccine candidate epitopes reveals low performance of common epitope prediction tools
Cited by: 61
Author(s): Marek Prachař, Sune Justesen, Daniel Bisgaard Steen-Jensen, Stephan Thorgrimsen, Erik Jurgons, Ole Winther, Frederik Otzen Bagger
Software Mentions: 2
Published: almost 4 years ago

10.3390/s110706533

Design and Analysis of Self-Adapted Task Scheduling Strategies in Wireless Sensor Networks
Cited by: 71
Author(s): Wenzhong Guo, Naixue Xiong, Han‐Chieh Chao, Sajid Hussain, Guolong Chen
Software Mentions: 2
Published: about 13 years ago

10.1186/1471-2105-14-S2-S13

Prediction of peptides binding to MHC class I and II alleles by temporal motif mining
Cited by: 27
Author(s): Cem Meydan, Hasan H. Otu, Uğur Sezerman
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-14-S8-S1

Integrating peptides' sequence and energy of contact residues information improves prediction of peptide and HLA-I binding with unknown alleles
Cited by: 2
Author(s): Fei Luo, Yangyang Gao, Yongqiong Zhu, Juan Liu
Software Mentions: 1
Published: over 11 years ago

10.1002/pmic.201700390

A Targeted LC‐MS Strategy for Low‐Abundant HLA Class‐I‐Presented Peptide Detection Identifies Novel Human Papillomavirus T‐Cell Epitopes
Cited by: 24
Author(s): Renata Blatnik, Nitya Mohan, Maria Bonsack, Lasse Gaarde Falkenby, Stéphanie Hoppe, Kathrin Josef, Alina Steinbach, Sara Becker, Wiebke Nadler, Marijana Ručević, Martin R. Larsen, Mogjiborahman Salek, Angelika B. Riemer
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-019-50171-7

Molecular Profiles and Metastasis Markers in Chinese Patients with Gastric Carcinoma
Cited by: 30
Author(s): Chao Chen, Shi Chen, Xiaochun Huang, Jie Zheng, Zhongyi Zhu, Qiaolian Li, Si Qiu, Zhiqing Huang, Zhenkun Zhuang, Riping Wu, Panhong Liu, Fengjie Wu, Shanyun Lin, Bo Li, Xiuqing Zhang, Qiang Chen
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-020-75410-0

Engineering a vector-based pan-Leishmania vaccine for humans: proof of principle
Cited by: 11
Author(s): Pedro Cecílio, James Oristian, Claudio Meneses, Tiago D. Serafim, Jesús G. Valenzuela, Anabela Cordeiro-da-Silva, Fabiano Oliveira
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pntd.0005344

Plasmodium vivax Cell Traversal Protein for Ookinetes and Sporozoites (PvCelTOS) gene sequence and potential epitopes are highly conserved among isolates from different regions of Brazilian Amazon
Cited by: 8
Author(s): Lana Bitencourt Chaves, Daiana de Souza Perce-da-Silva, Rodrigo Nunes Rodrigues-da-Silva, João Hermínio Martins da Silva, Gustavo Capatti Cassiano, Ricardo Luiz Dantas Machado, Lilian Rose Pratt-Riccio, Dalma Maria Banic, Josué da Costa Lima-Junior
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0144475

Epitope-Based Vaccine Target Screening against Highly Pathogenic MERS-CoV: An In Silico Approach Applied to Emerging Infectious Diseases
Cited by: 77
Author(s): Jiandong Shi, Jing Zhang, Sijin Li, Jing Sun, Yumei Teng, Man‐Li C. Wu, Jianfan Li, Yanhan Li, Ningzhu Hu, Haixuan Wang, Yunzhang Hu
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0029805

Class II MHC Self-Antigen Presentation in Human B and T Lymphocytes
Cited by: 26
Author(s): Cristina Maria Costantino, Eric Spooner, Hidde L. Ploegh, David A. Hafler
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0100440

Plasmodium vivax Antigen Discovery Based on Alpha-Helical Coiled Coil Protein Motif
Cited by: 9
Author(s): Nora Céspedes, Catherine Habel, Mary Lopez-Perez, Alejandro Castellanos, Andrey V. Kajava, Catherine Servis, Ingrid Felger, Rémy Moret, Myriam Arévalo‐Herrera, Giampietro Corradin, Sócrates Herrera
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0138729

Inferring Protective CD8+ T-Cell Epitopes for NS5 Protein of Four Serotypes of Dengue Virus Chinese Isolates Based on HLA-A, -B and -C Allelic Distribution: Implications for Epitope-Based Universal Vaccine Design
Cited by: 13
Author(s): Jiandong Shi, Jing Sun, Man‐Li C. Wu, Ningzhu Hu, Jianfan Li, Yanhan Li, Haixuan Wang, Yunzhang Hu
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0002402

A Detailed Analysis of the Murine TAP Transporter Substrate Specificity
Cited by: 36
Author(s): Anne Burgevin, Loredana Saveanu, Young S. Kim, Émilie Barilleau, Maya F. Kotturi, Alessandro Sette, Peter Van Endert, Bjoern Peters
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0204290

Association of HLA class I type with prevalence and outcome of patients with acute myeloid leukemia and mutated nucleophosmin
Cited by: 15
Author(s): Kateřina Kuželová, Barbora Brodská, Johannes Schetelig, Christoph Röllig, Zdeněk Ráčil, Juliane S. Walz, Grzegorz Helbig, Ota Fuchs, Milena Vraná, Pavla Pecherková, Cyril Šálek, Jiřı́ Mayer
Software Mentions: 1
Published: almost 6 years ago

10.1155/2017/2860867

B-CD8+T Cell Interactions in the Anti-Idiotypic Response against a Self-Antibody
Cited by: 2
Author(s): Darel Martínez, Amaury Pupo, Lianet Cabrera, Judith Raymond, Nichol E. Holodick, Ana Hernández
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0144515

Identification of Immunodominant Responses to the Plasmodium falciparum Antigens PfUIS3, PfLSA1 and PfLSAP2 in Multiple Strains of Mice
Cited by: 5
Author(s): Rhea J. Longley, Benedict R. Halbroth, Katie Ewer, Adrian V. S. Hill, Alexandra J. Spencer
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0127637

Altered HLA Class I Profile Associated with Type A/D Nucleophosmin Mutation Points to Possible Anti-Nucleophosmin Immune Response in Acute Myeloid Leukemia
Cited by: 26
Author(s): Kateřina Kuželová, Barbora Brodská, Ota Fuchs, Marie Dobrovolná, Petr Soukup, Petr Cetkovský
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0115343

T Cell Epitope Mapping of the E-Protein of West Nile Virus in BALB/c Mice
Cited by: 6
Author(s): Marina De Filette, Stefan Chabierski, Oliwia Andries, Sebastian Ulbert, Niek N. Sanders
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0222384

Lymphocyte proliferation induced by high-affinity peptides for HLA-B*51:01 in Behçet’s uveitis
Cited by: 3
Author(s): Toshikatsu Kaburaki, Hisae Nakahara, Rie Tanaka, Kimiko Okinaga, Hidetoshi Kawashima, Youichiro Hamasaki, Thanyada Rungrotmongkol, Supot Hannongbua, Hiroshi Noguchi, Makoto Aihara, Fujio Takeuchi
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2105-8-424

Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction
Cited by: 623
Author(s): Mette Voldby Larsen, Claus Lundegaard, Kasper Lamberth, Søren Buus, Ole Lund, Morten Nielsen
Software Mentions: 1
Published: almost 17 years ago

10.3389/fcimb.2014.00022

Cellular vaccines in listeriosis: role of the Listeria antigen GAPDH
Cited by: 21
Author(s): Ricardo Calderón-González, Elisabet Frande-Cabanes, Lucia Bronchalo-Vicente, M. Jesús Lecea-Cuello, Eduardo Pareja, Alexandre Bosch-Martinez, Mónica L. Fanarraga, Sonsoles Yáñez-Díaz, Eugenio Carrasco‐Marín, Carmen Alvarez-Domı́nguez
Software Mentions: 1
Published: over 10 years ago

10.3390/s17061317

Improving Multidimensional Wireless Sensor Network Lifetime Using Pearson Correlation and Fractal Clustering
Cited by: 20
Author(s): Fernando R. Almeida, Ângelo Brayner, Joel J. P. C. Rodrigues, José Everardo Bessa Maia
Software Mentions: 1
Published: over 7 years ago

10.3389/fimmu.2021.692937

Revelation of Potent Epitopes Present in Unannotated ORF Antigens of SARS-CoV-2 for Epitope-Based Polyvalent Vaccine Design Using Immunoinformatics Approach
Cited by: 8
Author(s): Patil Pranita Uttamrao, Chakkarai Sathyaseelan, L. Ponoop Prasad Patro, Thenmalarchelvi Rathinavelan
Software Mentions: 1
Published: about 3 years ago

10.3389/fimmu.2014.00529

In silico Derivation of HLA-Specific Alloreactivity Potential from Whole Exome Sequencing of Stem-Cell Transplant Donors and Recipients: Understanding the Quantitative Immunobiology of Allogeneic Transplantation
Cited by: 23
Author(s): Max Jameson-Lee, Vishal N. Kopardé, Phil Griffith, Allison F. Scalora, Juliana K. Sampson, Haniya Khalid, Nihar U. Sheth, Michael Batalo, Myrna G. Serrano, Catherine Roberts, Michael Heß, Gregory A. Buck, Michael C. Neale, Masoud H. Manjili, Amir A. Toor
Software Mentions: 1
Published: almost 10 years ago

10.3389/fimmu.2021.644637

NEPdb: A Database of T-Cell Experimentally-Validated Neoantigens and Pan-Cancer Predicted Neoepitopes for Cancer Immunotherapy
Cited by: 31
Author(s): Jiaqi Xia, Peng Bai, Weiliang Fan, Qi Ming Li, Yongzheng Li, Dehe Wang, Lei Yin, Yu Zhou
Software Mentions: 1
Published: over 3 years ago

10.3389/fimmu.2016.00232

Reconstitution of CD8 T Cells Protective against Cytomegalovirus in a Mouse Model of Hematopoietic Cell Transplantation: Dynamics and Inessentiality of Epitope Immunodominance
Cited by: 15
Author(s): Rafaela Holtappels, Niels A. W. Lemmermann, Jürgen Podlech, Stefan Ebert, Matthias J. Reddehase
Software Mentions: 1
Published: over 8 years ago

10.3389/fimmu.2017.01441

An Unexpected Major Role for Proteasome-Catalyzed Peptide Splicing in Generation of T Cell Epitopes: Is There Relevance for Vaccine Development?
Cited by: 13
Author(s): Anouk C.M. Platteel, Juliane Liepe, Willem van Eden, Michele Mishto, Alice J.A.M. Sijts
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2105-9-S1-S19

Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes
Cited by: 28
Author(s): Guanglan Zhang, Mohammad Asif Khan, Kellathur N. Srinivasan, A. T. Heiny, Kenneth X. Lee, Chee Keong Kwoh, J. Thomas August, Vladimir Brusic
Software Mentions: 1
Published: over 16 years ago

10.3389/fonc.2021.701777

Personalized Neoantigen-Pulsed DC Vaccines: Advances in Clinical Applications
Cited by: 17
Author(s): Lin Tang, Rui Zhang, Xiaoyu Zhang, Li Yang
Software Mentions: 1
Published: about 3 years ago

10.1186/1471-2105-7-131

EpiJen: a server for multistep T cell epitope prediction
Cited by: 144
Author(s): Irini Doytchinova, Peipei Guan, Darren R. Flower
Software Mentions: 1
Published: over 18 years ago

10.1186/s13073-016-0288-x

NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets
Cited by: 417
Author(s): Morten Nielsen, Massimo Andreatta
Software Mentions: 1
Published: over 8 years ago

10.1186/s43141-021-00148-9

Computational identification of significant immunogenic epitopes of the putative outer membrane proteins from Mycobacterium tuberculosis
Cited by: 1
Author(s): Shobana Sundar, Lokesh Thangamani, P. Shanmughavel
Software Mentions: 1
Published: over 3 years ago

10.1186/s13073-021-00872-4

Optimized polyepitope neoantigen DNA vaccines elicit neoantigen-specific immune responses in preclinical models and in clinical translation
Cited by: 30
Author(s): Lijin Li, Xiuli Zhang, Xiaoli Wang, Samuel W. Kim, John M. Herndon, Michelle Becker-Hapak, Beatriz M. Carreño, Nancy B. Myers, Mark Sturmoski, Michael D. McLellan, Christopher A. Miller, Tanner M. Johanns, Benjamin Tan, Gavin P. Dunn, Timothy P. Fleming, Ted H. Hansen, S. Peter Goedegebuure, William E. Gillanders
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-10-296

NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction
Cited by: 432
Author(s): Morten Nielsen, Ole Lund
Software Mentions: 1
Published: almost 15 years ago

10.5812/hepatmon.15342

GB Virus C/Hepatitis G Virus Envelope Glycoprotein E2: Computational Molecular Features and Immunoinformatics Study
Cited by: 11
Author(s): Malek Mohammad Ranjbar, Khodayar Ghorban, Seyed Moayed Alavian, Hossein Keyvani, Maryam Dadmanesh, Abbas Roayaei Ardakany, Mohammad Hassan Motedayen, Alireza Sazmand
Software Mentions: 1
Published: over 10 years ago

10.1186/1745-7580-3-5

Strength in numbers: achieving greater accuracy in MHC-I binding prediction by combining the results from multiple prediction tools
Cited by: 60
Author(s): Brett Trost, Mik Bickis, Anthony Kusalik
Software Mentions: 1
Published: over 17 years ago

10.1186/1745-7580-6-S1-S6

TAP Hunter: a SVM-based system for predicting TAP ligands using local description of amino acid sequence
Cited by: 15
Author(s): Tze Hau Lam, Hiroshi Mamitsuka, Ee Chee Ren, Joo Chuan Tong
Software Mentions: 1
Published: over 14 years ago

10.1186/1745-7580-6-S2-S3

State of the art and challenges in sequence based T-cell epitope prediction
Cited by: 52
Author(s): Claus Lundegaard, Ilka Hoof, Ole Lund, Morten Nielsen
Software Mentions: 1
Published: over 14 years ago

10.1186/s40425-019-0678-x

Cancer targeting by TCR gene-engineered T cells directed against Kita-Kyushu Lung Cancer Antigen-1
Cited by: 27
Author(s): Bridget C. Marcinkowski, Sanja Stevanović, Sarah R. Helman, Scott M. Norberg, Carylinda Serna, Benjamin Y. Jin, Nikolaos Gkitsas, Tejas Kadakia, Andrew C. Warner, Jeremy L. Davis, Lisa M. Rooper, Christian S. Hinrichs
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2172-13-50

Residue analysis of a CTL epitope of SARS-CoV spike protein by IFN-gamma production and bioinformatics prediction
Cited by: 8
Author(s): Jun Huang, Yanshuo Cao, Xianzhang Bu, Changyou Wu
Software Mentions: 1
Published: about 12 years ago

10.1186/s13321-015-0071-9

A multi-label approach to target prediction taking ligand promiscuity into account
Cited by: 28
Author(s): Avid M. Afzal, Hamse Y. Mussa, Richard E. Turner, Andreas Bender, Robert C. Glen
Software Mentions: 1
Published: over 9 years ago

10.1155/2019/2183510

A Comprehensive Survey of Genomic Alterations in Gastric Cancer Reveals Recurrent Neoantigens as Potential Therapeutic Targets
Cited by: 16
Author(s): Chao Chen, Qiming Zhou, Riping Wu, Bo Li, Qiang Chen, Xiuqing Zhang, Shi Chen
Software Mentions: 1
Published: almost 5 years ago

10.1155/2016/3832176

A Novel Peptide Binding Prediction Approach for HLA-DR Molecule Based on Sequence and Structural Information
Cited by: 4
Author(s): Li Zhao, Yi‐Lei Zhao, Gaofeng Pan, Jijun Tang, Fei Guo
Software Mentions: 1
Published: over 8 years ago

10.1186/s12865-018-0250-3

Low HLA binding of diabetes-associated CD8+ T-cell epitopes is increased by post translational modifications
Cited by: 29
Author(s): John Sidney, José Luis Vela, Dave Friedrich, Ravi V. Kolla, Matthias von Herrath, Johnna D. Wesley, Alessandro Sette
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.ppat.1005164

Antigen-Specific Th17 Cells Are Primed by Distinct and Complementary Dendritic Cell Subsets in Oropharyngeal Candidiasis
Cited by: 48
Author(s): Kerstin Trautwein-Weidner, André Gladiator, Florian Kirchner, Simone Becattini, Thomas Rülicke, Federica Sallusto, Salomé LeibundGut‐Landmann
Software Mentions: 1
Published: almost 9 years ago

10.1155/2020/7079356

An Immunoinformatics Study to Predict Epitopes in the Envelope Protein of SARS-CoV-2
Cited by: 10
Author(s): Renu Jakhar, S. K. Gakhar
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.ppat.1006184

Analysis of the T Cell Response to Zika Virus and Identification of a Novel CD8+ T Cell Epitope in Immunocompetent Mice
Cited by: 107
Author(s): Ryan D. Pardy, Maaran Michael Rajah, Stephanie A. Condotta, Nathan Taylor, Selena M. Sagan, Martin J. Richer
Software Mentions: 1
Published: over 7 years ago

10.1007/s00335-018-9771-6

Identifying neoantigens for use in immunotherapy
Cited by: 28
Author(s): Sharon Hutchison, Antonia L. Pritchard
Software Mentions: 1
Published: about 6 years ago

10.3390/ma6104847

Shear Behavior Models of Steel Fiber Reinforced Concrete Beams Modifying Softened Truss Model Approaches
Cited by: 22
Author(s): Jin Ha Hwang, Deuck Hang Lee, Hyunjin Ju, Kang Su Kim, Soo Yeon Seo, Joo Won Kang
Software Mentions: 1
Published: almost 11 years ago

10.1007/s10995-020-02903-9

SafeMotherMedicine: Aiming to Increase Women’s Empowerment in Use of Medications During Pregnancy and Breastfeeding
Cited by: 4
Author(s): Kristine Heitmann, Jan Schjøtt
Software Mentions: 1
Published: over 4 years ago

10.1186/s12859-017-1997-x

Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction
Cited by: 78
Author(s): Youngjoon Han, Dongsup Kim
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2105-13-313

EpicCapo: epitope prediction using combined information of amino acid pairwise contact potentials and HLA-peptide contact site information
Cited by: 10
Author(s): Thammakorn Saethang, Osamu Hirose, Ingorn Kimkong, Tran Anh Vu, Xuan Tho Dang, Lan Anh Nguyen, Tu Kien T. Le, Mamoru Kubo, Yoichi Yamada, Kenji Satou
Software Mentions: 1
Published: almost 12 years ago

10.3892/mmr.2015.3673

Identification of human leukemia antigen A*0201-restricted epitopes derived from epidermal growth factor pathway substrate number 8
Cited by: 6
Author(s): Bai-Shan Tang, Weijun Zhou, Junyan Du, Yanjie He, Yuhua Li
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2105-10-394

Derivation of an amino acid similarity matrix for peptide:MHC binding and its application as a Bayesian prior
Cited by: 174
Author(s): Young S. Kim, John Sidney, Clemencia Pinilla, Alessandro Sette, Bjoern Peters
Software Mentions: 1
Published: almost 15 years ago

Projects: cran: SMM

Papers Mentioning SMM 84