List of papers on computational immunology and others

this repository is inspired by Kevin Kaichuang Yang and Sean Peldom Zhang. Their works Machine-learning-for-proteins and papers_for_protein_design_using_DL are so unparalleled that I can't help but to follow their steps. I establish the repository mainly for systematically organizing these papers read by iqb members, so that anyone interested in cancer immunology and machine learning for protein can learn about the latest achievement in the field thorough the papers. I will try my best to keep this repository updated.
If you have any questions, please contact me at [tintinjiangiwls@gmail.com] or Kevin Chun CHAN [kevin@skblnw.com].

Any contributions and suggestions are welcomed!🎉🎉💗💗

Note: The papers are sorted by their themes and the time they are published.

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Content

• Reviews and Surveys
  • R-Cancer Immunology
  • R-Model and Technology
    • R-Protein Language Model
    • R-Drug Design
• Letters
• Cancer Immunology
• Model and Technology
  • protein language model
• Drug Design
• Covid-19
• Other

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Reviews-and-surveys

R Cancer Immunology

• T-cell antigen receptor genes and T-cell recognition
  -nature
  -Published: 01 August 1988
  -DOI: https://doi.org/10.1038/334395a0
  T-cell antigen receptor T-cell recognition

• Immunophilin-sensitive protein phosphatase action in cell signaling pathways
  -Cell
  -Published: 07 August 1992
  -DOI: https://doi.org/10.1016/0092-8674(92)90158-9
  Immunophilin-sensitive protein phosphatase cell signaling pathways

• Receptor Proximity, Not Intermolecular Orientation, Is Critical for Triggering T-cell Activation
  -Journal of Biological Chemistry
  -Published: 30 May 2001
  -DOI: https://doi.org/10.1074/jbc.270.37.21689
  T-cell receptor T-cell activation

• How T cells 'see' antigen
  -nature immunology
  -Published: 18 February 2005
  -DOI: https://doi.org/10.1038/ni1173
  T cells antigen

• How TCRs Bind MHCs, Peptides, and Coreceptors
  -Annual Review of Immunology
  -Published: 16 January 2006
  -DOI: https://doi.org/10.1146/annurev.immunol.23.021704.115658
  TCRs MHCs peptides coreceptors

• The HLA genomic loci map: expression, interaction, diversity and disease
  -Journal of Human Genetics
  -Published: 09 January 2009
  -DOI: https://doi.org/10.1038/jhg.2008.5
  HLA genomic loci expression interaction diversity disease

• Neoantigens in cancer immunotherapy
  -Science
  -Published: 03 April 2015
  -DOI: https://doi.org/10.1126/science.aaa4971
  neoantigens cancer immunotherapy

• Elements of cancer immunity and the cancer–immune set point
  -nature
  -Published:18 January 2017
  -DOI: https://doi.org/10.1038/nature21349
  cancer immunity cancer–immune set point

• Identification and Characterization of Neoantigens As Well As Respective Immune Responses in Cancer Patients
  -frontiersin.org
  -Published: 30 December 2017
  -DOI: https://doi.org/10.3389/fimmu.2017.01702
  neoantigens immune responses cancer patients

• Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy
  -Science
  -Published: 07 December 2018
  -DOI: https://doi.org/10.1126/science.aao4572
  HLA class I genotype cancer response checkpoint blockade immunotherapy

• TCR Signaling: Mechanisms of Initiation and Propagation
  -Trends in Biochemical Sciences
  -Published: 18 December 2017
  -DOI: https://doi.org/10.1016/j.tibs.2017.03.008
  TCR signaling initiation propagation

• Combining Immunotherapy and Radiotherapy for Cancer Treatment: Current Challenges and Future Directions
  -frontiersin.org
  -Published: 05 March 2018
  -DOI: https://doi.org/10.3389/fphar.2018.00185
  Immunotherapy Radiotherapy Cancer Treatment

• The hallmarks of successful anticancer immunotherapy
  -Science Translational Medicine
  -Published: 19 September 2018
  -DOI: https://doi.org/10.1126/scitranslmed.aat7807
  anticancer immunotherapy hallmarks

• Development of tumor mutation burden as an immunotherapy biomarker: utility for the oncology clinic
  -Annals of Oncology
  -Published: January 2019
  -DOI: https://doi.org/10.1093/annonc/mdy495
  Tumor mutation burden Immunotherapy Biomarker Oncology clinic

• The evolving landscape of biomarkers for checkpoint inhibitor immunotherapy
  -nature reviews cancer
  -Published: 12 February 2019
  -DOI: https://doi.org/10.1038/s41568-019-0116-x
  biomarkers checkpoint inhibitor immunotherapy

• Structure Based Prediction of Neoantigen Immunogenicity
  -frontiersin.org
  -Published: 28 August 2019
  -DOI: https://doi.org/10.3389/fimmu.2019.02047
  neoantigen immunogenicity

• Tumour-intrinsic resistance to immune checkpoint blockade
  -nature review immunology
  -Published: 30 September 2019
  -DOI: https://doi.org/10.1038/s41577-019-0218-4
  immune checkpoint blockade tumour-intrinsic resistance

• T Cell Recognition of Tumor Neoantigens and Insights Into T Cell Immunotherapy
  -frontiersin.org
  -Published: 10 February 2022
  -DOI: https://doi.org/10.3389/fimmu.2022.833017
  T cell neoantigen immunotherapy

R Model and Technology

R Protein Language Model

• Controllable protein design with language models
  -Nature Machine Learning
  -Published: 22 June 2022
  -DOI: https://doi.org/10.1038/s42256-022-00499-z
  protein language model protein design deep learning

• Linguistically inspired roadmap for building biologically reliable protein language models
  -Nature Machine Learning
  -Published: 06 April 2023
  -DOI: https://doi.org/10.1038/s42256-023-00637-1
  protein language model protein design deep learning

• On scientific understanding with artificial intelligence
  -nature reviews physics
  -Published: 11 October 2022
  -DOI: https://doi.org/10.1038/s42254-022-00518-3
  scientific understanding artificial intelligence

R Drug Design

• Deep Generative Molecular Design Reshapes Drug Discovery
  -Cell Reports Medicine
  -Published: 20 December 2022
  -DOI: https://doi.org/10.1016/j.xcrm.2022.100794
  generative model drug design deep learning

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Letters

• Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer
  -nature
  -Published: 05 July 2017
  -DOI: https://doi.org/10.1038/nature23003
  RNA mutanome vaccines poly-specific therapeutic immunity cancer

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Cancer Immunology

• HLA supertypes and supermotifs: a functional perspective on HLA polymorphism
  -Current Opinion in Immunology
  -Published: August 1998
  -DOI: https://doi.org/10.1016/S0952-7915(98)80124-6
  HLA supertypes supermotifs HLA polymorphism

• Thermodynamics of T cell receptor binding to peptide-MHC: Evidence for a general mechanism of molecular scanning
  -PNAS
  -Published: 28 September 1999
  -DOI: https://doi.org/10.1073/pnas.96.20.11446
  T cell receptor peptide-MHC molecular scanning

• Distinct Molecular Mechanisms Account for the Specificity of Two Different T-Cell Receptors
  -Biochemistry
  -Published: 1 April 2003
  -DOI: https://doi.org/10.1021/bi026864+
  T cell TCR specificity molecular mechanism

• Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study
  -PLOS Computational Biology
  -Published: 07 April 2014
  -DOI: https://doi.org/10.1371/journal.pcbi.1003748
  LC13 TCR HLA-B8 altered peptide ligands molecular dynamics simulation

• Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design
  -PLOS Computational Biology
  -Published: 18 September 2014
  -DOI: https://doi.org/10.1371/journal.pcbi.1003852
  T cell TCR antibody design variable domain orientations

• Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens
  -nature
  -Published: 26 November 2014
  -DOI: https://doi.org/10.1038/nature13988
  checkpoint blockade cancer immunotherapy tumour-specific mutant antigens

• A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells
  -Science
  -Published: 2 April 2015
  -DOI: https://doi.org/10.1126/science.aaa3828
  dendritic cell vaccine melanoma neoantigen-specific T cells

• How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire
  -PNAS
  -Published: 16 February 2016
  -DOI: https://doi.org/10.1073/pnas.1522069113
  HLA-A2 bias human αβ TCR repertoire

• T cell receptors for the HIV KK10 epitope from patients with differential immunologic control are functionally indistinguishable
  -PNAS
  -Published: 07 February 2018
  -DOI: https://doi.org/10.1073/pnas.1718659115
  T cell receptors HIV KK10 epitope differential immunologic control

• Improving T Cell Receptor On-Target Specificity via Structure-Guided Design
  -Molecular Therapy
  -Published: 04 April 2018
  -DOI: https://doi.org/10.1016/j.ymthe.2018.03.018
  T cell receptor on-target specificity structure-guided design

• Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial
  -nature
  -Published: 29 December 2018
  -DOI: https://doi.org/10.1038/s41586-018-0792-9
  neoantigen vaccine intratumoral T cell responses glioblastoma

• Neoantigen-directed immune escape in lung cancer evolution
  -nature
  -Published: 20 March 2019
  -DOI: https://doi.org/10.1038/s41586-019-1032-7
  neoantigen immune escape lung cancer

• Quantitative Prediction of the Landscape of T Cell Epitope Immunogenicity in Sequence Space
  -frontiersin.org
  -Published: 16 April 2019
  -DOI: https://doi.org/10.3389/fimmu.2019.00827
  T cell epitope immunogenicity sequence space

• A Public BCR Present in a Unique Dual-Receptor-Expressing Lymphocyte from Type 1 Diabetes Patients Encodes a Potent T Cell Autoantigen
  -Cell
  -Published: 30 May 2019
  -DOI: https://doi.org/10.1016/j.cell.2019.02.007
  BCR T cell autoantigen Type 1 Diabetes

• Exploration of HIV-1 fusion peptide–antibody VRC34.01 binding reveals fundamental neutralization sites
  -Physical Chemistry Chemical Physics
  -Published: 08 August 2019
  -DOI: https://doi.org/10.1039/C9CP02909E
  HIV-1 fusion peptide antibody neutralization sites

• MHC-II neoantigens shape tumour immunity and response to immunotherapy
  -nature
  -Published: 23 October 2019
  -DOI: https://doi.org/10.1038/s41586-019-1671-8
  MHC-II neoantigens tumour immunity immunotherapy

• A molecular basis for the T cell response in HLA-DQ2.2 mediated celiac disease
  -PNAS
  -Published: 23 January 2020
  -DOI: https://doi.org/10.1073/pnas.1914308117
  Celiac Disease HLA-DQ2.2 TCR Immunogenicity Gliadin Peptides

• Commensal bacteria stimulate antitumor responses via T cell cross-reactivity
  -JCI Insight
  -Published: 23 April 2020
  -DOI: https://doi.org/10.1172/jci.insight.135597
  Commensal bacteria antitumor responses T cell cross-reactivity

• High-affinity oligoclonal TCRs define effective adoptive T cell therapy targeting mutant KRAS-G12D
  -PNAS
  -Published: 27 May 2020
  -DOI: https://doi.org/10.1073/pnas.1921964117
  TCR T cell therapy mutant KRAS-G12D high-affinity oligoclonal

• Impact of Cysteine Residues on MHC Binding Predictions and Recognition by Tumor-Reactive T Cells
  -the Journal of Immunology
  -Published: 15 July 2020
  -DOI: https://doi.org/10.4049/jimmunol.1901173
  MHC T cell cysteine residues binding predictions

• Canonical T cell receptor docking on peptide–MHC is essential for T cell signaling
  -Science
  -Published: 04 June 2020
  -DOI: https://doi.org/10.1126/science.abe9124
  T cell receptor peptide–MHC T cell signaling

• Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors
  -frontiersin.org
  -Published: 22 October 2020
  -DOI: https://doi.org/10.3389/fimmu.2020.565096
  T cell receptor cross-reactivity antigen specificity

• Mutational landscape influences immunotherapy outcomes among patients with non-small-cell lung cancer with human leukocyte antigen supertype B44
  -nature cancer
  -Published: 16 November 2020
  -DOI: https://doi.org/10.1038/s43018-020-00140-1
  mutational landscape immunotherapy non-small-cell lung cancer human leukocyte antigen supertype B44

• Identification of bacteria-derived HLA-bound peptides in melanoma
  -nature
  -Published: 17 March 2021
  -DOI: https://doi.org/10.1038/s41586-021-03368-8
  bacteria-derived HLA-bound peptides melanoma

• Targeting a neoantigen derived from a common TP53 mutation
  -Science
  -Published: 01 March 2021
  -DOI: https://doi.org/10.1126/science.abc8697
  neoantigen TP53 mutation

• Neoantigen Controversies
  -Annual Review of Biomedical Data Science
  -Published: 08 July 2021
  -DOI: https://doi.org/10.1146/annurev-biodatasci-092820-112713
  neoantigen controversies

• Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers
  -nature
  -Published: 21 July 2021
  -DOI: https://doi.org/10.1038/s41586-021-03752-4
  neoantigen-specific TIL anti-PD-1 lung cancers

• Dynamics-Based Peptide–MHC Binding Optimization by a Convolutional Variational Autoencoder: A Use-Case Model for CASTELO
  -Journal of Chemical Theory and Computation
  -Published: 18 November 2021
  -DOI: https://doi.org/10.1021/acs.jctc.1c00870
  MHC T cell binding predictions convolutional variational autoencoder

• Evaluating performance of existing computational models in predicting CD8+ T cell pathogenic epitopes and cancer neoantigens
  -Briefings in Bioinformatics
  -Published: 25 April 2022
  -DOI: https://doi.org/10.1093/bib/bbac141
  CD8+ T cell pathogenic epitopes cancer neoantigens computational models

• Specific Genetic Polymorphisms Contributing in Differential Binding of Gliadin Peptides to HLA-DQ and TCR to Elicit Immunogenicity in Celiac Disease
  -Biochemical Genetics
  -Published: 27 April 2023
  -DOI: https://doi.org/10.1007/s10528-023-10377-x
  Celiac Disease HLA-DQ TCR Immunogenicity Gliadin Peptides

• Pan-KRAS inhibitor disables oncogenic signalling and tumour growth
  -nature
  -Published: 31 May 2023
  -DOI: https://doi.org/10.1038/s41586-023-06123-3
  KRAS pan-KRAS inhibitor oncogenic signalling tumour growth

• A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection
  -nature
  -Published: 19 July 2023
  -DOI: https://doi.org/10.1038/s41586-023-06331-x
  HLA SARS-CoV-2 asymptomatic infection

• A membrane-associated MHC-I inhibitory axis for cancer immune evasion
  -Cell
  -Published: 8 August 2023
  -DOI: https://doi.org/10.1016/j.cell.2023.07.026
  MHC-I cancer immune evasion membrane-associated inhibitory axis

• Chemical remodeling of a cellular chaperone to target the active state of mutant KRAS
  -Science
  -Published: 17 August 2023
  -DOI: https://doi.org/10.1126/science.adg9652
  KRAS chemical remodeling chaperone

• Quantitative approaches for decoding the specificity of the human T cell repertoire
  -frontiers in immunology
  -Published: 7 September 2023
  -DOI: https://doi.org/10.3389%2Ffimmu.2023.1228873
  T cell TCR specificity quantitative approaches

• Killing tumor-associated bacteria with a liposomal antibiotic generates neoantigens that induce anti-tumor immune responses
  -Nature Biotechnology
  -Published: 25 September 2023
  -DOI: https://doi.org/10.1038/s41587-023-01957-8
  tumor-associated bacteria liposomal antibiotic neoantigens anti-tumor immune responses

• The PTPN2/PTPN1 inhibitor ABBV-CLS-484 unleashes potent anti-tumour immunity
  -Nature
  -Published: 04 October 2023
  -DOI: https://doi.org/10.1038/s41586-023-06575-7
  PTPN2 PTPN1 ABBV-CLS-484 anti-tumour immunity

• Cancer- and infection-induced T cell exhaustion are distinct
  -nature immunology
  -Published: 14 November 2023
  -DOI: https://doi.org/10.1038/s41590-023-01624-9
  T cell exhaustion cancer infection

• Targeting of intracellular oncoproteins with peptide-centric CARs
  -nature
  -Published: 08 November 2023
  -DOI: https://doi.org/10.3389%2F
  peptide-centric chimeric antigen receptors

• Nanomedicine-based co-delivery of a calcium channel inhibitor and a small molecule tar- geting CD47 for lung cancer immunotherapy
  -nature communications
  -Published: 11 November 2023
  -DOI: https://doi.org/10.1038/s41467-023-42972-2
  calcium channel inhibitor CD47 lung cancer immunotherapy nanomedicine

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Model and Technology

protein language model

• DeepAntigen: a novel method for neoantigen prioritization via 3D genome and deep sparse learning
  -Bioinformatics
  -Published: 11 September 2020
  -DOI: https://doi.org/10.1093/bioinformatics/btaa686
  neoantigen 3D genome deep sparse learning

• Evaluating performance of existing computational models in predicting CD8+ T cell pathogenic epitopes and cancer neoantigens
  -Briefings in Bioinformatics
  -Published: 25 April 2022
  -DOI: https://doi.org/10.1093/bib/bbac141
  CD8+ T cell pathogenic epitopes cancer neoantigens computational models

• ProtGPT2 is a deep unsupervised language model for protein design
  -nature communications
  -Published: 27 July 2022
  -DOI: https://doi.org/10.1038/s41467-022-32007-7
  protein language model protein design deep learning

• Identification of potent antimicrobial peptides via a machine-learning pipeline that mines the entire space of peptide sequences
  -Nature Biomedical Engineering
  -Published: 12 January 2023
  -DOI: https://doi.org/10.1038/s41551-022-00991-2
  antimicrobial peptides machine-learning pipeline peptide sequences

• Improve the Protein Complex Prediction with Protein Language Models
  -bioRxiv
  -Published: 15 September 2022
  -DOI: https://doi.org/10.1101/2022.09.15.508065
  protein complex protein language model protein-protein interaction

• Active learning guided drug design lead optimization based on relative binding free energy modeling
  -Journal of Chemical Information and Modeling
  -Published: 04 January 2023
  -DOI: https://doi.org/10.1021/acs.jcim.2c01052
  active learning drug design lead optimization relative binding free energy modeling

• Efficient evolution of human antibodies from general protein language models
  -Nature Biotechnology
  -Published: 24 April 2023
  -DOI: https://doi.org/10.1038/s41587-023-01763-2
  protein language model antibody design deep learning

• Neural relational inference to learn long-range allosteric interactions in proteins from molecular dynamics simulations
  -nature communications
  -Published: 29 March 2022
  -DOI: https://doi.org/10.1038/s41467-022-29331-3
  protein allosteric interactions molecular dynamics simulations neural network

• AlphaDrug: Protein target specific de novo molecular generation
  -PNAS Nexus
  -Published: 01 April 2022
  -DOI: https://doi.org/10.1093/pnasnexus/pgac227
  protein target de novo molecular generation AlphaDrug

• Robust deep learning–based protein sequence design using ProteinMPNN
  -Science
  -Published: 15 September 2022
  -DOI: https://doi.org/10.1126/science.add2187
  protein sequence design deep learning ProteinMPNN

• Pre-Training of Equivariant Graph Matching Networks with Conformation Flexibility for Drug Binding
  -Advanced Science
  -Published: 06 October 2022
  -DOI: https://doi.org/10.1002/advs.202203796
  equivariant graph matching networks drug binding conformation flexibility

• ONE TRANSFORMER CAN UNDERSTAND BOTH 2D & 3D MOLECULAR DATA
  -arXiv
  -Published: 04 October 2022
  -DOI: https://arxiv.org/abs/2210.01765
  transformer 2D 3D molecular data

• Chemical complexity challenge: Is multi-instance machine learning a solution?
  -WIREs Computational Molecular Science
  -Published: 27 November 2023
  -DOI: https://doi.org/10.1002/wcms.1698
  multi-instance machine learning chemical complexity

• TCR-H: Machine Learning Prediction of T-cell Receptor Epitope Binding on Unseen Datasets
  -bioRxiv
  -Published: 28 November 2023
  -DOI: https://doi.org/10.1101/2023.11.28.569077
  TCR machine learning negative data bias

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Drug Design

• m¹A in CAG repeat RNA binds to TDP-43 and induces neurodegeneration
  -nature
  -Published: 08 November 2023
  -DOI: https://doi.org/10.1038/s41586-023-06701-5
  m1A CAG repeat RNA TDP-43 neurodegeneration

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Covid-19

• Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor
  -Nature
  -Published: 30 March 2020
  -DOI: http://dx.doi.org/10.1038/s41586-020-2180-5"
  SARS-COV-2 ACE2 spike protein receptor-binding domain crystal structure

Other

• Genetic risk converges on regulatory networks mediating early type 2 diabetes
  -nature
  -Published: 04 December 2023
  -DOI: https://doi.org/10.1038/s41586-023-06693-2
  type 2 diabetes genetic risk regulatory networks