4.6 Article

ProGeo-Neo v2.0: A One-Stop Software for Neoantigen Prediction and Filtering Based on the Proteogenomics Strategy

Related references

Note: Only part of the references are listed.
Review Immunology

Development of neoantigens: from identification in cancer cells to application in cancer vaccines

Nasim Ebrahimi et al.

Summary: The discovery and utilization of neoantigens in cancer vaccines show promising results in cancer immunotherapy as they specifically target tumor cells without harming healthy cells. Advances in genome sequencing and bioinformatics have made it possible to detect, identify, and design effective neoantigens for personalized cancer vaccines. Clinical trials on neoantigen-based vaccines are ongoing to assess their advantages and limitations in cancer treatment.

EXPERT REVIEW OF VACCINES (2022)

Review Oncology

Advances in the development of personalized neoantigen-based therapeutic cancer vaccines

Eryn Blass et al.

Summary: Immunotherapy has revolutionized cancer treatment with the development of immune-checkpoint inhibitors and personalized neoantigen vaccines. These vaccines trigger specific T cell responses against individual patient's tumors, showing promising tumor-specific immunogenicity and antitumor activity.

NATURE REVIEWS CLINICAL ONCOLOGY (2021)

Review Pharmacology & Pharmacy

Neoantigen vaccine platforms in clinical development: understanding the future of personalized immunotherapy

Suangson Supabphol et al.

Summary: Cancer neoantigens, derived from genetic alterations, are important targets for cancer immunotherapy. Advances in sequencing technologies and prediction algorithms have enabled the development of neoantigen vaccines, which are currently being evaluated in early phase clinical trials. Challenges to the success of neoantigen vaccines include limitations in identifying neoantigens and effectively targeting the immunosuppressive tumor microenvironment.

EXPERT OPINION ON INVESTIGATIONAL DRUGS (2021)

Review Oncology

MHC heterogeneity and response of metastases to immunotherapy

Ignacio Algarra et al.

Summary: Immunotherapy has proven to be effective in fighting cancer, but tumors and metastases can develop escape mechanisms to evade immune responses, such as downregulating the expression of MHC class I molecules. Understanding and reversing these escape mechanisms is crucial for personalized cancer treatment with immunotherapy.

CANCER AND METASTASIS REVIEWS (2021)

Review Immunology

Challenges targeting cancer neoantigens in 2021: a systematic literature review

Ina Chen et al.

Summary: Despite current limitations, advancements in sequencing, machine learning, and information sharing are likely to rapidly improve neoantigen prediction. The successful development of robust cancer neoantigen prediction strategies has the potential to significantly impact cancer neoantigen vaccine design.

EXPERT REVIEW OF VACCINES (2021)

Article Mathematical & Computational Biology

dbPepNeo: a manually curated database for human tumor neoantigen peptides

Xiaoxiu Tan et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2020)

Article Genetics & Heredity

ProGeo-neo: a customized proteogenomic workflow for neoantigen prediction and selection

Yuyu Li et al.

BMC MEDICAL GENOMICS (2020)

Article Oncology

High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets

Xiaoshan M. Shao et al.

CANCER IMMUNOLOGY RESEARCH (2020)

Review Biochemical Research Methods

A proteogenomic approach to target neoantigens in solid tumors

Ayushi Verma et al.

EXPERT REVIEW OF PROTEOMICS (2020)

Article Biotechnology & Applied Microbiology

A genome-wide survey of mutations in the Jurkat cell line

Louis Gioia et al.

BMC GENOMICS (2018)

Article Multidisciplinary Sciences

TSNAD: an integrated software for cancer somatic mutation and tumour-specific neoantigen detection

Zhan Zhou et al.

ROYAL SOCIETY OPEN SCIENCE (2017)

Review Oncology

Targeting neoantigens to augment antitumour immunity

Mark Yarchoan et al.

NATURE REVIEWS CANCER (2017)

Article Biotechnology & Applied Microbiology

Near-optimal probabilistic RNA-seq quantification

Nicolas L. Bray et al.

NATURE BIOTECHNOLOGY (2016)

Article Biochemical Research Methods

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

Stefka Tyanova et al.

NATURE PROTOCOLS (2016)

Article Genetics & Heredity

pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens

Jasreet Hundal et al.

GENOME MEDICINE (2016)

Article Biochemistry & Molecular Biology

UniProt: a hub for protein information

Alex Bateman et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemical Research Methods

OptiType: precision HLA typing from next-generation sequencing data

Andras Szolek et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq

Gloria M. Sheynkman et al.

MOLECULAR & CELLULAR PROTEOMICS (2013)

Article Genetics & Heredity

Derivation of HLA types from shotgun sequence datasets

Rene L. Warren et al.

GENOME MEDICINE (2012)

Article Biochemical Research Methods

Fast and accurate long-read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

Aaron McKenna et al.

GENOME RESEARCH (2010)

Article Biochemistry & Molecular Biology

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

Kai Wang et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemistry & Molecular Biology

NCBI GEO: archive for high-throughput functional genomic data

Tanya Barrett et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemistry & Molecular Biology

BLAST: at the core of a powerful and diverse set of sequence analysis tools

S McGinnis et al.

NUCLEIC ACIDS RESEARCH (2004)