Scientific Publications
How do I cite OpenCRAVAT?
Pagel KA et al. Integrated Informatics Analysis of Cancer-Related Variants. JCO Clinical Cancer Informatics 2020 4, 310-317.
In addition, OpenCRAVAT users are encouraged to cite individual annotations used in their study analysis.
How can I cite the annotations and tools included in my analysis?
The source information and citation for each module made available by OpenCRAVAT are described in their corresponding tile in the interactive open store. Or, alternatively, in the yml file within that module’s source directory.
Publications Citing CRAVAT
Kelly, Ronan J., et al. "Neoadjuvant nivolumab or nivolumab plus LAG-3 inhibitor relatlimab in resectable esophageal/gastroesophageal junction cancer: a phase Ib trial and ctDNA analyses." Nature medicine 30.4 (2024): 1023-1034.
Ablooglu, Ararat J., et al. "Intrinsic endothelial hyperresponsiveness to inflammatory mediators drives acute episodes in models of Clarkson disease." The Journal of Clinical Investigation 134.10 (2024).
Dou, Jinzhuang, et al. "Single-nucleotide variant calling in single-cell sequencing data with Monopogen." Nature biotechnology 42.5 (2024): 803-812.
Dressler, Franz F., et al. "Proteomic analysis of the urothelial cancer landscape." Nature Communications 15.1 (2024): 4513.
Murray, Joseph C., et al. "Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer." Clinical Cancer Research 30.2 (2024): 389-403.
Parker, Heidi G., et al. "Genome-wide analyses reveals an association between invasive urothelial carcinoma in the Shetland sheepdog and NIPAL1." npj Precision Oncology 8.1 (2024): 112.
Stan, A. et al. (2024). Detection of driver mutations and genomic signatures in endometrial cancers using artificial intelligence algorithms. Plos One, 19(2), e0299114. Public Library of Science, San Francisco, CA USA.
Dressler, F. F. et al. (2024). Proteomic analysis of the urothelial cancer landscape. Nature Communications, 15(1), 4513. Nature Publishing Group UK, London.
Murray, Joseph C., et al. "Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer." Clinical Cancer Research 30.2 (2024): 389-403.
Parker, Heidi G., et al. "Genome-wide analyses reveals an association between invasive urothelial carcinoma in the Shetland sheepdog and NIPAL1." npj Precision Oncology 8.1 (2024): 112.
Guarducci, Cristina, et al. "Selective CDK7 Inhibition Suppresses Cell Cycle Progression and MYC Signaling While Enhancing Apoptosis in Therapy-resistant Estrogen Receptor–positive Breast Cancer." Clinical Cancer Research 30.9 (2024): 1889-1905.
Stan, Anda, et al. "Detection of driver mutations and genomic signatures in endometrial cancers using artificial intelligence algorithms." Plos one 19.2 (2024): e0299114.
Karagianni, Korina, et al. "Recommendations for detection, validation, and evaluation of RNA editing events in cardiovascular and neurological/neurodegenerative diseases." Molecular Therapy-Nucleic Acids 35.1 (2024).
Karagianni, Korina, et al. "RNA editing regulates glutamatergic synapses in the frontal cortex of a molecular subtype of Amyotrophic Lateral Sclerosis." Molecular Medicine 30.1 (2024): 101.
Kassem, P. H. et al. (2024). Genomic landscape of hepatocellular carcinoma in Egyptian patients by whole exome sequencing. BMC Medical Genomics, 17(1), 202. Springer.
Wall, Patrick, and Trey Ideker. "Representing mutations for predicting cancer drug response." Bioinformatics 40.Supplement_1 (2024): i160-i168.
Zhang, Xi, et al. "Blood-based molecular and cellular biomarkers of early response to neoadjuvant PD-1 blockade in patients with non-small cell lung cancer." Cancer Cell International 24.1 (2024): 225.
Lim, Hyeyeun, et al. "Somatic mutations of esophageal adenocarcinoma: a comparison between Black and White patients." Scientific Reports 14.1 (2024): 8988.
Navapour, Leila, et al. "Identification of high-risk non-synonymous SNPs (nsSNPs) in DNAH1 and DNAH17 genes associated with male infertility: a bioinformatics analysis." Journal of Applied Genetics (2024): 1-14.
Winther-Sørensen, Marie, et al. "Determinants of plasma levels of proglucagon and the metabolic impact of glucagon receptor signalling: a UK Biobank study." Diabetologia (2024): 1-14.
Teixeira, Elisabete, et al. "Investigating USP42 Mutation as Underlying Cause of Familial Non-Medullary Thyroid Carcinoma." International Journal of Molecular Sciences 25.3 (2024): 1522.
Baraban, Ezra G., et al. "High-Grade, Nonsarcomatoid Chromophobe Renal Cell Carcinoma: A Series of 22 Cases With Novel Molecular Features on a Subset." Modern Pathology 37.5 (2024): 100472.
Boyd, Sonja, et al. "NGS of brush cytology samples improves the detection of high-grade dysplasia and cholangiocarcinoma in patients with primary sclerosing cholangitis: A retrospective and prospective study." Hepatology communications 8.4 (2024): e0415.
Zhang, Huayang, et al. "Pleiotropic effects of different exonic nucleotide changes at the same position contribute to hemophilia B phenotypic variation." Journal of Thrombosis and Haemostasis 22.4 (2024): 975-989.
Sheridan, Molly B., et al. "The clinical utility of sequencing the entirety of CFTR." Journal of Cystic Fibrosis (2024).
Koutsofti, Constantina, et al. "Massive Parallel DNA Sequencing of Patients with Inherited Cardiomyopathies in Cyprus and Suggestion of Digenic or Oligogenic Inheritance." Genes 15.3 (2024): 319.
Kuriakose, Santhosh, et al. "High prevalence of “non‐pathogenic” POLE mutation with poor prognosis in a cohort of endometrial cancer from South India." International Journal of Gynecology & Obstetrics (2024).
Dolin, Robert H., Bret SE Heale, and Srikar Chamala. "Genomics Clinical Decision Support with Fast Healthcare Interoperability Resources Genomics Operations." Advances in Molecular Pathology (2024).
Lin, Yu-Jen, et al. "Variant Impact Predictor database (VIPdb), version 2: Trends from 25 years of genetic variant impact predictors." bioRxiv (2024): 2024-06.
Kosobokova, Ekaterina N., et al. "Human Metastatic Melanoma Cell Lines Panel for In Vitro and In Vivo Investigations." Journal of Molecular Pathology 5.1 (2024): 11-27.
Vlachavas, Efstathios-Iason, et al. "Molecular and functional profiling unravels targetable vulnerabilities in colorectal cancer." bioRxiv (2024): 2024-04.
Shinde, Sonali S., et al. "Systems Approach for Identifying Drug Targets by Computational Approaches." Systems Biology Approaches: Prevention, Diagnosis, and Understanding Mechanisms of Complex Diseases (2024): 257-270.
Mamidi, Tarun Karthik Kumar, et al. "DITTO: An Explainable Machine-Learning Model for Transcript-Specific Variant Pathogenicity Prediction." (2024).
Krull, Jordan E., et al. "Follicular lymphoma B cells exhibit heterogeneous transcriptional states with associated somatic alterations and tumor microenvironments." Cell Reports Medicine 5.3 (2024).
Sabin, Carmen Alves. "Assessment of MuTect2 and VarScan2 for somatic mutation detection in exome sequencing."
Goyal, Yogesh, et al. "Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells." Nature 620.7974 (2023): 651-659.
Mensah, Martin A., et al. "Aberrant phase separation and nucleolar dysfunction in rare genetic diseases." Nature 614.7948 (2023): 564-571.
Li, Yize, et al. "Pan-cancer proteogenomics connects oncogenic drivers to functional states." Cell 186.18 (2023): 3921-3944.
Tsimberidou, Apostolia M., et al. "Molecular tumour boards—current and future considerations for precision oncology." Nature Reviews Clinical Oncology 20.12 (2023): 843-863.
Krysiak, Kilannin, et al. "CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase." Nucleic acids research 51.D1 (2023): D1230-D1241.
Johnson, Amber, et al. "Actionability classification of variants of unknown significance correlates with functional effect." npj Precision Oncology 7.1 (2023): 67.
Johnson, Amber, et al. "Actionability classification of variants of unknown significance correlates with functional effect." npj Precision Oncology 7.1 (2023): 67.
Mehta, Subina, et al. "A Galaxy of informatics resources for MS-based proteomics." Expert Review of Proteomics 20.11 (2023): 251-266.
Sashittal, Palash, et al. "ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model." Genome biology 24.1 (2023): 272.
Ghanem, Paola, et al. "Druggable genomic landscapes of high-grade gliomas." Frontiers in Medicine 10 (2023): 1254955.
Alcaniz, Joshua, et al. "Clinically relevant glioblastoma patient-derived xenograft models to guide drug development and identify molecular signatures." Frontiers in Oncology 13 (2023): 1129627.
Eng, Zing Hong, et al. "Changes in antioxidant status and DNA repair capacity are corroborated with molecular alterations in malignant thyroid tissue of patients with papillary thyroid cancer." Frontiers in Molecular Biosciences 10 (2023): 1237548.
Vellichirammal, Neetha Nanoth, et al. "The mutational landscape of a US Midwestern breast cancer cohort reveals subtype-specific cancer drivers and prognostic markers." Human Genomics 17.1 (2023): 64.
Tremmel, Roman, et al. "Translating pharmacogenomic sequencing data into drug response predictions—how to interpret variants of unknown significance." British Journal of Clinical Pharmacology (2023).
Kulandaisamy, A., S. A. Parvathy Dharshini, and M. Michael Gromiha. "Alz-Disc: A Tool to Discriminate Disease-causing and Neutral Mutations in Alzheimer's Disease." Combinatorial Chemistry & High Throughput Screening 26.4 (2023): 769-777.
Rasheed, Shayaan, et al. "Protein Arginine Methyltransferase 5 (PRMT5) Mutations in Cancer Cells." International journal of molecular sciences 24.7 (2023): 6042.
Gomez, Felicia, et al. "Ultra-deep sequencing reveals the mutational landscape of classical Hodgkin lymphoma." Cancer Research Communications 3.11 (2023): 2312-2330.
Watson, Alizhah J., et al. "F-box DNA Helicase 1 (FBH1) Contributes to the Destabilization of DNA Damage Repair Machinery in Human Cancers." Cancers 15.18 (2023): 4439.
Lunghi, Barbara, et al. "Whole-Exome Sequencing in a Family with an Unexplained Tendency for Venous Thromboembolism: Multicomponent Prediction of Low-Frequency Variant Deleteriousness and of Individual Protein Interaction." International Journal of Molecular Sciences 24.18 (2023): 13809.
Andus, Ingo, et al. "Establishment, characterization, and drug screening of low-passage patient individual non-small cell lung cancer in vitro models including the rare pleomorphic subentity." Frontiers in Oncology 13 (2023): 1089681.
Madsen, Allison T., and Deborah J. Good. "In Silico Examination of Single Nucleotide Missense Mutations in NHLH2, a Gene Linked to Infertility and Obesity." International Journal of Molecular Sciences 24.4 (2023): 3193.
Elangovan, Ashuvinee, et al. "WCRC-25: A novel luminal Invasive Lobular Carcinoma cell line model." bioRxiv (2023): 2023-09.
Botsis, Taxiarchis, et al. "Precision Oncology Core Data Model to Support Clinical Genomics Decision Making." JCO Clinical Cancer Informatics 7 (2023): e2200108.
Chandrashekar, K., et al. "Decision support system and web-application using supervised machine learning algorithms for easy cancer classifications." Cancer Informatics 22 (2023): 11769351221147244.
Huzar, Jared, et al. "Bootstrap confidence for molecular evolutionary estimates from tumor bulk sequencing data." Frontiers in Bioinformatics 3 (2023): 1090730.
Kontogianni, Georgia, et al. "A comprehensive analysis of cutaneous melanoma patients in Greece based on multi-omic data." Cancers 15.3 (2023): 815.
Sierk, Michael, et al. "3DVizSNP: a tool for rapidly visualizing missense mutations identified in high throughput experiments in iCn3D." BMC bioinformatics 24.1 (2023): 244.
Rasheed, Shayaan. "The investigation of PRMT5 in cancer through biochemical and computational approaches." (2023).
Xia, Huiming. "Improving Neoantigen Prioritization Methods for Personalized Cancer Vaccines." (2023).
Ostrander, Elaine, et al. "Genome-wide analyses reveals an association between invasive urothelial carcinoma in the Shetland sheepdog, NIPAL1, and the MAPK signaling pathway." (2023).
Lee, Seung Hyuk T., et al. "Changes of Mutations and Copy‐Number and Enhanced Cell Migration during Breast Tumorigenesis." Advanced biology 7.2 (2023): 2200072.
Yazar, Metin. "Computational Investigation of Structural and Functional Effects of Cancer Related Variants." PQDT-Global (2023).
Gensterblum-Miller, Elizabeth. "Molecular Analysis of Recurrent Translocations in Mucoepidermoid Carcinoma." (2023).
Horak, Peter, et al. "Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC)." Genetics in Medicine 24.5 (2022): 986-998.
Fejzo, Marlena S., et al. "Whole‐exome sequencing uncovers new variants in GDF15 associated with hyperemesis gravidarum." BJOG: An International Journal of Obstetrics & Gynaecology 129.11 (2022): 1845-1852.
Aksit, Melis A., et al. "Pleiotropic modifiers of age-related diabetes and neonatal intestinal obstruction in cystic fibrosis." The American Journal of Human Genetics 109.10 (2022): 1894-1908.
Hamid, Abdulaziz B., et al. "Pan-cancer analysis of co-occurring mutations in RAD52 and the BRCA1-BRCA2-PALB2 axis in human cancers." PLoS One 17.9 (2022): e0273736.
Thind, Amarinder Singh, et al. "Whole genome analysis reveals the genomic complexity in metastatic cutaneous squamous cell carcinoma." Frontiers in oncology 12 (2022): 919118.
Barrell, William B., et al. "Identification of a novel variant of the ciliopathic gene FUZZY associated with craniosynostosis." European Journal of Human Genetics 30.3 (2022): 282-290.
Dudová, Zdenka, et al. "The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization." BMC genomics 23.1 (2022): 156.
Tiberti, Matteo, et al. "The Cancermuts software package for the prioritization of missense cancer variants: a case study of AMBRA1 in melanoma." Cell Death & Disease 13.10 (2022): 872.
de Bruijn, Ino, et al. "Genome nexus: a comprehensive resource for the annotation and interpretation of genomic variants in cancer." JCO Clinical Cancer Informatics 6 (2022): e2100144.
Bult, Johanna AA, et al. "Low mutational burden of extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue in patients with primary Sjogren’s syndrome." Cancers 14.4 (2022): 1010.
Ruel, Louis-Jacques, et al. "Tumor mutational burden by whole-genome sequencing in resected NSCLC of never smokers." Cancer Epidemiology, Biomarkers & Prevention 31.12 (2022): 2219-2227.
Salomon-Perzyński, Aleksander, et al. "Tracking clonal evolution of multiple myeloma using targeted next-generation DNA sequencing." Biomedicines 10.7 (2022): 1674.
Zheng, Xinchang, et al. "CCAS: one-stop and comprehensive annotation system for individual cancer genome at multi-omics level." Frontiers in genetics 13 (2022): 956781.
Hurst, Carolyn D., et al. "Molecular profile of pure squamous cell carcinoma of the bladder identifies major roles for OSMR and YAP signalling." The Journal of Pathology: Clinical Research 8.3 (2022): 279-293.
Huang, Jinlong, et al. "Evidence for reduced BRCA2 functional activity in Homo sapiens after divergence from the chimpanzee-human last common ancestor." Cell Reports 39.5 (2022).
Zhu, Yuan, et al. "Discovery of pan-cancer related genes via integrative network analysis." Briefings in Functional Genomics 21.4 (2022): 325-338.
Chatterjee, Samadrita, Rajkumar Chakraborty, and Yasha Hasija. "Polymorphisms at site 469 of B-RAF protein associated with skin melanoma may be correlated with dabrafenib resistance: An in silico study." Journal of Biomolecular Structure and Dynamics 40.21 (2022): 10862-10877.
Cook, Ashley L., et al. "An isogenic cell line panel for sequence-based screening of targeted anticancer drugs." Iscience 25.6 (2022).
Hardison, Kimberly L., et al. "KAT5 histone acetyltransferase mutations in cancer cells." microPublication Biology 2022 (2022).
Pappula, Amrit L., et al. "In silico analysis of a SLC6A4 G100V mutation in lung cancers." Micropublication Biology 2022 (2022).
Krysiak, Kilannin, et al. "A community approach to the cancer-variant-interpretation bottleneck." Nature cancer 3.5 (2022): 522-525.
Bult, J. A. A., et al. "Low Mutational Burden of Extranodal Marginal Zone Lymphoma of Mucosa-Associated Lymphoid Tissue in Patients with Primary Sjogren’s Syndrome. Cancers 2022, 14, 1010." (2022).
Jahn, Stephan W., and Philipp J. Jost. "Challenges in integrating molecular profiles into clinical cancer care." memo-Magazine of European Medical Oncology 15.4 (2022): 303-306.
Ding, Kai. "Multi-omics profiling of breast cancer metastases to identify drivers and mechanisms of endocrine resistance for precision medicine." (2022).
Mosquera Orgueira, Adrián. "Identification of new genomic drivers and predictors of disease evolution in chronic lymphocytic leukemia." (2022).
Wang, Lihua, et al. "CDMPred: A Tool for Predicting Cancer Driver Mutations with High-Quality Passenger Mutations and Ensemble Learning." (2022).
Mahmoodi, Evanjelin, et al. "Entanglement Mapping: A Novel Method to Detect Interacting SNPs in Genome-Wide Studies." 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE, 2022.
Simanshu, Emil Lou. "RAS Internal Tandem Duplication Disrupts GAP-binding to Activate Oncogenic Signaling."
Hardison, Kimberly L., et al. "KAT5 histone acetyltransferase mutations in cancer cells."
Papadopoulos, Chetan Bettegowda, Nickolas Papadopoulos, and Bert Vogelstein. "An Isogenic Cell Line Panel for Sequence-based Screening of Targeted Anti-cancer Drugs."
Zuckerman, Brian L., et al. "Informatics Technologies for Cancer Research (ITCR) Case Study Report." (2022).
Forde, Patrick M., et al. "Durvalumab with platinum-pemetrexed for unresectable pleural mesothelioma: survival, genomic and immunologic analyses from the phase 2 PrE0505 trial." Nature medicine 27.11 (2021): 1910-1920.
Thind, Amarinder Singh, et al. "Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology." Briefings in bioinformatics 22.6 (2021): bbab259.
Tokheim, Collin, et al. "Systematic characterization of mutations altering protein degradation in human cancers." Molecular cell 81.6 (2021): 1292-1308.
Tokheim, Collin, et al. "Systematic characterization of mutations altering protein degradation in human cancers." Molecular cell 81.6 (2021): 1292-1308.
Nussinov, Ruth, et al. "A new precision medicine initiative at the dawn of exascale computing." Signal Transduction and Targeted Therapy 6.1 (2021): 3.
Wohler, Elizabeth, et al. "PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data." Orphanet journal of rare diseases 16 (2021): 1-10.
Pappula, Amrit L., et al. "A genome-wide profiling of glioma patients with an IDH1 mutation using the catalogue of somatic mutations in cancer database." Cancers 13.17 (2021): 4299.
Yazar, Metin, and Pemra Özbek. "In silico tools and approaches for the prediction of functional and structural effects of single-nucleotide polymorphisms on proteins: an expert review." OMICS: A Journal of Integrative Biology 25.1 (2021): 23-37.
Pillich, Rudolf T., et al. "NDEx: accessing network models and streamlining network biology workflows." Current protocols 1.9 (2021): e258.
Tang, Jie, et al. "Single-cell exome sequencing reveals multiple subclones in metastatic colorectal carcinoma." Genome Medicine 13 (2021): 1-14.
Raimondi, Daniele, et al. "Current cancer driver variant predictors learn to recognize driver genes instead of functional variants." BMC biology 19 (2021): 1-12.
Navapour, Leila, and Navid Mogharrab. "In silico screening and analysis of nonsynonymous SNPs in human CYP1A2 to assess possible associations with pathogenicity and cancer susceptibility." Scientific Reports 11.1 (2021): 4977.
Borchert, Florian, et al. "Knowledge bases and software support for variant interpretation in precision oncology." Briefings in Bioinformatics 22.6 (2021): bbab134.
Rogers, Mark F., Tom R. Gaunt, and Colin Campbell. "Prediction of driver variants in the cancer genome via machine learning methodologies." Briefings in bioinformatics 22.4 (2021): bbaa250.
Li, Ling, et al. "Protein synthesis inhibitor omacetaxine is effective against hepatocellular carcinoma." JCI insight 6.12 (2021).
Erkizan, Hayriye Verda, et al. "Exome sequencing identifies novel somatic variants in African American esophageal squamous cell carcinoma." Scientific Reports 11.1 (2021): 14814.
Milanese, Jean-Sébastien, et al. "ETumorMetastasis: a network-based algorithm predicts clinical outcomes using whole-exome sequencing data of cancer patients." Genomics, Proteomics and Bioinformatics 19.6 (2021): 973-985.
Krebs, Fanny S., et al. "Swiss-PO: a new tool to analyze the impact of mutations on protein three-dimensional structures for precision oncology." NPJ precision oncology 5.1 (2021): 19.
Park, Kyung-Sun, et al. "A population-based analysis of BRCA1/2 genes and associated breast and ovarian cancer risk in Korean patients: a multicenter cohort study." Cancers 13.9 (2021): 2192.
Tang, Yun-Yun, et al. "Identification of driver genes based on gene mutational effects and network centrality." BMC bioinformatics 22 (2021): 1-16.
Chen, Lihua, et al. "Identification of somatic genetic alterations using whole-exome sequencing of uterine leiomyosarcoma tumors." Frontiers in Oncology 11 (2021): 687899.
Jagodzińska-Mucha, Paulina, et al. "Mutational landscape of primary and recurrent Ewing sarcoma." Contemporary Oncology/Współczesna Onkologia 25.4 (2021): 241-248.
ElHefnawi, Mahmoud, et al. "Complete genome sequence and bioinformatics analysis of nine Egyptian females with clinical information from different geographic regions in Egypt." Gene 769 (2021): 145237.
Shah, Osama Shiraz, et al. "Identifying genomic alterations in patients with stage IV breast cancer using MammaSeq: an international collaborative study." Clinical Breast Cancer 21.3 (2021): 210-217.
Banerjee, Shayantan, Karthik Raman, and Balaraman Ravindran. "Sequence neighborhoods enable reliable prediction of pathogenic mutations in cancer genomes." Cancers 13.10 (2021): 2366.
Graber, Meghan, et al. "Comprehensive genetic analysis of DGAT2 mutations and gene expression patterns in human cancers." Biology 10.8 (2021): 714.
Fuiten, Allison M., et al. "Genetic analysis of multiple primary melanomas arising within the boundaries of congenital nevi depigmentosa." Pigment cell & melanoma research 34.6 (2021): 1123-1130.
Simpson, Claire L., et al. "Myopia in african Americans is significantly linked to chromosome 7p15. 2-14.2." Investigative ophthalmology & visual science 62.9 (2021): 16-16.
Kader, Bnar Abdul, et al. "EZH2 inhibition in glioblastoma stem cells increases the expression of neuronal genes and the neuronal developmental regulators ZIC2, ZNF423 and MAFB." bioRxiv (2021): 2021-11.
Kader, Bnar Abdul, et al. "EZH2 inhibition in glioblastoma stem cells increases the expression of neuronal genes and the neuronal developmental regulators ZIC2, ZNF423 and MAFB." bioRxiv (2021): 2021-11.
Akin-Bali, D. F., et al. "Comprehensive Mutation Analysis of the RAS/RAF/MEK/ERK Pathway in Paediatric Leukaemia and Significant Inferences." HK J Paediatr (New Series) 26.2 (2021): 75-87.
Nicholas, Thomas J., et al. "OncoGEMINI: software for investigating tumor variants from multiple biopsies with integrated cancer annotations." Genome Medicine 13 (2021): 1-11.
Zuradelli, Monica, et al. "How I faced my prostate cancer: a molecular biologist’s perspective." NPJ Precision Oncology 5.1 (2021): 88.
Agajanian, Steven. "Development of integrated machine learning and data science approaches for the prediction of cancer mutation and autonomous drug discovery of anti-cancer therapeutic agents." (2021).
Zhang, Xi, et al. "Blood-based Genomic and Cellular Determinants of Response to Neoadjuvant PD-1 Blockade in Patients with Non-Small-Cell Lung Cancer." medRxiv (2021): 2021-12.
Monica, Zuradelli, et al. "How I faced my prostate cancer: a molecular biologist’s perspective." NPJ Precision Oncology 5.1 (2021).
Dong, Zhipeng. "ULTRALOW-FREQUENCY MUTATIONAL VARIATIONS REFLECT SPATIAL HETEROGENEITY OF GLIOBLASTOMAS." (2021).
Krysiak, Kilannin, et al. "Evolution of the open-access CIViC knowledgebase is driven by the needs of the cancer variant interpretation community." bioRxiv (2021): 2021-06.
Al Khleifat, Ahmad, et al. "SnpReportR: A Tool for Clinical Reporting of RNAseq Expression and Variants." (2021).
Bonneville, Russell. "Data-Driven Insights into Cancer as a Dynamic Process." (2021).
Bonneville, Russell. "Data-Driven Insights into Cancer as a Dynamic Process." (2021).
Raghu, Aarthy, et al. "Identification of novel somatic cell-free DNA variants by next-generation sequencing in breast cancer patients." International Journal of Molecular and Immuno Oncology 6.1 (2021): 16-26.
Ceesay, Abdoulie K. "Computational Investigation on Structural and Functional Impact of Oncogenes and Tumor Suppressor Genes on Cancer." PQDT-Global (2021).
Banerjee, S., K. Raman, and B. Ravindran. "Sequence Neighborhoods Enable Reliable Prediction of Pathogenic Mutations in Cancer Genomes. Cancers 2021, 13, 2366." (2021).
Graber, M., et al. "Comprehensive Genetic Analysis of DGAT2 Mutations and Gene Expression Patterns in Human Cancers. Biology 2021, 10, 714." (2021).
Duarte Rute, Víctor Manuel. "Evaluación del rendimiento y comparativa de varios métodos de predicción de patogenicidad y priorización de variantes genéticas." (2021).
Anagnostou, Valsamo, et al. "Multimodal genomic features predict outcome of immune checkpoint blockade in non-small-cell lung cancer." Nature cancer 1.1 (2020): 99-111.
Lyu, Jie, et al. "DORGE: Discovery of Oncogenes and tumoR suppressor genes using Genetic and Epigenetic features." Science advances 6.46 (2020): eaba6784.
Chen, Hu, et al. "Comprehensive assessment of computational algorithms in predicting cancer driver mutations." Genome biology 21 (2020): 1-17.
Savage, Paul, et al. "Chemogenomic profiling of breast cancer patient-derived xenografts reveals targetable vulnerabilities for difficult-to-treat tumors." Communications biology 3.1 (2020): 310.
Nelakurti, Devi D., et al. "Comprehensive analysis of MEN1 mutations and their role in cancer." Cancers 12.9 (2020): 2616.
Perry, Jay, et al. "Comprehensive mutational and phenotypic characterization of new metastatic cutaneous squamous cell carcinoma cell lines reveal novel drug susceptibilities." International Journal of Molecular Sciences 21.24 (2020): 9536.
Nelson, Andrew C., et al. "RAS internal tandem duplication disrupts GTPase-activating protein (GAP) binding to activate oncogenic signaling." Journal of Biological Chemistry 295.28 (2020): 9335-9348.
Sjaarda, Calvin P., et al. "Exome sequencing identifies de novo splicing variant in XRCC6 in sporadic case of autism." Journal of Human Genetics 65.3 (2020): 287-296.
Zia, Ayisha, and Sajid Rashid. "Systems biology and integrated computational methods for cancer-associated mutation analysis." 'Essentials of Cancer Genomic, Computational Approaches and Precision Medicine (2020): 335-362.
Chakraborty, Payel, et al. "Novel somatic mutations of the CDH1 gene associated with gastric cancer: prediction of pathogenicity using comprehensive in silico methods." Current Pharmacogenomics and Personalized Medicine (Formerly Current Pharmacogenomics) 17.3 (2020): 182-196.
Abbaspourkharyeki, Malek, Naveen Jayaram Anvekar, and Nallur B. Ramachandra. "The possible role of point mutations and activation of the CDC27 gene in progression of multiple myeloma." Meta Gene 26 (2020): 100761.
Warner, Jeremy L., and Juli D. Klemm. "Informatics Tools for Cancer Research and Care: Bridging the Gap Between Innovation and Implementation." JCO Clinical Cancer Informatics 4 (2020).
Huang, Jinlong, et al. "Selection for Decreased BRCA2 Functional Activity in Homo sapiens After Divergence from the Chimpanzee-Human Last Common Ancestor." bioRxiv (2020): 2020-11.
Kim, Artem. "Exploration of interaction between common and rare variants in genetic susceptibility to holoprosencephaly." (2020).
NAIR, BJ BIPIN, and V. ROHITH. "Transcription Analysis of Primary Genes Causing Endometrial Cancer from Cell Line Analysis." International Journal of Pharmaceutical Research (09752366) 12.3 (2020).
ElHefnawi, Mahmoud, et al. "Complete genome sequence and analysis of nine Egyptian females with clinical information from different geographic regions in Egypt." bioRxiv (2020): 2020-03.
Abbaspourkharyeki, Malek, Naveen Jayaram Anvekar, and Nallur B. Ramachandra. "Genomic landscape of a case of multiple myeloma by whole exome sequencing." (2020): 13-21.
Ma, Yiliang. "Everyone’s Variant Annotation Tool: EVAT." (2020).
Moon, SeongRyeol, et al. "Oncogenic signaling pathways and hallmarks of cancer in Korean patients with acral melanoma." Computers in Biology and Medicine 154 (2023): 106602.