1000 Genomes Project C, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA: An integrated map of genetic variation from 1,092 human genomes. Nature. 2012, 491 (7422): 56-65. 10.1038/nature11632.
Google Scholar
Capriotti E, Nehrt NL, Kann MG, Bromberg Y: Bioinformatics for personal genome interpretation. Brief Bioinform. 2012, 13 (4): 495-512. 10.1093/bib/bbr070.
PubMed Central
PubMed
Google Scholar
Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, Shendure J: Exome sequencing as a tool for Mendelian disease gene discovery. Nature reviews Genetics. 2011, 12 (11): 745-755. 10.1038/nrg3031.
CAS
PubMed
Google Scholar
Stratton MR, Campbell PJ, Futreal PA: The cancer genome. Nature. 2009, 458 (7239): 719-724. 10.1038/nature07943.
PubMed Central
CAS
PubMed
Google Scholar
Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S, Biankin AV, Bignell GR, Bolli N, Borg A, Borresen-Dale AL, et al: Signatures of mutational processes in human cancer. Nature. 2013, 500 (7463): 415-421. 10.1038/nature12477.
PubMed Central
CAS
PubMed
Google Scholar
Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin ML, Ordonez GR, Bignell GR, et al: A comprehensive catalogue of somatic mutations from a human cancer genome. Nature. 2010, 463 (7278): 191-196. 10.1038/nature08658.
PubMed Central
CAS
PubMed
Google Scholar
Ciriello G, Miller ML, Aksoy BA, Senbabaoglu Y, Schultz N, Sander C: Emerging landscape of oncogenic signatures across human cancers. Nature genetics. 2013, 45 (10): 1127-1133. 10.1038/ng.2762.
PubMed Central
CAS
PubMed
Google Scholar
Garraway LA, Lander ES: Lessons from the cancer genome. Cell. 2013, 153 (1): 17-37. 10.1016/j.cell.2013.03.002.
CAS
PubMed
Google Scholar
Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA, Kinzler KW: Cancer genome landscapes. Science. 2013, 339 (6127): 1546-1558. 10.1126/science.1235122.
PubMed Central
CAS
PubMed
Google Scholar
Cancer Genome Atlas Research N, Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM: The Cancer Genome Atlas Pan-Cancer analysis project. Nature genetics. 2013, 45 (10): 1113-1120. 10.1038/ng.2764.
Google Scholar
Raphael BJ, Dobson JR, Oesper L, Vandin F: Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine. Genome medicine. 2014, 6 (1): 5-10.1186/gm524.
PubMed Central
PubMed
Google Scholar
Fernald GH, Capriotti E, Daneshjou R, Karczewski KJ, Altman RB: Bioinformatics challenges for personalized medicine. Bioinformatics. 2011, 27 (13): 1741-1748. 10.1093/bioinformatics/btr295.
PubMed Central
CAS
PubMed
Google Scholar
Ding L, Wendl MC, McMichael JF, Raphael BJ: Expanding the computational toolbox for mining cancer genomes. Nature reviews Genetics. 2014, 15 (8): 556-570. 10.1038/nrg3767.
PubMed Central
CAS
PubMed
Google Scholar
Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, et al: Computational approaches to identify functional genetic variants in cancer genomes. Nature methods. 2013, 10 (8): 723-729. 10.1038/nmeth.2562.
PubMed Central
CAS
PubMed
Google Scholar
Pabinger S, Dander A, Fischer M, Snajder R, Sperk M, Efremova M, Krabichler B, Speicher MR, Zschocke J, Trajanoski Z: A survey of tools for variant analysis of next-generation genome sequencing data. Briefings in bioinformatics. 2014, 15 (2): 256-278. 10.1093/bib/bbs086.
PubMed Central
PubMed
Google Scholar
Wang Q, Jia P, Li F, Chen H, Ji H, Hucks D, Dahlman KB, Pao W, Zhao Z: Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers. Genome medicine. 2013, 5 (10): 91-10.1186/gm495.
PubMed Central
PubMed
Google Scholar
Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25 (14): 1754-1760. 10.1093/bioinformatics/btp324.
PubMed Central
CAS
PubMed
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome biology. 2009, 10 (3): R25-10.1186/gb-2009-10-3-r25.
PubMed Central
PubMed
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S: The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009, 25 (16): 2078-2079. 10.1093/bioinformatics/btp352.
PubMed Central
PubMed
Google Scholar
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, et al: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome research. 2010, 20 (9): 1297-1303. 10.1101/gr.107524.110.
PubMed Central
CAS
PubMed
Google Scholar
Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK: VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome research. 2012, 22 (3): 568-576. 10.1101/gr.129684.111.
PubMed Central
CAS
PubMed
Google Scholar
Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G: Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nature biotechnology. 2013, 31 (3): 213-219. 10.1038/nbt.2514.
CAS
PubMed
Google Scholar
Bansal V: A statistical method for the detection of variants from next-generation resequencing of DNA pools. Bioinformatics. 2010, 26 (12): i318-324. 10.1093/bioinformatics/btq214.
PubMed Central
CAS
PubMed
Google Scholar
Wei Z, Wang W, Hu P, Lyon GJ, Hakonarson H: SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data. Nucleic acids research. 2011, 39 (19): e132-10.1093/nar/gkr599.
PubMed Central
CAS
PubMed
Google Scholar
Shiraishi Y, Sato Y, Chiba K, Okuno Y, Nagata Y, Yoshida K, Shiba N, Hayashi Y, Kume H, Homma Y, et al: An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data. Nucleic acids research. 2013, 41 (7): e89-10.1093/nar/gkt126.
PubMed Central
CAS
PubMed
Google Scholar
Roth A, Ding J, Morin R, Crisan A, Ha G, Giuliany R, Bashashati A, Hirst M, Turashvili G, Oloumi A, et al: JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. Bioinformatics. 2012, 28 (7): 907-913. 10.1093/bioinformatics/bts053.
PubMed Central
CAS
PubMed
Google Scholar
Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, Ley TJ, Mardis ER, Wilson RK, Ding L: SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics. 2012, 28 (3): 311-317. 10.1093/bioinformatics/btr665.
PubMed Central
CAS
PubMed
Google Scholar
Saunders CT, Wong WS, Swamy S, Becq J, Murray LJ, Cheetham RK: Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics. 2012, 28 (14): 1811-1817. 10.1093/bioinformatics/bts271.
CAS
PubMed
Google Scholar
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K: dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001, 29 (1): 308-311. 10.1093/nar/29.1.308.
PubMed Central
CAS
PubMed
Google Scholar
Cingolani P, Patel VM, Coon M, Nguyen T, Land SJ, Ruden DM, Lu X: Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift. Frontiers in genetics. 2012, 3: 35-
PubMed Central
PubMed
Google Scholar
Wang K, Li M, Hakonarson H: ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic acids research. 2010, 38 (16): e164-10.1093/nar/gkq603.
PubMed Central
PubMed
Google Scholar
Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM: A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012, 6 (2): 80-92. 10.4161/fly.19695.
PubMed Central
CAS
PubMed
Google Scholar
McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F: Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics. 2010, 26 (16): 2069-2070. 10.1093/bioinformatics/btq330.
PubMed Central
CAS
PubMed
Google Scholar
Wilks C, Cline MS, Weiler E, Diehkans M, Craft B, Martin C, Murphy D, Pierce H, Black J, Nelson D, et al: The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data. Database : the journal of biological databases and curation. 2014, 2014:
Google Scholar
International Cancer Genome C, Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, Bernabe RR, Bhan MK, Calvo F, Eerola I, et al: International network of cancer genome projects. Nature. 2010, 464 (7291): 993-998. 10.1038/nature08987.
Google Scholar
Watson IR, Takahashi K, Futreal PA, Chin L: Emerging patterns of somatic mutations in cancer. Nature reviews Genetics. 2013, 14 (10): 703-718. 10.1038/nrg3539.
PubMed Central
CAS
PubMed
Google Scholar
Wheeler DA, Wang L: From human genome to cancer genome: the first decade. Genome research. 2013, 23 (7): 1054-1062. 10.1101/gr.157602.113.
PubMed Central
CAS
PubMed
Google Scholar
Cancer Genome Atlas Research N: Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008, 455 (7216): 1061-1068. 10.1038/nature07385.
Google Scholar
Cancer Genome Atlas N: Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012, 487 (7407): 330-337. 10.1038/nature11252.
Google Scholar
Cancer Genome Atlas N: Comprehensive molecular portraits of human breast tumours. Nature. 2012, 490 (7418): 61-70. 10.1038/nature11412.
Google Scholar
Biankin AV, Waddell N, Kassahn KS, Gingras MC, Muthuswamy LB, Johns AL, Miller DK, Wilson PJ, Patch AM, Wu J, et al: Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nature. 2012, 491 (7424): 399-405. 10.1038/nature11547.
PubMed Central
CAS
PubMed
Google Scholar
Cancer Genome Atlas Research N: Integrated genomic analyses of ovarian carcinoma. Nature. 2011, 474 (7353): 609-615. 10.1038/nature10166.
Google Scholar
Cancer Genome Atlas Research N: Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012, 489 (7417): 519-525. 10.1038/nature11404.
Google Scholar
Stephens PJ, Tarpey PS, Davies H, Van Loo P, Greenman C, Wedge DC, Nik-Zainal S, Martin S, Varela I, Bignell GR, et al: The landscape of cancer genes and mutational processes in breast cancer. Nature. 2012, 486 (7403): 400-404.
PubMed Central
CAS
PubMed
Google Scholar
Sadelain M, Papapetrou EP, Bushman FD: Safe harbours for the integration of new DNA in the human genome. Nature reviews Cancer. 2012, 12 (1): 51-58.
CAS
Google Scholar
Lawrence MS, Stojanov P, Mermel CH, Robinson JT, Garraway LA, Golub TR, Meyerson M, Gabriel SB, Lander ES, Getz G: Discovery and saturation analysis of cancer genes across 21 tumour types. Nature. 2014, 505 (7484): 495-501. 10.1038/nature12912.
PubMed Central
CAS
PubMed
Google Scholar
Davoli T, Xu AW, Mengwasser KE, Sack LM, Yoon JC, Park PJ, Elledge SJ: Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. Cell. 2013, 155 (4): 948-962. 10.1016/j.cell.2013.10.011.
PubMed Central
CAS
PubMed
Google Scholar
Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, Xie M, Zhang Q, McMichael JF, Wyczalkowski MA, et al: Mutational landscape and significance across 12 major cancer types. Nature. 2013, 502 (7471): 333-339. 10.1038/nature12634.
PubMed Central
CAS
PubMed
Google Scholar
Tamborero D, Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Kandoth C, Reimand J, Lawrence MS, Getz G, Bader GD, Ding L, et al: Comprehensive identification of mutational cancer driver genes across 12 tumor types. Scientific reports. 2013, 3: 2650-
PubMed Central
PubMed
Google Scholar
An O, Pendino V, D'Antonio M, Ratti E, Gentilini M, Ciccarelli FD: NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes. Database : the journal of biological databases and curation. 2014, 2014: bau015-
PubMed
Google Scholar
Porta-Pardo E, Hrabe T, Godzik A: Cancer3D: understanding cancer mutations through protein structures. Nucleic acids research. 2014
Google Scholar
Capriotti E, Altman RB: Improving the prediction of disease-related variants using protein three-dimensional structure. BMC Bioinformatics. 2011, 12 (Suppl 4): S3-10.1186/1471-2105-12-S4-S3.
PubMed Central
CAS
PubMed
Google Scholar
Lahti JL, Tang GW, Capriotti E, Liu T, Altman RB: Bioinformatics and variability in drug response: a protein structural perspective. J R Soc Interface. 2012, 9 (72): 1409-1437. 10.1098/rsif.2011.0843.
PubMed Central
CAS
PubMed
Google Scholar
Li B, Seligman C, Thusberg J, Miller JL, Auer J, Whirl-Carrillo M, Capriotti E, Klein TE, Mooney SD: In silico comparative characterization of pharmacogenomic missense variants. BMC Genomics. 2014, 15 (Suppl 4): S4-10.1186/1471-2164-15-S4-S4.
PubMed Central
PubMed
Google Scholar
Rose PW, Bi C, Bluhm WF, Christie CH, Dimitropoulos D, Dutta S, Green RK, Goodsell DS, Prlic A, Quesada M, et al: The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res. 2013, 41 (Database): D475-482.
PubMed Central
CAS
PubMed
Google Scholar
Porta-Pardo E, Godzik A: e-Driver: a novel method to identify protein regions driving cancer. Bioinformatics. 2014, 30 (21): 3109-3114. 10.1093/bioinformatics/btu499.
PubMed Central
PubMed
Google Scholar
Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, et al: The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer discovery. 2012, 2 (5): 401-404. 10.1158/2159-8290.CD-12-0095.
PubMed
Google Scholar
Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, et al: Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Science signaling. 2013, 6 (269): pl1-
PubMed Central
PubMed
Google Scholar
Goldman M, Craft B, Swatloski T, Ellrott K, Cline M, Diekhans M, Ma S, Wilks C, Stuart J, Haussler D, et al: The UCSC Cancer Genomics Browser: update 2013. Nucleic acids research. 2013, 41 (Database): D949-954.
PubMed Central
CAS
PubMed
Google Scholar
Park YK, Kang TW, Baek SJ, Kim KI, Kim SY, Lee D, Kim YS: CaGe: A Web-Based Cancer Gene Annotation System for Cancer Genomics. Genomics & informatics. 2012, 10 (1): 33-39. 10.5808/GI.2012.10.1.33.
CAS
Google Scholar
Cheng WC, Chung IF, Chen CY, Sun HJ, Fen JJ, Tang WC, Chang TY, Wong TT, Wang HW: DriverDB: an exome sequencing database for cancer driver gene identification. Nucleic acids research. 2014, 42 (Database): D1048-1054.
PubMed Central
CAS
PubMed
Google Scholar
Gundem G, Perez-Llamas C, Jene-Sanz A, Kedzierska A, Islam A, Deu-Pons J, Furney SJ, Lopez-Bigas N: IntOGen: integration and data mining of multidimensional oncogenomic data. Nature methods. 2010, 7 (2): 92-93. 10.1038/nmeth0210-92.
CAS
PubMed
Google Scholar
Rubio-Perez C, Tamborero D, Schroeder MP, Antolin AA, Deu-Pons J, Perez-Llamas C, Mestres J, Gonzalez-Perez A, Lopez-Bigas N: In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities. Cancer cell. 2015, 27 (3): 382-396. 10.1016/j.ccell.2015.02.007.
CAS
PubMed
Google Scholar
Gonzalez-Perez A, Lopez-Bigas N: Functional impact bias reveals cancer drivers. Nucleic acids research. 2012, 40 (21): e169-10.1093/nar/gks743.
PubMed Central
CAS
PubMed
Google Scholar
Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M: Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic acids research. 2014, 42 (Database): D199-205.
PubMed Central
CAS
PubMed
Google Scholar
Akavia UD, Litvin O, Kim J, Sanchez-Garcia F, Kotliar D, Causton HC, Pochanard P, Mozes E, Garraway LA, Pe'er D: An integrated approach to uncover drivers of cancer. Cell. 2010, 143 (6): 1005-1017. 10.1016/j.cell.2010.11.013.
PubMed Central
CAS
PubMed
Google Scholar
Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, Bignell G, Davies H, Teague J, Butler A, Stevens C, et al: Patterns of somatic mutation in human cancer genomes. Nature. 2007, 446 (7132): 153-158. 10.1038/nature05610.
PubMed Central
CAS
PubMed
Google Scholar
Dees ND, Zhang Q, Kandoth C, Wendl MC, Schierding W, Koboldt DC, Mooney TB, Callaway MB, Dooling D, Mardis ER, et al: MuSiC: identifying mutational significance in cancer genomes. Genome research. 2012, 22 (8): 1589-1598. 10.1101/gr.134635.111.
PubMed Central
CAS
PubMed
Google Scholar
Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, et al: Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 2013, 499 (7457): 214-218. 10.1038/nature12213.
PubMed Central
CAS
PubMed
Google Scholar
Hua X, Xu H, Yang Y, Zhu J, Liu P, Lu Y: DrGaP: a powerful tool for identifying driver genes and pathways in cancer sequencing studies. American journal of human genetics. 2013, 93 (3): 439-451. 10.1016/j.ajhg.2013.07.003.
PubMed Central
CAS
PubMed
Google Scholar
Youn A, Simon R: Identifying cancer driver genes in tumor genome sequencing studies. Bioinformatics. 2011, 27 (2): 175-181. 10.1093/bioinformatics/btq630.
PubMed Central
CAS
PubMed
Google Scholar
Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, et al: Somatic mutations affect key pathways in lung adenocarcinoma. Nature. 2008, 455 (7216): 1069-1075. 10.1038/nature07423.
PubMed Central
CAS
PubMed
Google Scholar
Reimand J, Bader GD: Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. Molecular systems biology. 2013, 9: 637-
PubMed Central
PubMed
Google Scholar
Tamborero D, Gonzalez-Perez A, Lopez-Bigas N: OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes. Bioinformatics. 2013, 29 (18): 2238-2244. 10.1093/bioinformatics/btt395.
CAS
PubMed
Google Scholar
Tian R, Basu MK, Capriotti E: ContrastRank: a new method for ranking putative cancer driver genes and classification of tumor samples. Bioinformatics. 2014, 30 (17): i572-i578. 10.1093/bioinformatics/btu466.
PubMed Central
CAS
PubMed
Google Scholar
Ng PC, Henikoff S: SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003, 31 (13): 3812-3814. 10.1093/nar/gkg509.
PubMed Central
CAS
PubMed
Google Scholar
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR: A method and server for predicting damaging missense mutations. Nature methods. 2010, 7 (4): 248-249. 10.1038/nmeth0410-248.
PubMed Central
CAS
PubMed
Google Scholar
Reva B, Antipin Y, Sander C: Determinants of protein function revealed by combinatorial entropy optimization. Genome biology. 2007, 8 (11): R232-10.1186/gb-2007-8-11-r232.
PubMed Central
PubMed
Google Scholar
1000 Genomes Project Consortium: A map of human genome variation from population-scale sequencing. Nature. 2010, 467 (7319): 1061-1073. 10.1038/nature09534.
Google Scholar
Compiani M, Capriotti E: Computational and theoretical methods for protein folding. Biochemistry. 2013, 52 (48): 8601-8624. 10.1021/bi4001529.
CAS
PubMed
Google Scholar
Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J: A general framework for estimating the relative pathogenicity of human genetic variants. Nature genetics. 2014, 46 (3): 310-315. 10.1038/ng.2892.
PubMed Central
CAS
PubMed
Google Scholar
Capriotti E, Arbiza L, Casadio R, Dopazo J, Dopazo H, Marti-Renom MA: Use of estimated evolutionary strength at the codon level improves the prediction of disease-related protein mutations in humans. Hum Mutat. 2008, 29 (1): 198-204. 10.1002/humu.20628.
PubMed
Google Scholar
Capriotti E, Calabrese R, Casadio R: Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics. 2006, 22 (22): 2729-2734. 10.1093/bioinformatics/btl423.
CAS
PubMed
Google Scholar
Capriotti E, Calabrese R, Fariselli P, Martelli PL, Altman RB, Casadio R: WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation. BMC Genomics. 2013, 14 (Suppl 3): S6-10.1186/1471-2164-14-S3-S6.
PubMed Central
PubMed
Google Scholar
Bromberg Y, Yachdav G, Rost B: SNAP predicts effect of mutations on protein function. Bioinformatics. 2008, 24 (20): 2397-2398. 10.1093/bioinformatics/btn435.
PubMed Central
CAS
PubMed
Google Scholar
Capriotti E, Altman RB, Bromberg Y: Collective judgment predicts disease-associated single nucleotide variants. BMC Genomics. 2013, 14 (Suppl 3): S2-10.1186/1471-2164-14-S3-S2.
PubMed Central
PubMed
Google Scholar
Gonzalez-Perez A, Lopez-Bigas N: Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. American journal of human genetics. 2011, 88 (4): 440-449. 10.1016/j.ajhg.2011.03.004.
PubMed Central
CAS
PubMed
Google Scholar
Shihab HA, Rogers MF, Gough J, Mort M, Cooper DN, Day IN, Gaunt TR, Campbell C: An Integrative Approach to Predicting the Functional Effects of Non-Coding and Coding Sequence Variation. Bioinformatics. 2015
Google Scholar
Capriotti E, Altman RB: A new disease-specific machine learning approach for the prediction of cancer-causing missense variants. Genomics. 2011, 98 (4): 310-317. 10.1016/j.ygeno.2011.06.010.
PubMed Central
CAS
PubMed
Google Scholar
Carter H, Chen S, Isik L, Tyekucheva S, Velculescu VE, Kinzler KW, Vogelstein B, Karchin R: Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. Cancer research. 2009, 69 (16): 6660-6667. 10.1158/0008-5472.CAN-09-1133.
PubMed Central
CAS
PubMed
Google Scholar
Kaminker JS, Zhang Y, Watanabe C, Zhang Z: CanPredict: a computational tool for predicting cancer-associated missense mutations. Nucleic Acids Res. 2007, 35 (Web Server): W595-598. 10.1093/nar/gkm405.
PubMed Central
PubMed
Google Scholar
Shihab HA, Gough J, Cooper DN, Day IN, Gaunt TR: Predicting the functional consequences of cancer-associated amino acid substitutions. Bioinformatics. 2013, 29 (12): 1504-1510. 10.1093/bioinformatics/btt182.
PubMed Central
CAS
PubMed
Google Scholar
Gonzalez-Perez A, Deu-Pons J, Lopez-Bigas N: Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation. Genome medicine. 2012, 4 (11): 89-10.1186/gm390.
PubMed Central
PubMed
Google Scholar
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, et al: Pfam: the protein families database. Nucleic acids research. 2014, 42 (Database): D222-230.
PubMed Central
CAS
PubMed
Google Scholar
Harris SL, Levine AJ: The p53 pathway: positive and negative feedback loops. Oncogene. 2005, 24 (17): 2899-2908. 10.1038/sj.onc.1208615.
CAS
PubMed
Google Scholar
Yuan TL, Cantley LC: PI3K pathway alterations in cancer: variations on a theme. Oncogene. 2008, 27 (41): 5497-5510. 10.1038/onc.2008.245.
PubMed Central
CAS
PubMed
Google Scholar
Rajagopalan H, Bardelli A, Lengauer C, Kinzler KW, Vogelstein B, Velculescu VE: Tumorigenesis: RAF/RAS oncogenes and mismatch-repair status. Nature. 2002, 418 (6901): 934-10.1038/418934a.
CAS
PubMed
Google Scholar
Sparks AB, Morin PJ, Vogelstein B, Kinzler KW: Mutational analysis of the APC/beta-catenin/Tcf pathway in colorectal cancer. Cancer research. 1998, 58 (6): 1130-1134.
CAS
PubMed
Google Scholar
Gazdar AF, Shigematsu H, Herz J, Minna JD: Mutations and addiction to EGFR: the Achilles 'heal' of lung cancers?. Trends in molecular medicine. 2004, 10 (10): 481-486. 10.1016/j.molmed.2004.08.008.
CAS
PubMed
Google Scholar
Momand J, Zambetti GP, Olson DC, George D, Levine AJ: The mdm-2 oncogene product forms a complex with the p53 protein and inhibits p53-mediated transactivation. Cell. 1992, 69 (7): 1237-1245. 10.1016/0092-8674(92)90644-R.
CAS
PubMed
Google Scholar
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, et al: Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America. 2005, 102 (43): 15545-15550. 10.1073/pnas.0506580102.
PubMed Central
CAS
PubMed
Google Scholar
Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, et al: The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic acids research. 2014, 42 (Database): D358-363.
PubMed Central
CAS
PubMed
Google Scholar
Razick S, Magklaras G, Donaldson IM: iRefIndex: a consolidated protein interaction database with provenance. BMC bioinformatics. 2008, 9: 405-10.1186/1471-2105-9-405.
PubMed Central
PubMed
Google Scholar
Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, et al: The Reactome pathway knowledgebase. Nucleic acids research. 2014, 42 (Database): D472-477.
PubMed Central
CAS
PubMed
Google Scholar
Ciriello G, Cerami E, Sander C, Schultz N: Mutual exclusivity analysis identifies oncogenic network modules. Genome research. 2012, 22 (2): 398-406. 10.1101/gr.125567.111.
PubMed Central
CAS
PubMed
Google Scholar
Miller CA, Settle SH, Sulman EP, Aldape KD, Milosavljevic A: Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors. BMC medical genomics. 2011, 4: 34-10.1186/1755-8794-4-34.
PubMed Central
PubMed
Google Scholar
Zhao J, Zhang S, Wu LY, Zhang XS: Efficient methods for identifying mutated driver pathways in cancer. Bioinformatics. 2012, 28 (22): 2940-2947. 10.1093/bioinformatics/bts564.
CAS
PubMed
Google Scholar
Szczurek E, Beerenwinkel N: Modeling mutual exclusivity of cancer mutations. PLoS computational biology. 2014, 10 (3): e1003503-10.1371/journal.pcbi.1003503.
PubMed Central
PubMed
Google Scholar
Leiserson MD, Blokh D, Sharan R, Raphael BJ: Simultaneous identification of multiple driver pathways in cancer. PLoS computational biology. 2013, 9 (5): e1003054-10.1371/journal.pcbi.1003054.
PubMed Central
CAS
PubMed
Google Scholar
Bashashati A, Haffari G, Ding J, Ha G, Lui K, Rosner J, Huntsman DG, Caldas C, Aparicio SA, Shah SP: DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer. Genome biology. 2012, 13 (12): R124-10.1186/gb-2012-13-12-r124.
PubMed Central
PubMed
Google Scholar
Cerami E, Demir E, Schultz N, Taylor BS, Sander C: Automated network analysis identifies core pathways in glioblastoma. PloS one. 2010, 5 (2): e8918-10.1371/journal.pone.0008918.
PubMed Central
PubMed
Google Scholar
Jia P, Zhao Z: VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data. PLoS computational biology. 2014, 10 (2): e1003460-10.1371/journal.pcbi.1003460.
PubMed Central
PubMed
Google Scholar
Vandin F, Upfal E, Raphael BJ: De novo discovery of mutated driver pathways in cancer. Genome research. 2012, 22 (2): 375-385. 10.1101/gr.120477.111.
PubMed Central
CAS
PubMed
Google Scholar
Wendl MC, Wallis JW, Lin L, Kandoth C, Mardis ER, Wilson RK, Ding L: PathScan: a tool for discerning mutational significance in groups of putative cancer genes. Bioinformatics. 2011, 27 (12): 1595-1602. 10.1093/bioinformatics/btr193.
PubMed Central
CAS
PubMed
Google Scholar
Leiserson MD, Vandin F, Wu HT, Dobson JR, Eldridge JV, Thomas JL, Papoutsaki A, Kim Y, Niu B, McLellan M, et al: Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes. Nature genetics. 2015, 47 (2): 106-114.
PubMed Central
CAS
PubMed
Google Scholar
Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, Haussler D, Stuart JM: Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics. 2010, 26 (12): i237-245. 10.1093/bioinformatics/btq182.
PubMed Central
CAS
PubMed
Google Scholar
Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, Buetow KH: PID: the Pathway Interaction Database. Nucleic acids research. 2009, 37 (Database): D674-679. 10.1093/nar/gkn653.
PubMed Central
CAS
PubMed
Google Scholar
Hofree M, Shen JP, Carter H, Gross A, Ideker T: Network-based stratification of tumor mutations. Nature methods. 2013, 10 (11): 1108-1115. 10.1038/nmeth.2651.
CAS
PubMed
Google Scholar
Nowell PC: The clonal evolution of tumor cell populations. Science. 1976, 194 (4260): 23-28. 10.1126/science.959840.
CAS
PubMed
Google Scholar
Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, Cook K, Stepansky A, Levy D, Esposito D, et al: Tumour evolution inferred by single-cell sequencing. Nature. 2011, 472 (7341): 90-94. 10.1038/nature09807.
PubMed Central
CAS
PubMed
Google Scholar
Zong C, Lu S, Chapman AR, Xie XS: Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science. 2012, 338 (6114): 1622-1626. 10.1126/science.1229164.
PubMed Central
CAS
PubMed
Google Scholar
Carter SL, Cibulskis K, Helman E, McKenna A, Shen H, Zack T, Laird PW, Onofrio RC, Winckler W, Weir BA, et al: Absolute quantification of somatic DNA alterations in human cancer. Nature biotechnology. 2012, 30 (5): 413-421. 10.1038/nbt.2203.
PubMed Central
CAS
PubMed
Google Scholar
Hajirasouliha I, Mahmoody A, Raphael BJ: A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data. Bioinformatics. 2014, 30 (12): i78-86. 10.1093/bioinformatics/btu284.
PubMed Central
CAS
PubMed
Google Scholar
Jiao W, Vembu S, Deshwar AG, Stein L, Morris Q: Inferring clonal evolution of tumors from single nucleotide somatic mutations. BMC bioinformatics. 2014, 15: 35-10.1186/1471-2105-15-35.
PubMed Central
PubMed
Google Scholar
Roth A, Khattra J, Yap D, Wan A, Laks E, Biele J, Ha G, Aparicio S, Bouchard-Cote A, Shah SP: PyClone: statistical inference of clonal population structure in cancer. Nature methods. 2014, 11 (4): 396-398. 10.1038/nmeth.2883.
CAS
PubMed
Google Scholar
Fischer A, Vazquez-Garcia I, Illingworth CJ, Mustonen V: High-definition reconstruction of clonal composition in cancer. Cell reports. 2014, 7 (5): 1740-1752. 10.1016/j.celrep.2014.04.055.
PubMed Central
CAS
PubMed
Google Scholar
Miller CA, White BS, Dees ND, Griffith M, Welch JS, Griffith OL, Vij R, Tomasson MH, Graubert TA, Walter MJ, et al: SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution. PLoS computational biology. 2014, 10 (8): e1003665-10.1371/journal.pcbi.1003665.
PubMed Central
PubMed
Google Scholar
Mali P, Esvelt KM, Church GM: Cas9 as a versatile tool for engineering biology. Nature methods. 2013, 10 (10): 957-963. 10.1038/nmeth.2649.
PubMed Central
CAS
PubMed
Google Scholar
El Emam K: Methods for the de-identification of electronic health records for genomic research. Genome medicine. 2011, 3 (4): 25-10.1186/gm239.
PubMed Central
PubMed
Google Scholar
Paltoo DN, Rodriguez LL, Feolo M, Gillanders E, Ramos EM, Rutter JL, Sherry S, Wang VO, Bailey A, Baker R, et al: Data use under the NIH GWAS data sharing policy and future directions. Nature genetics. 2014, 46 (9): 934-938. 10.1038/ng.3062.
PubMed Central
PubMed
Google Scholar
Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, et al: Finding Our Way through Phenotypes. PLoS biology. 2015, 13 (1): e1002033-10.1371/journal.pbio.1002033.
PubMed Central
PubMed
Google Scholar
Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, Ding M, Bamford S, Cole C, Ward S, et al: COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic acids research. 2014
Google Scholar
Zhang J, Baran J, Cros A, Guberman JM, Haider S, Hsu J, Liang Y, Rivkin E, Wang J, Whitty B, et al: International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data. Database : the journal of biological databases and curation. 2011, 2011: bar026-
PubMed
Google Scholar
Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, Rahman N, Stratton MR: A census of human cancer genes. Nature reviews Cancer. 2004, 4 (3): 177-183. 10.1038/nrc1299.
PubMed Central
CAS
PubMed
Google Scholar