Comprehensive Characterization of Cancer Driver Genes and Mutations

Steven J. M. Jones | Christopher A. Miller | Joshua M. Stuart | Richard A. Moore | Amy Y. Chen | Benjamin E. Gross | Matthew H Bailey | Katherine C. Sexton | Ludmila V. Danilova | Joseph A. Galbraith | Lisle E. Mose | Christopher K. Wong | Zachary J. Heins | Ashton C. Berger | David I Heiman | Elizabeth R. Duffy | Michael J. Kendrick | Sheila M. Reynolds | V. Thorsson | E. Giné | S. Gabriel | C. Sander | A. Godzik | R. Wilson | R. Fulton | E. Mardis | R. Gibbs | P. Spellman | R. Mural | G. Getz | M. Meyerson | L. Fulton | N. Nagarajan | D. Schadendorf | J. Cheville | P. Carroll | M. Rubin | C. Fan | C. Perou | D. Murawa | N. Girard | J. Weinstein | G. Mills | P. Park | Erwin G. Van Meir | D. Brat | J. Olson | T. Mikkelsen | N. Lehman | M. Prados | D. Muzny | M. Morgan | L. Lewis | H. Dinh | J. Santibanez | L. Donehower | D. Wheeler | L. Ding | M. McLellan | M. Wendl | Heather K. Schmidt | M. Lawrence | R. Beroukhim | R. Kucherlapati | P. Laird | L. Cope | D. Weisenberger | D. V. Berg | B. Taylor | N. Schultz | M. Ladanyi | D. Hayes | K. Hoadley | S. Balu | Yan Shi | R. Penny | T. Shelton | S. Morris | M. Ferguson | E. Campo | R. Berkowitz | T. Ley | H. Noushmehr | J. Schein | M. Wilkerson | C. Adebamowo | Ekta Khurana | B. O'neill | A. Tischler | B. Karlan | M. Marra | N. Thiessen | A. Mes-Masson | F. Saad | D. Beer | T. Giordano | A. Berchuck | J. Ajani | A. Kibel | F. Cheng | I. Shmulevich | Wei Zhang | R. Karchin | G. Sica | C. Morrison | T. Knijnenburg | A. G. Robertson | Angela Tam | P. Mieczkowski | F. Khuri | C. Kandoth | K. Shannon | Hui Shen | J. Parker | O. Mariani | A. Gonzalez-Perez | N. López-Bigas | C. Tokheim | L. Schmidt | I. Wistuba | G. Ha | D. Huntsman | C. Rubio-Perez | M. Aymerich | D. Tamborero | A. Jimeno | Jaegil Kim | G. Saksena | Douglas Voet | M. Noble | Pei Lin | David I. Heiman | L. Mularoni | R. Govindan | Jianjiong Gao | S. O. Sumer | Yichao Sun | Kane Tse | S. Signoretti | Z. Ju | J. Kocher | T. Ho | Juok Cho | A. Mungall | K. Mungall | E. Appelbaum | C. Fronick | Fengmei Zhao | R. Postier | D. Levine | S. Heath | Adrian Ally | M. Balasundaram | Noreen Dhalla | Darlene Lee | Michael Mayo | R. Akbani | B. Broom | J. Bowen | J. Gastier-Foster | T. Lichtenberg | L. Wise | John A. Demchok | Margi Sheth | H. Sofia | Liming Yang | S. Schumacher | J. Luketich | G. Sauter | W. Richards | R. Bueno | W. Rathmell | R. Thompson | C. Creighton | P. Tamboli | Kyle Chang | Donna Morton | H. Doddapaneni | W. Hale | A. Cherniack | Payal Sipahimalani | R. Carlsen | Candace D. Carter | J. Auman | Donghui Tan | Corbin D. Jones | S. Jefferys | T. Bodenheimer | A. Hoyle | J. Simons | Phillip H. Lai | M. Bootwalla | D. Maglinte | Hailei Zhang | N. Gehlenborg | S. Frazer | C. Benz | C. Yau | Yiling Lu | C. Shelton | J. Gardner | M. Sherman | D. Mallery | J. Paulauskis | Erin E. Curley | C. Vocke | R. Worrell | B. Czerniak | M. Iacocca | B. Rabeno | J. Myers | J. Eckman | Jodi Harr | Kelinda Tucker | L. A. Zach | R. Dhir | T. Pihl | Zhining Wang | R. Tarnuzzer | J. Zhang | J. Slotta-Huspenina | S. Somiari | A. Rao | L. Omberg | M. Schiffman | Therese Bocklage | L. Rozek | T. Schlomm | M. Goodman | Yi Han | Sandy Lee | A. Unterberg | A. Luna | H. Pass | I. Cortés-Ciriano | A. Shabunin | M. Wiznerowicz | G. Barnett | E. Reznik | H. Al-Ahmadie | S. Roman-Roman | R. Rintoul | M. Marino | P. Troncoso | P. Pinto | R. Sheridan | A. Sloan | E. Swisher | T. Hinoue | S. Singer | J. Wilmott | R. Scolyer | J. Barnholtz-Sloan | J. Melamed | D. Bell | M. Birrer | P. Disaia | H. Gabra | Pat Glenn | A. Godwin | K. Smith-McCune | A. Sood | J. Drummond | Jun Li | S. Meng | P. Yena | Min Wang | Wanding Zhou | P. Westervelt | J. Dipersio | L. Danilova | M. Couce | F. Meric-Bernstam | T. Owonikoko | S. Ramalingam | R. Simon | M. Graefen | H. Huland | T. Skelly | A. Lazar | Wenbin Liu | J. Gershenwald | L. Haydu | Linghua Wang | Eduard Porta-Pardo | G. Gao | A. Colaprico | Yuexin Liu | Varsha Dhankani | R. Bowlby | Ken Chen | Samantha J. Caesar-Johnson | Ina Felau | M. Kasapi | C. Hutter | J. Zenklusen | Sudha Chudamani | Jia Liu | Laxmi Lolla | R. Naresh | Qiang Sun | Yunhu Wan | Ye Wu | T. DeFreitas | S. Meier | Brady Bernard | N. Chambwe | R. Kramer | Kalle Leinonen | Michael Miller | A. Hegde | R. Kanchi | Anil Korkut | Han Liang | Shiyun Ling | Kwok-Shing Ng | Jing Wang | Jiexin Zhang | Adam Abeshouse | J. Armenia | D. Chakravarty | W. Chatila | Ritika Kundra | Konnor C. La | Moriah G. Nissan | Angelica Ochoa | Sarah M. Phillips | F. Sánchez-Vega | Jioajiao Wang | Hongxin Zhang | Pavana Anur | Myron Peto | Denise Brooks | K. Kasaian | Yussanne Ma | S. Sadeghi | Tina Wong | A. Berger | C. Cibulskis | Steven E Schumacher | J. Shih | M. Kucherlapati | Amy H. Perou | J. Roach | Matthew G. Soloway | Umadevi Veluvolu | Michelle Bellair | K. Covington | R. Glenn | Jianhong Hu | V. Korchina | Wei Li | Xiuping Liu | E. Shinbrot | Liu Xi | J. Hess | M. Cordes | D. Crain | Kevin R Lau | E. Thompson | M. Gerken | N. Ramirez | E. Zmuda | N. Corcoran | T. Costello | C. Hovens | A. Carvalho | A. Longatto-Filho | R. Reis | C. Scapulatempo-Neto | H. C. Silveira | D. O. Vidal | Andrew Burnette | J. Eschbacher | B. Hermes | Ardene Noss | Rosy Singh | Matthew L. Anderson | Patricia D. Castro | M. Ittmann | B. Kohl | X. Le | Richard A. Thorp | C. Andry | V. Lyadov | O. Paklina | G. Setdikova | M. Tavobilov | C. McPherson | D. Cramer | C. Feltmate | N. Horowitz | M. Muto | C. Raut | A. Malykh | Wendi Barrett | K. Devine | Jordonna Fulop | Q. Ostrom | K. Shimmel | Yingli Wolinsky | F. Giuliante | C. Hagedorn | B. Deyarmin | L. Kvecher | C. Larson | A. Vicha | T. Zelinka | Joseph Bennett | P. Swanson | M. Latour | L. Lacombe | B. Têtu | A. Bergeron | M. McGraw | S. Staugaitis | J. Chabot | H. Hibshoosh | Timothy C. Wang | O. Potapova | Olga Voronina | L. Desjardins | X. Sastre | M. Stern | E. Lipp | S. McCall | Roger R. McLendon | A. Secord | M. Behera | K. Delman | S. Force | K. Magliocca | S. Maithel | A. Pickens | Dong-Myung Shin | Hongzhen Zhang | Wil Eijckenboom | A. Gillis | E. Korpershoek | L. Looijenga | W. Oosterhuis | H. Stoop | E. Zwarthoff | C. Calatozzolo | L. Cuppini | S. Cuzzubbo | F. DiMeco | G. Finocchiaro | L. Mattei | A. Perin | B. Pollo | Chu Chen | J. Houck | Pawadee Lohavanichbutr | A. Hartmann | C. Stoehr | R. Stoehr | H. Taubert | S. Wach | B. Wullich | W. Kycler | K. Chung | Julie M Martin | E. Baudin | G. Bubley | S. Kalkanis | L. Scarpace | A. Guillermo | Phan Thi Hong Hanh | Bui Duc Phu | Yufang Tang | H. Colman | K. Evason | P. Dottino | J. Martignetti | H. Juhl | Teniola Akeredolu | Serghei Stepa | K. Kang | F. Beuschlein | A. Breggia | M. Borad | A. Bryce | V. Chandan | M. Farnell | N. Giama | Karla J. Kopp | C. Moser | D. Nagorney | D. O'Brien | G. Petersen | F. Que | M. Rivera | L. Roberts | R. Smallridge | T. Smyrk | M. Stanton | M. Torbenson | Ju Dong Yang | Lizhi Zhang | F. Brimo | Ana Maria Angulo Gonzalez | C. Behrens | J. Bondaruk | B. Esmaeli | J. Fujimoto | Charles C. Guo | C. Moran | L. Ramondetta | D. Rice | T. Thompson | A. Tsao | P. Hersey | V. Jakrot | Huihui Fan | Hai Hu | N. Wentzensen | N. V. Tien | N. V. Bằng | N. P. Hung | A. Gopalan | Bhuvanesh Singh | C. Landen | K. Jeong | C. Shelley | S. Asa | R. Kelley | A. Deimling | M. Quinn | C. Brewer | D. Rassl | C. Jungk | D. Bertrand | M. Fassnacht | G. Manikhas | W. Linehan | J. Elder | R. Kefford | G. Long | E. Kebebew | R. Dhanasekaran | D. Tirapelli | Joong-Won Park | O. Bathe | Monique Albert | I. Alexopoulou | J. Catto | D. Chesla | S. Cottingham | J. Engel | Edna M. Mora Pinero | J. Parfitt | S. Porten | Mario E. Quintero-Aguiló | K. V. Kessel | T. Carey | P. Ng | C. Bradford | G. Wolf | W. Urba | W. Grizzle | D. Zhou | Song Cao | Q. Gao | R. Madan | C. Bifulco | D. Hoon | C. Shriver | G. Carpino | E. Gaudio | K. Pacak | K. Roggin | A. Kovatich | K. Fong | G. McKercher | R. Saw | A. Spillane | J. Hooke | S. Adebamowo | Kıvanç Birsoy | K. Becker | K. Junker | J. Simko | K. Sexton | Chayaporn Suphavilai | C. Carlotti | S. Baylin | Sue Bell | Amy Davis | R. Duell | Ashley Fehrenbach | J. Hilty | A. Kastl | A. Kendler | Theresa Naska | Kelly Senecal | Suzanne Sifri | R. Warnick | Felicia Williams | S. Gilbert | A. Boussioutas | Wen-Wei Liang | E. Allen | I. D. Bruijn | R. Holt | A. C. D. Carvalho | José H. Fregnani | A. D. Rose | Antonia Sepulveda | Tao Su | W. Edenfield | A. Rienzo | Keun-Young Ahn | Erik Castle | J. Copland | T. Flotte | R. Broaddus | H. Kakavand | Kenneth Lee | G. Mann | Jonathan Stretch | M. Synott | J. Thompson | T. Chan | R. Ghossein | V. Reuter | Thomas B. Broudy | Cyrus Mirsaidi | P. Nair | Paul Drwiega | Judy Miller | Jennifer L. Smith | H. Zaren | A. Metwalli | Hannah P. Yang | C. Goparaju | N. Botnariuc | I. Caraman | M. Cernat | I. Chemencedji | A. Clipca | Serghei Doruc | Ghenadie Gorincioi | Sergiu Mura | Maria Pirtac | Irina Stancul | Diana Tcaciuc | A. Arnaout | John M S Bartlett | H. Sekhon | G. Thomas | Raina A Tamakawa | N. Hayward | H. Timmers | A. Antenucci | F. Facciolo | G. Grazi | R. Merola | R. Krijger | A. Gimenez-Roqueplo | A. Piché | S. Chevalier | C. Farver | N. Pennell | D. Raymond | Cathy Schilero | Kathy Smolenski | J. Borgia | M. Liptay | M. Pool | C. Seder | Mikhail Dinkin | D. Alvaro | M. Bragazzi | V. Cardinale | M. Dubina | F. Moiseenko | K. Janssen | M. Abdel-Rahman | Dina Aziz | C. Cebulla | Bahavna Kumar | James Lang | Randy Mandt | P. Nguyen | R. Pilarski | K. Rai | L. Schoenfield | P. Wakely | P. Hansen | R. Lechan | James Powers | J. Waldmann | P. Tennstedt | Oluwole Olabode | Mark Nelson | J. Chan | J. Phillips | Ruth Steele | Francis A. Carey | I. Forgie | M. Mannelli | M. Carney | Brenda Hernandez | B. Campos | Laura S. Jacobus | M. Knudson | T. Knutson | Deqin Ma | M. Milhem | H. Rosenthal | L. Landrum | R. Mannel | K. Moore | K. Moxley | Joan L. Walker | R. Zuna | M. Feldman | Federico Valdivieso | J. S. Santos | R. Kemp | A. Sankarankuty | K. Agnew | J. Creaney | B. Robinson | Eryn M. Godwin | S. Kendall | Cassaundra Shipman | Andrea Haddad | Jeff Moyer | Lisa A. Peterson | M. Prince | R. Bowman | I. Yang | R. Korst | J. Fantacone-Campbell | B. Drake | B. V. Tine | J. I. Lee | A. Mariamidze | B. Reardon | Venkata Yellapantula | Zixing Wang | E. M. Liu | M. Moncrieff | D. Bigner | T. Patel | J. Henderson | Scott VandenBerg | A. Bossler | Michael Ryan | A. Weerasinghe | Sohini Sengupta | J. Ko | Carrie L. Cibulskis | Walid K. Chatila | Elizabeth L. Appelbaum | Matthew H. Bailey | Fang-fang Wang | N. D. Aredes | A. Sharp | C. Herold‐Mende | J. Marks | R. Moore | Christopher Logothetis | E. Chuah | K. Leraas | R. Sigmund | Josh M Stuart | J. Fulop | Carrie Cibulskis | Beth Hermes | B. Têtu | V. Yellapantula | Ana C. de Carvalho | Antonia R Sepulveda | Qingsong Gao | R. McLendon | C. Guo | K. Chang | Jay Bowen | John M. S. Bartlett | I. Bruijn | Antonia R. Sepulveda | O. Olabode | N. V. Bang | J. Yang | A. Longatto‐Filho | Stephen Baylin | E. Porta-Pardo | J. D. Yang | Yi Han | Walker Hale | A. D. Carvalho | K. Jeong | R. Wilson | Mary McGraw | A. Deimling | D. Muzny | Augustin Luna | Steven J. M. Jones | Karan J. Rai | C. Schilero | G. Petersen | J. Parker | A. G. Robertson | R. Thompson | Tara J. Skelly | Daniel Cramer | Collin J Tokheim | G. Mckercher | Robert W. Holt | M. Stern | A. González-Pérez | Rehan Akbani | Nils Gehlenborg | Praveen Nair | Moiz Bootwalla | David W. Chesla

[1]  Adrian V. Lee,et al.  An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics , 2018, Cell.

[2]  Steven J. M. Jones,et al.  The Immune Landscape of Cancer , 2018, Immunity.

[3]  Li Ding,et al.  Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. , 2018, Cell systems.

[4]  Ken Chen,et al.  Systematic Functional Annotation of Somatic Mutations in Cancer. , 2018, Cancer cell.

[5]  Moriah H Nissan,et al.  OncoKB: A Precision Oncology Knowledge Base. , 2017, JCO precision oncology.

[6]  D. Schadendorf,et al.  Binimetinib versus dacarbazine in patients with advanced NRAS-mutant melanoma (NEMO): a multicentre, open-label, randomised, phase 3 trial. , 2017, The Lancet. Oncology.

[7]  Alexander Lex,et al.  UpSetR: an R package for the visualization of intersecting sets and their properties , 2017, bioRxiv.

[8]  Hannah Carter,et al.  CRAVAT: cancer-related analysis of variants toolkit , 2013, Bioinform..

[9]  J. Sosman,et al.  Novel Targeted Therapies for Metastatic Melanoma , 2017, Cancer journal.

[10]  Trey Ideker,et al.  Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer. , 2017, Cancer discovery.

[11]  C. Sander,et al.  3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets , 2017, Genome Medicine.

[12]  Gill Bejerano,et al.  M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity , 2016, Nature Genetics.

[13]  D. Cacchiarelli,et al.  Phenotypic Characterization of a Comprehensive Set of MAPK1/ERK2 Missense Mutants. , 2016, Cell reports.

[14]  Matthew J. Betts,et al.  Insights into cancer severity from biomolecular interaction mechanisms , 2016, Scientific Reports.

[15]  P. Park,et al.  A molecular portrait of microsatellite instability across multiple cancers , 2016, Nature Communications.

[16]  Li Ding,et al.  Protein-structure-guided discovery of functional mutations across 19 cancer types , 2016, Nature Genetics.

[17]  David L. Masica,et al.  Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure. , 2016, Cancer research.

[18]  K. Kinzler,et al.  Evaluating the evaluation of cancer driver genes , 2016, Proceedings of the National Academy of Sciences.

[19]  Ken Chen,et al.  Hotspot mutations delineating diverse mutational signatures and biological utilities across cancer types , 2016, BMC Genomics.

[20]  A. Gonzalez-Perez,et al.  OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations , 2016, Genome Biology.

[21]  David C. Jones,et al.  Landscape of somatic mutations in 560 breast cancer whole genome sequences , 2016, Nature.

[22]  Robert D. Finn,et al.  The Pfam protein families database: towards a more sustainable future , 2015, Nucleic Acids Res..

[23]  J. Buxbaum,et al.  A SPECTRAL APPROACH INTEGRATING FUNCTIONAL GENOMIC ANNOTATIONS FOR CODING AND NONCODING VARIANTS , 2015, Nature Genetics.

[24]  James Y. Zou.  Analysis of protein-coding genetic variation in 60,706 humans , 2015, Nature.

[25]  David L. Masica,et al.  Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST‐Indel) , 2015, Human mutation.

[26]  Joaquín Dopazo,et al.  A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces , 2015, PLoS Comput. Biol..

[27]  E. V. Van Allen,et al.  Next-generation sequencing to guide cancer therapy , 2015, Genome Medicine.

[28]  Gary D Bader,et al.  Pathway and network analysis of cancer genomes , 2015, Nature Methods.

[29]  B. Vogelstein,et al.  PD-1 blockade in tumors with mismatch repair deficiency. , 2015, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[30]  G. Kempermann.  Faculty Opinions recommendation of Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. , 2015 .

[31]  Jun S. Liu,et al.  The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans , 2015, Science.

[32]  Nicolai J. Birkbak,et al.  Clonal status of actionable driver events and the timing of mutational processes in cancer evolution , 2015, Science Translational Medicine.

[33]  Martin L. Miller,et al.  Mutational landscape determines sensitivity to PD-1 blockade in non–small cell lung cancer , 2015, Science.

[34]  Jessica Zucman-Rossi,et al.  Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets , 2015, Nature Genetics.

[35]  Kern Rei Chng,et al.  Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles , 2015, Nucleic acids research.

[36]  R. Verhaak,et al.  The landscape and therapeutic relevance of cancer-associated transcript fusions , 2014, Oncogene.

[37]  Gary D Bader,et al.  Analysis working group of the International Cancer Genome Consortium , 2015 .

[38]  Dmitry A. Gordenin,et al.  Hypermutation in human cancer genomes: footprints and mechanisms , 2014, Nature Reviews Cancer.

[39]  Adam Godzik,et al.  e-Driver: a novel method to identify protein regions driving cancer , 2014, Bioinform..

[40]  Benjamin J. Raphael,et al.  Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin , 2014, Cell.

[41]  Benjamin J. Raphael,et al.  Expanding the computational toolbox for mining cancer genomes , 2014, Nature Reviews Genetics.

[42]  G. Linette,et al.  Effect of selumetinib vs chemotherapy on progression-free survival in uveal melanoma: a randomized clinical trial. , 2014, JAMA.

[43]  Kai Ye,et al.  MSIsensor: microsatellite instability detection using paired tumor-normal sequence data , 2014, Bioinform..

[44]  J. Shendure,et al.  A general framework for estimating the relative pathogenicity of human genetic variants , 2014, Nature Genetics.

[45]  S. Gabriel,et al.  Discovery and saturation analysis of cancer genes across 21 tumor types , 2014, Nature.

[46]  Dennis C. Friedrich,et al.  Whole-exome sequencing and clinical interpretation of formalin-fixed , paraffin-embedded tumor samples to guide precision cancer medicine , 2014 .

[47]  Renato Martins,et al.  Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens. , 2014, The Journal of molecular diagnostics : JMD.

[48]  Peter J. Park,et al.  The Landscape of Microsatellite Instability in Colorectal and Endometrial Cancer Genomes , 2013, Cell.

[49]  Alex M. Fichtenholtz,et al.  Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing , 2013, Nature Biotechnology.

[50]  G. Mills,et al.  CanDrA: Cancer-Specific Driver Missense Mutation Annotation with Optimized Features , 2013, PloS one.

[51]  Benjamin J. Raphael,et al.  Mutational landscape and significance across 12 major cancer types , 2013, Nature.

[52]  Gary D Bader,et al.  Comprehensive identification of mutational cancer driver genes across 12 tumor types , 2013, Scientific Reports.

[53]  S. Gabriel,et al.  Pan-cancer patterns of somatic copy-number alteration , 2013, Nature Genetics.

[54]  P. A. Futreal,et al.  Emerging patterns of somatic mutations in cancer , 2013, Nature Reviews Genetics.

[55]  David Tamborero,et al.  OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes , 2013, Bioinform..

[56]  David T. W. Jones,et al.  Signatures of mutational processes in human cancer , 2013, Nature.

[57]  Gary D Bader,et al.  Computational approaches to identify functional genetic variants in cancer genomes , 2013, Nature Methods.

[58]  Mark Diekhans,et al.  MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures , 2013, Human Genetics.

[59]  Steven A. Roberts,et al.  Mutational heterogeneity in cancer and the search for new cancer genes , 2014 .

[60]  H. Carter,et al.  Identifying Mendelian disease genes with the Variant Effect Scoring Tool , 2013, BMC Genomics.

[61]  K. Kinzler,et al.  Cancer Genome Landscapes , 2013, Science.

[62]  C. Berking,et al.  MEK162 for patients with advanced melanoma harbouring NRAS or Val600 BRAF mutations: a non-randomised, open-label phase 2 study. , 2013, The Lancet. Oncology.

[63]  I. Adzhubei,et al.  Predicting Functional Effect of Human Missense Mutations Using PolyPhen‐2 , 2013, Current protocols in human genetics.

[64]  Gary D Bader,et al.  Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers , 2013 .

[65]  Tom R. Gaunt,et al.  Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models , 2012, Human mutation.

[66]  Steven A. Roberts,et al.  Mutational heterogeneity in cancer and the search for new cancer-associated genes , 2013 .

[67]  A. Bashashati,et al.  DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer , 2012, Genome Biology.

[68]  A. Gonzalez-Perez,et al.  Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation , 2012, Genome Medicine.

[69]  Lincoln D. Stein,et al.  Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes , 2012, Nature.

[70]  Matthew B. Callaway,et al.  MuSiC: Identifying mutational significance in cancer genomes , 2012, Genome research.

[71]  C. Drake,et al.  Safety and activity of anti-PD-L1 antibody in patients with advanced cancer. , 2012, The New England journal of medicine.

[72]  A. Børresen-Dale,et al.  The landscape of cancer genes and mutational processes in breast cancer , 2012, Nature.

[73]  Gangning Liang,et al.  DNA methylation screening identifies driver epigenetic events of cancer cell survival. , 2012, Cancer cell.

[74]  A. Sivachenko,et al.  Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer , 2012, Nature Genetics.

[75]  Joshua F. McMichael,et al.  Clonal evolution in relapsed acute myeloid leukemia revealed by whole genome sequencing , 2011, Nature.

[76]  C. Sander,et al.  Predicting the functional impact of protein mutations: application to cancer genomics , 2011, Nucleic acids research.

[77]  Hannah Carter,et al.  CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer , 2011, Bioinform..

[78]  H. Hakonarson,et al.  ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data , 2010, Nucleic acids research.

[79]  L. Stein,et al.  A human functional protein interaction network and its application to cancer data analysis , 2010, Genome Biology.

[80]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[81]  Leyla Isik,et al.  Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. , 2009, Cancer research.

[82]  W. Franklin,et al.  Phase I pharmacokinetic and pharmacodynamic study of the oral, small-molecule mitogen-activated protein kinase kinase 1/2 inhibitor AZD6244 (ARRY-142886) in patients with advanced cancers. , 2008, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[83]  N. Schork,et al.  Prediction of cancer driver mutations in protein kinases. , 2008, Cancer research.

[84]  E. Birney,et al.  Patterns of somatic mutation in human cancer genomes , 2007, Nature.

[85]  Marc A. Martí-Renom,et al.  MODBASE: a database of annotated comparative protein structure models and associated resources , 2005, Nucleic Acids Res..

[86]  Jaime Prilusky,et al.  FoldIndex copyright: a simple tool to predict whether a given protein sequence is intrinsically unfolded , 2005, Bioinform..

[87]  J. Beckmann,et al.  FoldIndex©: a simple tool to predict whether a given protein sequence is intrinsically unfolded , 2005 .

[88]  K. Kinzler,et al.  Cancer genes and the pathways they control , 2004, Nature Medicine.

[89]  T. Hubbard,et al.  A census of human cancer genes , 2004, Nature Reviews Cancer.

[90]  S. Henikoff,et al.  Accounting for human polymorphisms predicted to affect protein function. , 2002, Genome research.

[91]  S. Bull,et al.  Tumor microsatellite instability and clinical outcome in young patients with colorectal cancer. , 2000, The New England journal of medicine.