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1. Full Text SeqLib: A C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly
by Wala, Jeremiah and Beroukhim, Rameen
Bioinformatics, ISSN 1367-4803, 2017, Volume 33, Issue 5, pp. 751 - 753
Sequence Alignment | Software | High-Throughput Nucleotide Sequencing - methods | Chromosomes | Sequence Analysis, DNA - methods | Index Medicus | Applications Notes
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2. Full Text CANCER The oncogene makes its escape
by Wala, Jeremiah and Beroukhim, Rameen
Science (American Association for the Advancement of Science), ISSN 0036-8075, 03/2016, Volume 351, Issue 6280, pp. 1398 - 1399
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Sequence Deletion | Translocation, Genetic | Proto-Oncogenes - genetics | Precursor T-Cell Lymphoblastic Leukemia-Lymphoma - genetics | Humans | Chromosome Aberrations | Gene Expression Regulation, Leukemic | Index Medicus
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3. Full Text Pan-cancer patterns of somatic copy number alteration
by Zack, Travis I and Schumacher, Steven E and Carter, Scott L and Cherniack, Andrew D and Saksena, Gordon and Tabak, Barbara and Lawrence, Michael S and Zhang, Cheng-Zhong and Wala, Jeremiah and Mermel, Craig H and Sougnez, Carrie and Gabriel, Stacey B and Hernandez, Bryan and Shen, Hui and Laird, Peter W and Getz, Gad and Meyerson, Matthew and Beroukhim, Rameen
Nature genetics, ISSN 1061-4036, 10/2013, Volume 45, Issue 10, pp. 1134 - 1140
Life Sciences & Biomedicine | Genetics & Heredity | Science & Technology | Genetic Predisposition to Disease | Genetic Association Studies | Mutagenesis | Neoplasms - genetics | Epigenesis, Genetic | Humans | Ploidies | Gene Regulatory Networks | DNA Copy Number Variations | Copy number variations | Pancreatic cancer | Genetic aspects | Research | Tumor proteins | Health aspects | Risk factors | Studies | Genes | DNA methylation | Genomes | Chromosomes | Estimates | Cancer | Index Medicus
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4. Full Text Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas
by Campbell, Joshua D and Alexandrov, Anton and Kim, Jaegil and Wala, Jeremiah and Berger, Alice H and Pedamallu, Chandra Sekhar and Shukla, Sachet A and Guo, Guangwu and Brooks, Angela N and Murray, Bradley A and Imielinski, Marcin and Hu, Xin and Ling, Shiyun and Akbani, Rehan and Rosenberg, Mara and Cibulskis, Carrie and Ramachandran, Aruna and Collisson, Eric A and Kwiatkowski, David J and Lawrence, Michael S and Weinstein, John N and Verhaak, Roel G.W and Wu, Catherine J and Hammerman, Peter S and Cherniack, Andrew D and Getz, Gad and Artyomov, Maxim N and Schreiber, Robert and Govindan, Ramaswamy and Meyerson, Matthew and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network
Nature genetics, ISSN 1061-4036, 06/2016, Volume 48, Issue 6, pp. 607 - 616
Life Sciences & Biomedicine | Genetics & Heredity | Science & Technology | Adenocarcinoma | Usage | Squamous cell carcinoma | Nucleotide sequencing | Risk factors | DNA sequencing | Genomics | Lung cancer | Colleges & universities | Quality control | Defense contracts | Genomes | Mutation | Grants | Signatures | Tumors | Smoking | Index Medicus
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5. Full Text Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes
by Chapuy, Bjoern and Stewart, Chip and Dunford, Andrew J and Kim, Jaegil and Kamburov, Atanas and Redd, Robert A and Lawrence, Mike S and Roemer, Margaretha G. M and Li, Amy J and Ziepert, Marita and Staiger, Annette M and Wala, Jeremiah A and Ducar, Matthew D and Leshchiner, Ignaty and Rheinbay, Ester and Taylor-Weiner, Amaro and Coughlin, Caroline A and Hess, Julian M and Pedamallu, Chandra S and Livitz, Dimitri and Rosebrock, Daniel and Rosenberg, Mara and Tracy, Adam A and Horn, Heike and Van Hummelen, Paul and Feldman, Andrew L and Link, Brian K and Novak, Anne J and Cerhan, James R and Habermann, Thomas M and Siebert, Reiner and Rosenwald, Andreas and Thorner, Aaron R and Meyerson, Matthew L and Golub, Todd R and Beroukhim, Rameen and Wulf, Gerald G and Ott, German and Rodig, Scott J and Monti, Stefano and Neuberg, Donna S and Loeffler, Markus and Pfreundschuh, Michael and Trümper, Lorenz and Getz, Gad and Shipp, Margaret A
Nature medicine, ISSN 1078-8956, 05/2018, Volume 24, Issue 5, pp. 679 - 690
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Medicine, Research & Experimental | Science & Technology | Cell Biology | Research & Experimental Medicine | Lymphoma, Large B-Cell, Diffuse - pathology | Genes, Neoplasm | Humans | Mutation Rate | Treatment Outcome | DNA Copy Number Variations - genetics | Gene Rearrangement - genetics | Mutation - genetics | Lymphoma, Large B-Cell, Diffuse - genetics | Genetic Heterogeneity | Oncology, Experimental | Development and progression | Genetic aspects | Non-Hodgkin's lymphomas | B cells | Research | Identification and classification | Health aspects | Cancer | Deactivation | Stability | Transcription | Pathogenesis | Copy number | p53 Protein | Malignancy | Inactivation | Clustering | Lymphoma | Molecular chains | Genomic instability | Alterations | Lymphocytes B | Genetic analysis | New combinations | Adults | Mutation | Signatures | B-cell lymphoma | Index Medicus
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6. Full Text SvABA: Genome-wide detection of structural variants and indels by local assembly
by Wala, Jeremiah A and Bandopadhayay, Pratiti and Greenwald, Noah F and O’Rourke, Ryan and Sharpe, Ted and Stewart, Chip and Schumacher, Steve and Li, Yilong and Weischenfeldt, Joachim and Yao, Xiaotong and Nusbaum, Chad and Campbell, Peter and Getz, Gad and Meyerson, Matthew and Zhang, Cheng-Zhong and Imielinski, Marcin and Beroukhim, Rameen
Genome research, ISSN 1088-9051, 04/2018, Volume 28, Issue 4, pp. 581 - 591
Biochemistry & Molecular Biology | Genetics & Heredity | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Insertion | Genomes | Gene deletion | Computer applications | Cancer | Index Medicus | Method
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7. Full Text The genomic landscape and evolution of endometrial carcinoma progression and abdominopelvic metastasis
by Gibson, William J and Hoivik, Erling A and Halle, Mari K and Taylor-Weiner, Amaro and Cherniack, Andrew D and Berg, Anna and Holst, Frederik and Zack, Travis I and Werner, Henrica M.J and Staby, Kjersti M and Rosenberg, Mara and Stefansson, Ingunn M and Kusonmano, Kanthida and Chevalier, Aaron and Mauland, Karen K and Trovik, Jone and Krakstad, Camilla and Giannakis, Marios and Hodis, Eran and Woie, Kathrine and Bjorge, Line and Vintermyr, Olav K and Wala, Jeremiah A and Lawrence, Michael S and Getz, Gad and Carter, Scott L and Beroukhim, Rameen and Salvesen, Helga B
Nature genetics, ISSN 1061-4036, 08/2016, Volume 48, Issue 8, pp. 848 - 855
Life Sciences & Biomedicine | Genetics & Heredity | Science & Technology | Complications and side effects | Genome-wide association studies | Endometrial cancer | Gene mutations | Genetic aspects | Metastasis | Health aspects | Risk factors | Methods | Studies | Biomedical research | Biopsy | Software | Mutation | Patients | Tumors | Index Medicus | Precursor | Cancer genomics | Cancer evolution | Cancer
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8. Full Text Patterns of somatic structural variation in human cancer genomes
by Li, Yilong and Roberts, Nicola D and Wala, Jeremiah A and Shapira, Ofer and Schumacher, Steven E and Kumar, Kiran and Khurana, Ekta and Waszak, Sebastian and Korbel, Jan O and Haber, James E and Imielinski, Marcin and Weischenfeldt, Joachim and Beroukhim, Rameen and Campbell, Peter J and Akdemir, Kadir C and Alvarez, Eva G and Baez-Ortega, Adrian and Boutros, Paul C and Bowtell, David D. L and Brors, Benedikt and Burns, Kathleen H and Chan, Kin and Chen, Ken and Cortes-Ciriano, Isidro and Dueso-Barroso, Ana and Dunford, Andrew J and Edwards, Paul A and Estivill, Xavier and Etemadmoghadam, Dariush and Feuerbach, Lars and Fink, J. Lynn and Frenkel-Morgenstern, Milana and Garsed, Dale W and Gerstein, Mark and Gordenin, Dmitry A and Haan, David and Hess, Julian M and Hutter, Barbara and Jones, David T. W and Ju, Young Seok and Kazanov, Marat D and Klimczak, Leszek J and Koh, Youngil and Lee, Eunjung Alice and Lee, Jake June-Koo and Lynch, Andy G and Macintyre, Geoff and Markowetz, Florian and Martincorena, Inigo and Martinez-Fundichely, Alexander and Meyerson, Matthew and Miyano, Satoru and Nakagawa, Hidewaki and Navarro, Fabio C. P and Ossowski, Stephan and Park, Peter J and Pearson, John and Puiggros, Montserrat and Rippe, Karsten and Roberts, Steven A and Rodriguez-Martin, Bernardo and Scully, Ralph and Shackleton, Mark and Sidiropoulos, Nikos and Sieverling, Lina and Stewart, Chip and Torrents, David and Tubio, Jose M. C and Villasante, Izar and Waddell, Nicola and Yang, Lixing and Yao, Xiaotong and Yoon, Sung-Soo and Zamora, Jorge and Zhang, Cheng-Zhong and PCAWG Consortium and PCAWG Struct Variation Working Grp and PCAWG Structural Variation Working Group
Nature (London), ISSN 0028-0836, 02/2020, Volume 578, Issue 7793, pp. 112 - 121
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Genetic Variation | Telomerase - genetics | Neoplasms - genetics | Genomics | Humans | Mutagenesis, Insertional | Gene Rearrangement - genetics | Genome, Human - genetics | Size distribution | Inversions | Genomes | Gene sequencing | Consortia | Liver cancer | Chromosome translocations | Replicating | Reproduction (copying) | Gene rearrangement | Mutation | Variation | Chromosomes | Telomerase | Deoxyribonucleic acid--DNA | Cancer | Tumors | Index Medicus | Cancer genomics | Genomic instability
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9. Full Text The oncogene makes its escape
by Wala, Jeremiah and Beroukhim, Rameen
Science (American Association for the Advancement of Science), ISSN 0036-8075, 03/2016, Volume 351, Issue 6280, pp. 1398 - 1399
Cellular biology | Gene expression | Deoxyribonucleic acid--DNA | Cancer
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10. Full Text Genomic heterogeneity and exceptional response to dual pathway inhibition in anaplastic thyroid cancer
by Gibson, William J and Ruan, Daniel T and Paulson, Vera A and Barletta, Justine A and Hanna, Glenn J and Kraft, Stefan and Calles, Antonio and Nehs, Matthew A and Moore, Francis D and Taylor-Weiner, Amaro and Wala, Jeremiah A and Zack, Travis I and Lee, Thomas C and Fennessy, Fiona M and Alexander, Erik K and Thomas, Tom and Janne, Pasi A and Garraway, Levi A and Carter, Scott L and Beroukhim, Rameen and Lorch, Jochen H and Allen, Eliezer M.Van
Clinical cancer research, ISSN 1078-0432, 05/2017, Volume 23, Issue 9, pp. 2367 - 2373
Life Sciences & Biomedicine | Oncology | Science & Technology | TOR protein | Autopsies | Transcription | MAP kinase | Raf protein | AKT protein | Drug development | Ribonucleic acid--RNA | 1-Phosphatidylinositol 3-kinase | Gene sequencing | Thyroid carcinoma | Thyroid cancer | Pathways | Autopsy | Experimental design | Diagnostic systems | Mutation | Inhibition | Deoxyribonucleic acid--DNA | Tumors | DNA sequencing | Cancer | Thyroid | Index Medicus
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