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1. Full Text Oncotator: Cancer Variant Annotation Tool
by Ramos, Alex H and Lichtenstein, Lee and Gupta, Manaswi and Lawrence, Michael S and Pugh, Trevor J and Saksena, Gordon and Meyerson, Matthew and Getz, Gad
Human Mutation, ISSN 1059-7794, 04/2015, Volume 36, Issue 4, pp. E2423 - E2429
Oncotator is a tool for annotating genomic point mutations and short nucleotide insertions/deletions (indels) with variant‐ and gene‐centric information... 
annotation | database | cancer | TCGA | oncotator | Database | Oncotator | Annotation | Cancer | SIGNATURES | LANDSCAPE | SOMATIC MUTATIONS | GENOME | POINT MUTATIONS | PROSTATE-CANCER | GENES | GENETICS & HEREDITY | LUNG ADENOCARCINOMA | CONSEQUENCES | SEQUENCING DATA | Genetic Variation | Neoplasms - metabolism | Computational Biology - methods | Neoplasms - genetics | Humans | Databases, Genetic | Neoplasms - diagnosis | Internet | Genomics - methods | Web Browser | Genomics | Mutation | Index Medicus
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2. Full Text Integrative Clinical Genomics of Advanced Prostate Cancer
by Robinson, Brian D and Robinson, Dan and Van Allen, Eliezer M and Wu, Yi-Mi and Schultz, Nikolaus and Lonigro, Robert J and Mosquera, Juan-Miguel and Montgomery, Bruce and Taplin, Mary-Ellen and Pritchard, Colin C and Attard, Gerhardt and Beltran, Himisha and Abida, Wassim and Bradley, Robert K and Vinson, Jake and Cao, Xuhong and Vats, Pankaj and Kunju, Lakshmi P and Hussain, Maha and Feng, Felix Y and Tomlins, Scott A and Cooney, Kathleen A and Smith, David C and Brennan, Christine and Siddiqui, Javed and Mehra, Rohit and Chen, Yu and Rathkopf, Dana E and Morris, Michael J and Solomon, Stephen B and Durack, Jeremy C and Reuter, Victor E and Gopalan, Anuradha and Gao, Jianjiong and Loda, Massimo and Lis, Rosina T and Bowden, Michaela and Balk, Stephen P and Gaviola, Glenn and Sougnez, Carrie and Gupta, Manaswi and Yu, Evan Y and Mostaghel, Elahe A and Cheng, Heather H and Mulcahy, Hyojeong and True, Lawrence D and Plymate, Stephen R and Dvinge, Heidi and Ferraldeschi, Roberta and Flohr, Penny and Miranda, Susana and Zafeiriou, Zafeiris and Tunariu, Nina and Mateo, Joaquin and Perez-Lopez, Raquel and Demichelis, Francesca and Schiffman, Marc and Nanus, David M and Tagawa, Scott T and Sigaras, Alexandros and Eng, Kenneth W and Elemento, Olivier and Sboner, Andrea and Heath, Elisabeth I and Scher, Howard I and Pienta, Kenneth J and Kantoff, Philip and de Bono, Johann S and Rubin, Mark A and Nelson, Peter S and Garraway, Levi A and Sawyers, Charles L and Chinnaiyan, Arul M
Cell, ISSN 0092-8674, 05/2015, Volume 161, Issue 5, pp. 1215 - 1228
Toward development of a precision medicine framework for metastatic, castration-resistant prostate cancer (mCRPC), we established a multi-institutional... 
HETEROGENEITY | INHIBITION | BIOCHEMISTRY & MOLECULAR BIOLOGY | INCREASED SURVIVAL | MUTATIONS | REARRANGEMENTS | ETS GENE FUSIONS | CHEMOTHERAPY | DISCOVERY | ENZALUTAMIDE | ABIRATERONE | CELL BIOLOGY | Neoplasm Metastasis - genetics | Neoplasm Metastasis - drug therapy | Neoplasm Metastasis - pathology | Humans | Gene Expression Profiling - methods | Male | Mutation | Prostatic Neoplasms, Castration-Resistant - drug therapy | Prostatic Neoplasms, Castration-Resistant - genetics | Prostatic Neoplasms, Castration-Resistant - pathology | Cohort Studies | Genetic research | Genetic aspects | Prostate cancer | Cancer | Index Medicus | precision oncology | transcriptome sequencing | whole exome sequencing | prostate cancer genomics
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3. Full Text The Molecular Taxonomy of Primary Prostate Cancer
by Abeshouse, Adam and Ahn, Jaeil and Akbani, Rehan and Ally, Adrian and Amin, Samirkumar and Andry, Christopher D and Annala, Matti and Aprikian, Armen and Armenia, Joshua and Arora, Arshi and Auman, J. Todd and Balasundaram, Miruna and Balu, Saianand and Barbieri, Christopher E and Bauer, Thomas and Benz, Christopher C and Bergeron, Alain and Beroukhim, Rameen and Berrios, Mario and Bivol, Adrian and Bodenheimer, Tom and Boice, Lori and Bootwalla, Moiz S and Borges dos Reis, Rodolfo and Boutros, Paul C and Bowen, Jay and Bowlby, Reanne and Boyd, Jeffrey and Bradley, Robert K and Breggia, Anne and Brimo, Fadi and Bristow, Christopher A and Brooks, Denise and Broom, Bradley M and Bryce, Alan H and Bubley, Glenn and Burks, Eric and Butterfield, Yaron S.N and Button, Michael and Canes, David and Carlotti, Carlos G and Carlsen, Rebecca and Carmel, Michel and Carroll, Peter R and Carter, Scott L and Cartun, Richard and Carver, Brett S and Chan, June M and Chang, Matthew T and Chen, Yu and Cherniack, Andrew D and Chevalier, Simone and Chin, Lynda and Cho, Juok and Chu, Andy and Chuah, Eric and Chudamani, Sudha and Cibulskis, Kristian and Ciriello, Giovanni and Clarke, Amanda and Cooperberg, Matthew R and Corcoran, Niall M and Costello, Anthony J and Cowan, Janet and Crain, Daniel and Curley, Erin and David, Kerstin and Demchok, John A and Demichelis, Francesca and Dhalla, Noreen and Dhir, Rajiv and Doueik, Alexandre and Drake, Bettina and Dvinge, Heidi and Dyakova, Natalya and Felau, Ina and Ferguson, Martin L and Frazer, Scott and Freedland, Stephen and Fu, Yao and Gabriel, Stacey B and Gao, Jianjiong and Gardner, Johanna and Gastier-Foster, Julie M and Gehlenborg, Nils and Gerken, Mark and Gerstein, Mark B and Getz, Gad and Godwin, Andrew K and Gopalan, Anuradha and Graefen, Markus and Graim, Kiley and Gribbin, Thomas and Guin, Ranabir and Gupta, Manaswi and Hadjipanayis, Angela and Haider, Syed and Hamel, Lucie and Hayes, D. Neil and Heiman, David I and ... and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network
Cell, ISSN 0092-8674, 11/2015, Volume 163, Issue 4, pp. 1011 - 1025
There is substantial heterogeneity among primary prostate cancers, evident in the spectrum of molecular abnormalities and its variable clinical course. As part... 
ACTIVE ANDROGEN RECEPTOR | WHOLE-GENOME | DNA METHYLATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | SPOP | GENOMIC ABERRATIONS | RADICAL PROSTATECTOMY | RECURRENCE | EXPRESSION PROFILES | MUTATIONS | ETS GENE FUSIONS | CELL BIOLOGY | Prostatic Neoplasms - metabolism | Prostatic Neoplasms - pathology | Signal Transduction | Epigenesis, Genetic | Humans | Receptors, Androgen - metabolism | Gene Expression Regulation, Neoplastic | ras Proteins - metabolism | Gene Fusion | Male | Phosphatidylinositol 3-Kinases - metabolism | Neoplasm Metastasis - genetics | Prostatic Neoplasms - genetics | DNA Repair | Mutation | Epigenetic inheritance | Prostate cancer | Analysis | Genomics | Index Medicus
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4. Full Text Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma
by Raphael, Benjamin J and Hruban, Ralph H and Aguirre, Andrew J and Moffitt, Richard A and Yeh, Jen Jen and Stewart, Chip and Robertson, A. Gordon and Cherniack, Andrew D and Gupta, Manaswi and Getz, Gad and Gabriel, Stacey B and Meyerson, Matthew and Cibulskis, Carrie and Fei, Suzanne S and Hinoue, Toshinori and Shen, Hui and Laird, Peter W and Ling, Shiyun and Lu, Yiling and Mills, Gordon B and Akbani, Rehan and Loher, Phillipe and Londin, Eric R and Rigoutsos, Isidore and Telonis, Aristeidis G and Gibb, Ewan A and Goldenberg, Anna and Mezlini, Aziz M and Hoadley, Katherine A and Collisson, Eric and Lander, Eric and Murray, Bradley A and Hess, Julian and Rosenberg, Mara and Bergelson, Louis and Zhang, Wei and Zhang, Hailei and Zhang, Jiashan (Julia) and Zhang, Lizhi and Cho, Juok and Tiao, Grace and Kim, Seong Hoon and Kim, Hark and Kim, Jaegil and Kim, Paula and Kim, Yong Hoon and Livitz, Dimitri and Leshchiner, Ignaty and Reardon, Brendan and Van Allen, Eliezer and Kamburov, Atanas and Beroukhim, Rameen and Saksena, Gordon and Schumacher, Steven E and Noble, Michael S and Heiman, David I and Gehlenborg, Nils and Lawrence, Michael S and Adsay, Volkan and Petersen, Gloria and Klimstra, David and Bardeesy, Nabeel and Leiserson, Mark D.M and Bowlby, Reanne and Kasaian, Katayoon and Birol, Inanc and Mungall, Andrew J and Mungall, Karen L and Sadeghi, Sara and Weinstein, John N and Spellman, Paul T and Liu, Yuexin and Liu, Jia and Amundadottir, Laufey T and Tepper, Joel and Singhi, Aatur D and Dhir, Rajiv and Paul, Drwiega and Smyrk, Thomas and Bowen, Jay and Frick, Jessica and Gastier-Foster, Julie M and Gerken, Mark and Lau, Kevin and Leraas, Kristen M and Lichtenberg, Tara M and Ramirez, Nilsa C and Renkel, Jeremy and Sherman, Mark and Wise, Lisa and Yena, Peggy and Zmuda, Erik and Shih, Juliann and Ally, Adrian and Balasundaram, Miruna and Carlsen, Rebecca and Chu, Andy and Chuah, Eric and Clarke, Amanda and Dhalla, Noreen and ... and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network. Electronic address: andrew_aguirre@dfci.harvard.edu and Cancer Genome Atlas Research Network
Cancer Cell, ISSN 1535-6108, 08/2017, Volume 32, Issue 2, pp. 185 - 203.e13
We performed integrated genomic, transcriptomic, and proteomic profiling of 150 pancreatic ductal adenocarcinoma (PDAC) specimens, including samples with... 
molecular subtypes | pancreatic cancer | PDAC | tumor cellularity | genomics | miRNA | RPPA | KRAS | heterogeneity | TCGA | PHASE PROTEIN ARRAY | HEREDITARY PANCREATITIS | CANCER GENES | LONG NONCODING RNA | DNA METHYLATION | ONCOLOGY | HNF1A-AS1 REGULATES PROLIFERATION | MUTATIONAL LANDSCAPE | TUMOR-SUPPRESSOR | COPY-NUMBER ALTERATION | SEQUENCING REVEALS | CELL BIOLOGY | Pancreatic Neoplasms - metabolism | Proto-Oncogene Proteins p21(ras) - genetics | Humans | Carcinoma, Pancreatic Ductal - metabolism | Gene Expression Regulation, Neoplastic | Pancreatic Neoplasms - genetics | Gene Expression Profiling | Transcriptome - genetics | Proteome - analysis | Mutation - genetics | Carcinoma, Pancreatic Ductal - genetics | DNA Methylation | Epigenesis, Genetic - genetics | Genomics - methods | Adenocarcinoma | RNA | Analysis | Pancreatic cancer | Genomics | Stem cells | Genetic aspects | Tumor proteins | Transforming growth factors | Cancer | MicroRNA | Index Medicus
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5. Full Text Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma
by Fishbein, Lauren and Leshchiner, Ignaty and Walter, Vonn and Danilova, Ludmila and Robertson, A. Gordon and Johnson, Amy R and Lichtenberg, Tara M and Murray, Bradley A and Ghayee, Hans K and Else, Tobias and Ling, Shiyun and Jefferys, Stuart R and de Cubas, Aguirre A and Wenz, Brandon and Korpershoek, Esther and Amelio, Antonio L and Makowski, Liza and Rathmell, W. Kimryn and Gimenez-Roqueplo, Anne-Paule and Giordano, Thomas J and Asa, Sylvia L and Tischler, Arthur S and Akbani, Rehan and Ally, Adrian and Amar, Laurence and Arachchi, Harindra and Auchus, Richard J and Auman, J. Todd and Baertsch, Robert and Balasundaram, Miruna and Balu, Saianand and Bartsch, Detlef K and Baudin, Eric and Bauer, Thomas and Beaver, Allison and Benz, Christopher and Beroukhim, Rameen and Beuschlein, Felix and Bodenheimer, Tom and Boice, Lori and Bowen, Jay and Bowlby, Reanne and Brooks, Denise and Carlsen, Rebecca and Carter, Suzie and Cassol, Clarissa A and Cherniack, Andrew D and Chin, Lynda and Cho, Juok and Chuah, Eric and Chudamani, Sudha and Cope, Leslie and Crain, Daniel and Curley, Erin and de Krijger, Ronald R and Demchok, John A and Deutschbein, Timo and Dhalla, Noreen and Dimmock, David and Dinjens, Winand N.M and Eng, Charis and Eschbacher, Jennifer and Fassnacht, Martin and Felau, Ina and Feldman, Michael and Ferguson, Martin L and Fiddes, Ian and Frazer, Scott and Gabriel, Stacey B and Gardner, Johanna and Gastier-Foster, Julie M and Gehlenborg, Nils and Gerken, Mark and Getz, Gad and Geurts, Jennifer and Goldman, Mary and Graim, Kiley and Gupta, Manaswi and Haan, David and Hahner, Stefanie and Hantel, Constanze and Haussler, David and Hayes, D. Neil and Heiman, David I and Hoadley, Katherine A and Holt, Robert A and Hoyle, Alan P and Huang, Mei and Hunt, Bryan and Hutter, Carolyn M and Jones, Steven J.M and Jones, Corbin D and Kasaian, Katayoon and Kebebew, Electron and Kim, Jaegil and Kimes, Patrick and Knijnenburg, Theo and Lander, Eric and Lawrence, Michael S and Lechan, Ronald and ... and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network
Cancer Cell, ISSN 1535-6108, 02/2017, Volume 31, Issue 2, pp. 181 - 193
We report a comprehensive molecular characterization of pheochromocytomas and paragangliomas (PCCs/PGLs), a rare tumor type. Multi-platform integration... 
metastasis | CSDE1 | pheochromocytoma | genomics | expression subtypes | MAML3 | TCGA | paraganglioma | sequencing | molecular profiling | RET | SPORADIC PHEOCHROMOCYTOMA | STEM-CELLS | ONCOLOGY | GENE-EXPRESSION | DIFFERENTIATION | CANCER | TUMORS | CARCINOMA | SOMATIC MUTATIONS | RNA-BINDING PROTEIN | CELL BIOLOGY | RNA-Binding Proteins - genetics | Paraganglioma - genetics | Pheochromocytoma - etiology | Humans | Middle Aged | Gene Fusion | Male | Transcription Factors - genetics | DNA-Binding Proteins - genetics | Pol1 Transcription Initiation Complex Proteins - genetics | Paraganglioma - etiology | Aged, 80 and over | Adult | Female | Pheochromocytoma - genetics | Aged | Mutation | Nuclear Proteins - genetics | Proto-Oncogene Proteins c-ret - genetics | Gene mutations | Analysis | Disease susceptibility | Pheochromocytoma | Index Medicus
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6. Full Text Tubercular myelofibrosis: A rare presentation of a common disease
by Kumar, Nilesh and Kannauje, Pankaj and Chaubey, Manaswi and Gupta, K K
The Journal of the Association of Physicians of India, ISSN 0004-5772, 01/2016, Volume 64, Issue 1, p. 50
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7. Full Text Multi-environment model estimation for motility analysis of Caenorhabditis elegans
by Sznitman, Raphael and Gupta, Manaswi and Hager, Gregory D and Arratia, Paulo E and Sznitman, Josué
PLoS ONE, ISSN 1932-6203, 2010, Volume 5, Issue 7, pp. e11631 - e11631
The nematode Caenorhabditis elegans is a well-known model organism used to investigate fundamental questions in biology. Motility assays of this small... 
SYSTEM | GENE | GAIT | MULTIDISCIPLINARY SCIENCES | TRACKING | NEMATODE C. ELEGANS | BEHAVIORAL PHENOTYPES | LOCOMOTION | MACHINE VISION | LINEAGE | Caenorhabditis elegans - physiology | Algorithms | Animals | Models, Statistical | Locomotion - physiology | Caenorhabditis elegans | Image processing | Locomotives | Models | Equipment and supplies | Nematoda | Microfluidics | Computer programs | Statistical analysis | Oligodendrocyte-myelin glycoprotein | Motility | Segmentation | Computational fluid dynamics | Laboratories | Pattern recognition | Substrates | Computer science | Studies | Image segmentation | Statistical models | Morphology | Nematodes | Environment | International conferences | Standard deviation | Swimming | Mathematical models | Behavior | Localization | Index Medicus | Computer Science - Computer Vision and Pattern Recognition
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