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1. Full Text Detection and localization of surgically resectable cancers with a multi-analyte blood test
by Cohen, Joshua D and Li, Lu and Wang, Yuxuan and Thoburn, Christopher and Afsari, Bahman and Danilova, Ludmila and Douville, Christopher and Javed, Ammar A and Wong, Fay and Mattox, Austin and Hruban, Ralph. H and Wolfgang, Christopher L and Goggins, Michael G and Molin, Marco Dal and Wang, Tian-Li and Roden, Richard and Klein, Alison P and Ptak, Janine and Dobbyn, Lisa and Schaefer, Joy and Silliman, Natalie and Popoli, Maria and Vogelstein, Joshua T and Browne, James D and Schoen, Robert E and Brand, Randall E and Tie, Jeanne and Gibbs, Peter and Wong, Hui-Li and Mansfield, Aaron S and Jen, Jin and Hanash, Samir M and Falconi, Massimo and Allen, Peter J and Zhou, Shibin and Bettegowda, Chetan and Diaz, Luis A and Tomasetti, Cristian and Kinzler, Kenneth W and Vogelstein, Bert and Lennon, Anne Marie and Papadopoulos, Nickolas
Science (American Association for the Advancement of Science), ISSN 0036-8075, 02/2018, Volume 359, Issue 6378, pp. 926 - 930
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Early Detection of Cancer - economics | Costs and Cost Analysis | Circulating Tumor DNA - genetics | Early Detection of Cancer - methods | Neoplasms - surgery | Humans | Neoplasms - diagnosis | Polymerase Chain Reaction - methods | Neoplasms - blood | Neoplasms - genetics | Hematologic Tests - economics | Neoplasm Proteins - blood | Mutation | Medical examination | Diagnosis | Methods | Blood | Ovarian cancer | Cancer | Stomach | Liver | Biological evolution | Blood tests | Health risks | Patients | Esophagus | Proteins | Liver cancer | Sensitivity | Lungs | Surgery | Biomarkers | Pancreas | Localization | Evolution & development | Deoxyribonucleic acid--DNA | Index Medicus
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2. Full Text Inferring causal molecular networks: empirical assessment through a community-based effort
by Bohler, Anwesha and Evelo, Chris and Kutmon, M and HPN-DREAM Consortium and The HPN-DREAM Consortium
Nature methods, ISSN 1548-7091, 04/2016, Volume 13, Issue 4, pp. 310 - 318
GENE NETWORKS | BAYESIAN NETWORKS | MODELS | SENSITIVITY | VALIDATION | ALGORITHMS | INFERENCE | EXPRESSION DATA | CHALLENGES | SIGNALING NETWORKS | Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biochemical Research Methods | Science & Technology | Signal Transduction | Humans | Computational Biology | Gene Expression Profiling | Gene Regulatory Networks | Systems Biology | Protein Interaction Mapping - methods | Algorithms | Neoplasms - genetics | Models, Biological | Computer Simulation | Software | Tumor Cells, Cultured | Causality | Biological research | Physiological aspects | Cellular signal transduction | Research | Molecular biology | Phosphotransferases | Biology, Experimental | Proteins | Cancer | Index Medicus | Medicin och hälsovetenskap
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3. Full Text A simple and reproducible breast cancer prognostic test
by Marchionni, Luigi and Afsari, Bahman and Geman, Donald and Leek, Jeffrey T
BMC genomics, ISSN 1471-2164, 05/2013, Volume 14, Issue 1, pp. 336 - 336
Gene expression analysis | Genomics | Prediction | Biomarkers | Breast cancer | Top scoring pair | Personalized medicine | Reproducible research | MammaPrint | Genetics & Heredity | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Computational Biology - methods | Reproducibility of Results | Breast Neoplasms - genetics | Prognosis | Humans | Breast Neoplasms - diagnosis | Gene Expression Profiling | Software | Cohort Studies | Medical research | Pharmacogenetics | Medicine, Experimental | Diagnosis | Gene expression | Genetic screening | Cancer | Index Medicus
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4. Full Text SwitchBox: An R package for k-Top Scoring Pairs classifier development
by Afsari, Bahman and Fertig, Elana J and Geman, Donald and Marchionni, Luigi
Bioinformatics, ISSN 1367-4803, 01/2015, Volume 31, Issue 2, pp. 273 - 274
Breast Neoplasms - classification | Computational Biology - methods | Algorithms | Breast Neoplasms - genetics | Humans | Gene Expression Regulation, Neoplastic | Female | Gene Expression Profiling - methods | Neoplasm Recurrence, Local - genetics | Biomarkers, Tumor - genetics | Neoplasm Recurrence, Local - diagnosis | Support Vector Machine | Index Medicus | Applications Notes
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5. Full Text A novel functional splice variant of AKT3 defined by analysis of alternative splice expression in HPV-positive oropharyngeal cancers
by Guo, Theresa and Sakai, Akihiro and Afsari, Bahman and Considine, Michael and Danilova, Ludmila and Favorov, Alexander V and Yegnasubramanian, Srinivasan and Kelley, Dylan Z and Flam, Emily and Ha, Patrick K and Khan, Zubair and Wheelan, Sarah J and Gutkind, J. Silvio and Fertig, Elana J and Gaykalova, Daria A and Califano, Joseph
Cancer research (Chicago, Ill.), ISSN 0008-5472, 10/2017, Volume 77, Issue 19, pp. 5248 - 5258
Life Sciences & Biomedicine | Oncology | Science & Technology | Prognosis | Alternative Splicing | Follow-Up Studies | Carcinoma, Squamous Cell - genetics | Carcinoma, Squamous Cell - pathology | Carcinoma, Squamous Cell - virology | Humans | Middle Aged | Male | Oropharyngeal Neoplasms - pathology | Case-Control Studies | Proto-Oncogene Proteins c-akt - genetics | Papillomavirus Infections - pathology | Young Adult | Adult | Female | Papillomavirus Infections - virology | Oropharyngeal Neoplasms - genetics | Survival Rate | Oropharyngeal Neoplasms - virology | Papillomaviridae - isolation & purification | Papillomavirus Infections - genetics | Adolescent | Aged | Biomarkers, Tumor - genetics | Neoplasm Staging | Alternative splicing | Squamous cell carcinoma | Statistical analysis | Splicing | Genes | Genomes | Statistical methods | Gene expression | Ribonucleic acid--RNA | Carcinogenesis | Incidence | Gene sequencing | Carcinogens | DNA methylation | Head and neck cancer | Tumorigenesis | Mutation | Methylation | In vitro methods and tests | Deoxyribonucleic acid--DNA | Cancer | Tumors | CpG islands | Index Medicus | oropharynx squamous cell carcinoma | outlier analysis | alternative splice expression | AKT3 | HPV
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6. Full Text RANK DISCRIMINANTS FOR PREDICTING PHENOTYPES FROM RNA EXPRESSION
by Bahman Afsari and Ulisses M. Braga-Neto and Donald Geman
The annals of applied statistics, ISSN 1932-6157, 9/2014, Volume 8, Issue 3, pp. 1469 - 1491
Datasets | Discriminants | Phenotypes | Genes | Leukemia | Gene expression | Bioinformatics | Prostate | Tumors | Cancer | Rank discriminant | Cancer classification | Order statistics | Statistics & Probability | Physical Sciences | Mathematics | Science & Technology | order statistics | gene expression | rank discriminant
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7. Full Text Learning Dysregulated Pathways in Cancers from Differential Variability Analysis
by Bahman Afsari and Donald Geman and Elana J. Fertig
Cancer Informatics, ISSN 1176-9351, 10/2014, Volume 2014, Issue Suppl. 5, pp. 61 - 67
Variability analysis | Gene set analysis | Gene expression | Multivariate analysis | Development and progression | Algorithms | Analysis | Cancer
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8. Full Text Non-invasive detection of urothelial cancer through the analysis of driver gene mutations and aneuploidy
by Springer, Simeon U and Chen, Chung-Hsin and Del Carmen Rodriguez Pena, Maria and Li, Lu and Douville, Christopher and Wang, Yuxuan and Cohen, Joshua David and Taheri, Diana and Silliman, Natalie and Schaefer, Joy and Ptak, Janine and Dobbyn, Lisa and Papoli, Maria and Kinde, Isaac and Afsari, Bahman and Tregnago, Aline C and Bezerra, Stephania M and Vandenbussche, Christopher and Fujita, Kazutoshi and Ertoy, Dilek and Cunha, Isabela W and Yu, Lijia and Bivalacqua, Trinity J and Grollman, Arthur P and Diaz, Luis A and Karchin, Rachel and Danilova, Ludmila and Huang, Chao-Yuan and Shun, Chia-Tung and Turesky, Robert J and Yun, Byeong Hwa and Rosenquist, Thomas A and Pu, Yeong-Shiau and Hruban, Ralph H and Tomasetti, Cristian and Papadopoulos, Nickolas and Kinzler, Ken W and Vogelstein, Bert and Dickman, Kathleen G and Netto, George J
eLife, ISSN 2050-084X, 03/2018, Volume 7
Biology | Life Sciences & Biomedicine - Other Topics | Life Sciences & Biomedicine | Science & Technology | Urinary Bladder Neoplasms - urine | Early Detection of Cancer - methods | Urinary Bladder Neoplasms - diagnosis | Carcinoma, Transitional Cell - diagnosis | Carcinoma, Transitional Cell - urine | Humans | Middle Aged | Child, Preschool | Aneuploidy | Male | Genetic Testing - methods | Young Adult | Telomerase - genetics | Urinary Bladder Neoplasms - genetics | Sensitivity and Specificity | Adolescent | Aged, 80 and over | Adult | Female | Aged | Mutation | Child | Carcinoma, Transitional Cell - genetics | Urine | Urothelial cancer | Copy number | Invasiveness | Genes | Cytology | Genomes | FDA approval | Bladder cancer | Urology | Medicine | Pathology | Toxicology | Cellular biology | Public health | Deoxyribonucleic acid--DNA | DNA sequencing | Tumors | Index Medicus
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9. Full Text Integrated analysis of whole-genome ChIP-Seq and RNA-Seq data of primary head and neck tumor samples associates HPV integration sites with open chromatin marks
by Kelley, Dylan Z and Flam, Emily L and Izumchenko, Evgeny and Danilova, Ludmila V and Wulf, Hildegard A and Guo, Theresa and Singman, Dzov A and Afsari, Bahman and Skaist, Alyza M and Considine, Michael and Welch, Jane A and Stavrovskaya, Elena and Bishop, Justin A and Westra, William H and Khan, Zubair and Koch, Wayne M and Sidransky, David and Wheelan, Sarah J and Califano, Joseph A and Favorov, Alexander V and Fertig, Elana J and Gaykalova, Daria A
Cancer research (Chicago, Ill.), ISSN 0008-5472, 12/2017, Volume 77, Issue 23, pp. 6538 - 6550
Life Sciences & Biomedicine | Oncology | Science & Technology | Virus Integration - genetics | Head and Neck Neoplasms - virology | Humans | Chromatin - pathology | Sequence Analysis, DNA | Genome, Human - genetics | Papillomaviridae - genetics | Chromatin Immunoprecipitation | Base Sequence | Cell Line, Tumor | Head and Neck Neoplasms - genetics | Chromatin - genetics | Gene Expression Regulation, Neoplastic - genetics | Enrichment | Chromatin | Squamous cell carcinoma | Integration | Head | Immunoprecipitation | Genomes | Tumor cell lines | Gene expression | Ribonucleic acid--RNA | Gene sequencing | Human papillomavirus | Alterations | Xenografts | Head and neck cancer | Tumorigenesis | Aberration | Mutation | Protocol (computers) | Cancer | Tumors | Index Medicus | Chromatin immunoprecipitation | HPV integration | high-throughput data | histone code | head and neck squamous cell carcinoma
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10. Full Text A multimodality test to guide the management of patients with a pancreatic cyst
by Springer, Simeon and Masica, David L and Molin, Marco Dal and Douville, Christopher and Thoburn, Christopher J and Afsari, Bahman and Li, Lu and Cohen, Joshua D and Thompson, Elizabeth and Allen, Peter J and Klimstra, David S and Schattner, Mark A and Max Schmidt, C and Yip-Schneider, Michele and Simpson, Rachel E and Castillo, Carlos Fernandez-Del and Mino-Kenudson, Mari and Brugge, William and Brand, Randall E and Singhi, Aatur D and Scarpa, Aldo and Lawlor, Rita and Salvia, Roberto and Zamboni, Giuseppe and Hong, Seung-Mo and Hwang, Dae Wook and Jang, Jin-Young and Kwon, Wooil and Swan, Niall and Geoghegan, Justin and Falconi, Massimo and Crippa, Stefano and Doglioni, Claudio and Paulino, Jorge and Schulick, Richard D and Edil, Barish H and Park, Walter and Yachida, Shinichi and Hijioka, Susumu and van Hooft, Jeanin and He, Jin and Weiss, Matthew J and Burkhart, Richard and Makary, Martin and Canto, Marcia I and Goggins, Michael G and Ptak, Janine and Dobbyn, Lisa and Schaefer, Joy and Sillman, Natalie and Popoli, Maria and Klein, Alison P and Tomasetti, Cristian and Karchin, Rachel and Papadopoulos, Nickolas and Kinzler, Kenneth W and Vogelstein, Bert and Wolfgang, Christopher L and Hruban, Ralph H and Lennon, Anne Marie
Science translational medicine, ISSN 1946-6234, 2019, Volume 11, Issue 501, p. eaav4772
Life Sciences & Biomedicine | Medicine, Research & Experimental | Science & Technology | Cell Biology | Research & Experimental Medicine | Learning algorithms | Cysts | Surgery | Management | Pancreas | Patients | Morbidity | Biochemical markers | Index Medicus
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