Now showing items 1-16 of 16

    • Bayesian Adaptive Clinical Trials 

      Zhang, Yifan (2014-10-22)
      Bayesian adaptive designs are emerging as popular approach to develop adaptive clinical trials. In this dissertation, I describe the mathematical steps for computing the theoretical optimal adaptive designs in biomarker-integrated ...
    • BRCA1 Recruitment to Transcriptional Pause Sites Is Required for R-Loop-Driven DNA Damage Repair 

      Hatchi, Elodie; Skourti-Stathaki, Konstantina; Ventz, Steffen; Pinello, Luca; Yen, Angela; Kamieniarz-Gdula, Kinga; Dimitrov, Stoil; Pathania, Shailja; McKinney, Kristine M.; Eaton, Matthew L.; Kellis, Manolis; Hill, Sarah J.; Parmigiani, Giovanni; Proudfoot, Nicholas J.; Livingston, David M. (Cell Press, 2015)
      Summary The mechanisms contributing to transcription-associated genomic instability are both complex and incompletely understood. Although R-loops are normal transcriptional intermediates, they are also associated with ...
    • Comparative Lesion Sequencing Provides Insights into Tumor Evolution 

      Jones, Siân; Chen, Wei-dong; Parmigiani, Giovanni; Diehl, Frank; Beerenwinkel, Niko; Antal, Tibor; Traulsen, Arne; Nowak, Martin A.; Siegel, Christopher; Velculescu, Victor E.; Kinzler, Kenneth W.; Vogelstein, Bert; Willis, Joseph; Markowitz, Sanford D. (Proceedings of the National Academy of Sciences, 2008)
      We show that the times separating the birth of benign, invasive, and metastatic tumor cells can be determined by analysis of the mutations they have in common. When combined with prior clinical observations, these analyses ...
    • Completing the Results of the 2013 Boston Marathon 

      Hammerling, Dorit; Cefalu, Matthew; Cisewski, Jessi; Dominici, Francesca; Parmigiani, Giovanni; Paulson, Charles; Smith, Richard L. (Public Library of Science, 2014)
      The 2013 Boston marathon was disrupted by two bombs placed near the finish line. The bombs resulted in three deaths and several hundred injuries. Of lesser concern, in the immediate aftermath, was the fact that nearly 6,000 ...
    • curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome 

      Ganzfried, Benjamin Frederick; Riester, Markus; Haibe-Kains, Benjamin; Risch, Thomas; Tyekucheva, Svitlana; Jazic, Ina; Wang, Xin Victoria; Ahmadifar, Mahnaz; Birrer, Michael James; Parmigiani, Giovanni; Huttenhower, Curtis; Waldron, Levi D. (Oxford University Press, 2013)
      This article introduces a manually curated data collection for gene expression meta-analysis of patients with ovarian cancer and software for reproducible preparation of similar databases. This resource provides uniformly ...
    • Estimation of Sequencing Error Rates in Short Reads 

      Blades, Natalie; Sultana, Razvan; Ding, Jie; Parmigiani, Giovanni; Wang, Xin Victoria (BioMed Central, 2012)
      Background: Short-read data from next-generation sequencing technologies are now being generated across a range of research projects. The fidelity of this data can be affected by several factors and it is important to have ...
    • Heterogeneity of genomic evolution and mutational profiles in multiple myeloma 

      Bolli, Niccolo; Avet-Loiseau, Hervé; Wedge, David C.; Van Loo, Peter; Alexandrov, Ludmil B.; Martincorena, Inigo; Dawson, Kevin J.; Iorio, Francesco; Nik-Zainal, Serena; Bignell, Graham R.; Hinton, Jonathan W.; Li, Yilong; Tubio, Jose M.C.; McLaren, Stuart; O' Meara, Sarah; Butler, Adam P.; Teague, Jon W.; Mudie, Laura; Anderson, Elizabeth; Rashid, Naim; Tai, Yu-Tzu; Shammas, Masood A.; Sperling, Adam S.; Fulciniti, Mariateresa; Richardson, Paul G.; Parmigiani, Giovanni; Magrangeas, Florence; Minvielle, Stephane; Moreau, Philippe; Attal, Michel; Facon, Thierry; Futreal, P Andrew; Anderson, Kenneth C.; Campbell, Peter J.; Munshi, Nikhil C. (Nature Pub. Group, 2014)
      Multiple myeloma is an incurable plasma cell malignancy with a complex and incompletely understood molecular pathogenesis. Here we use whole-exome sequencing, copy-number profiling and cytogenetics to analyse 84 myeloma ...
    • Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma 

      Sausen, Mark; Leary, Rebecca J.; Jones, Siân; Wu, Jian; Reynolds, C. Patrick; Liu, Xueyuan; Blackford, Amanda; Parmigiani, Giovanni; Diaz, Luis A.; Papadopoulos, Nickolas; Vogelstein, Bert; Kinzler, Kenneth W.; Velculescu, Victor E.; Hogarty, Michael D. (2012)
      Neuroblastomas are tumors of peripheral sympathetic neurons and are the most common solid tumor in children. To determine the genetic basis for neuroblastoma we performed whole-genome sequencing (6 cases), exome sequencing ...
    • Integrating Diverse Genomic Data Using Gene Sets 

      Tyekucheva, Svitlana; Marchionni, Luigi; Karchin, Rachel; Parmigiani, Giovanni (BioMed Central, 2011)
      We introduce and evaluate data analysis methods to interpret simultaneous measurement of multiple genomic features made on the same biological samples. Our tools use gene sets to provide an interpretable common scale for ...
    • Modular network construction using eQTL data: an analysis of computational costs and benefits 

      Ho, Yen-Yi; Cope, Leslie M.; Parmigiani, Giovanni (Frontiers Media S.A., 2014)
      Background: In this paper, we consider analytic methods for the integrated analysis of genomic DNA variation and mRNA expression (also named as eQTL data), to discover genetic networks that are associated with a complex ...
    • Recent Enhancements to the Genetic Risk Prediction Model BRCAPRO 

      Mazzola, Emanuele; Blackford, Amanda; Parmigiani, Giovanni; Biswas, Swati (Libertas Academica, 2015)
      BRCAPRO is a widely used model for genetic risk prediction of breast cancer. It is a function within the R package BayesMendel and is used to calculate the probabilities of being a carrier of a deleterious mutation in one ...
    • Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues 

      Waldron, Levi D.; Simpson, Peter; Parmigiani, Giovanni; Huttenhower, Curtis (BioMed Central, 2012)
      Background: With over 20 million formalin-fixed, paraffin-embedded (FFPE) tissue samples archived each year in the United States alone, archival tissues remain a vast and under-utilized resource in the genomic study of ...
    • Simplifying clinical use of the genetic risk prediction model BRCAPRO 

      Biswas, Swati; Atienza, Philamer; Chipman, Jonathan; Hughes, Kevin S.; Barrera, Angelica M. Gutierrez; Amos, Christopher I.; Arun, Banu; Parmigiani, Giovanni (Springer Nature, 2013)
      Purpose: Health care providers need simple tools to identify patients at genetic risk of breast and ovarian cancers. Genetic risk prediction models such as BRCAPRO could fill this gap if incorporated into Electronic Medical ...
    • Statistical Methods to Adjust for Measurement Error in Risk Prediction Models and Observational Studies 

      Braun, Danielle (2014-02-25)
      The first part of this dissertation focuses on methods to adjust for measurement error in risk prediction models. In chapter one, we propose a nonparametric adjustment for measurement error in time to event data. Measurement ...
    • Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma 

      Gartner, Jared J.; Parker, Stephen C. J.; Prickett, Todd D.; Dutton-Regester, Kenneth Adam; Stitzel, Michael L.; Lin, Jimmy C.; Davis, Sean; Simhadri, Vijaya L.; Jha, Sujata; Katagiri, Nobuko; Gotea, Valer; Teer, Jamie K.; Wei, Xiaomu; Morken, Mario A.; Bhanot, Umesh K.; Chen, Guo; Elnitski, Laura L.; Davies, Michael A.; Gershenwald, Jeffrey E.; Carter, Hannah; Karchin, Rachel; Robinson, William; Robinson, Steven; Rosenberg, Steven A.; Collins, Francis S.; Parmigiani, Giovanni; Komar, Anton A.; Kimchi-Sarfaty, Chava; Hayward, Nicholas K.; Margulies, Elliott H.; Samuels, Yardena; Becker, Jesse; Benjamin, Betty; Blakesley, Robert; Bouffard, Gerry; Brooks, Shelise; Coleman, Holly; Dekhtyar, Mila; Gregory, Michael; Guan, Xiaobin; Gupta, Jyoti; Han, Joel; Hargrove, April; Ho, Shi-ling; Johnson, Taccara; Legaspi, Richelle; Lovett, Sean; Maduro, Quino; Masiello, Cathy; Maskeri, Baishali; McDowell, Jenny; Montemayor, Casandra; Mullikin, James; Park, Morgan; Riebow, Nancy; Schandler, Karen; Schmidt, Brian; Sison, Christina; Stantripop, Mal; Thomas, James; Thomas, Pam; Vemulapalli, Meg; Young, Alice (Proceedings of the National Academy of Sciences, 2013)
      Synonymous mutations, which do not alter the protein sequence, have been shown to affect protein function [Sauna ZE, Kimchi-Sarfaty C (2011) Nat Rev Genet 12(10):683–691]. However, synonymous mutations are rarely investigated ...
    • Why tyrosine kinase inhibitor resistance is common in advanced gastrointestinal stromal tumors 

      Tomasetti, Cristian; Demetri, George D; Parmigiani, Giovanni (F1000Research, 2013)
      Background: Most patients with advanced gastrointestinal stromal tumors (GIST) develop drug resistance to tyrosine kinase inhibitors (TKIs) within two years of starting therapy, whereas most chronic myeloid leukemia (CML) ...