Reverse Ecology:
Computational Integration of Genomes, Organisms, and Environments

IGERT Events







Events

  • Biology of Aging Seminar Download Biology of Aging Seminar to my desktop calendar

    April 17, 2014 12:00 PM - 1:00 PM Dr. Joshua Dubnau from Cold Spring Harbor Laboratory will speak on: "The transposon storm hypothesis of neurodegeneration" Sidney Frank Hall, Room 220 (Nathan Marcuvitz Auditorium) NSGP (Neuroscience Graduate Program), Open to the Public, Graduate School, Audience, Biology and Medicine, Lectures, Conferences, and Meetings, MCB Graduate Program, Dept: MCB, MMI, BioMed: Office of Graduate and Postdoctoral Studies, Dept: MPPB, Dept: EEB, BioMed: PathoGrad, Departments, Seminars
  • Biology of Aging Seminar Series Download Biology of Aging Seminar Series to my desktop calendar

    April 17, 2014 12:00 PM - 1:00 PM The next seminar of the semester will be held Thursday, April 17, at 12:00pm in Sidney Frank Hall, 185 Meeting St., Nathan Marcuvitz Auditorium (room 220). Joshua Dubnau of the Cold Spring Harbor Laboratory will speak on “The transposon storm hypothesis of neurodegeneration.” Sidney Frank Hall, Room 220 (Nathan Marcuvitz Auditorium) Lectures, Conferences, and Meetings, Dept: MCB, Departments, Seminars
  • MCB Graduate Program Thesis Defense Download MCB Graduate Program Thesis Defense to my desktop calendar

    April 18, 2014 2:00 PM - 3:00 PM Jessica Chery will defend her PhD Thesis: "The function of the CLAMP zinc finger protein in targeting MSL Complex to the X-chromosome during dosage compensation in Drosophila melanogaster" Advisor: Erica Larschan Building for Environmental Research & Teaching (BERT), Room 130 NSGP (Neuroscience Graduate Program), Open to the Public, Graduate School, Audience, Biology and Medicine, MCB Graduate Program, Thesis Defense, Dept: MCB, MMI, BioMed: Office of Graduate and Postdoctoral Studies, Dept: MPPB, Dept: EEB, BioMed: PathoGrad, Departments
  • Applied Math Degree Days Download Applied Math Degree Days to my desktop calendar

    April 18, 2014 4:30 PM - 6:00 PM The Applied Math DUG hosts Elena Jakubiak '98 Ph.D. (Development/Visualization Design Engineer at BBN Technologies) and William Hermann '12 (Buzzfeed Scientific Data Analyst) for the Applied Math Degree Days Event. Students interested in learning about what they can do with an applied math education are welcome to hear from and talk to Brown applied math alumni. Smith-Buonanno, Room 101 Dept: Applied Mathematics, Departments
  • Brown Statistics C. M. Colver Lecture - Title to be announced Download Brown Statistics C. M. Colver Lecture - Title to be announced to my desktop calendar

    April 21, 2014 3:30 PM - 4:30 PM Brown Statistics C. M. Colver Lectureship Series Ji Zhu, PhD Professor of Statistics Professor of Electrical Engineering and Computer Science Department of Statistics University of Michigan http://www.stat.brown.edu/Seminars.aspx 121 South Main, Room 245 Open to the Public, Audience, Dept: Applied Mathematics, Biology and Medicine, Lectures, Conferences, and Meetings, BioMed: Biostatistics, Departments, Lectures, Seminars
  • Brown Statistics C.M. Colver Lecture: “On Consistency of Community Detection in Networks” Download Brown Statistics C.M. Colver Lecture: “On Consistency of Community Detection in Networks” to my desktop calendar

    April 21, 2014 3:30 PM - 4:30 PM Brown Statistics C.M. Colver Lectureship Series “On Consistency of Community Detection in Networks” Ji Zhu, PhD Professor of Statistics Professor of Electrical Engineering and Computer Sciences University of Michigan Community detection is a fundamental problem in network analysis, with applications in many diverse areas.  The stochastic block model is a common tool for model-based community detection, and asymptotic tools for checking consistency of community detection under the block model have been recently developed by Bickel and Chen (2009).  However, the block model is limited by its assumption that all nodes within a community are stochastically equivalent, and provides a poor fit to networks with hubs or highly varying node degrees within communities, which are common in practice.  The degree-corrected block model (Karrer and Newman 2010) was proposed to address this shortcoming, and allows variation in node degrees within a community while preserving the overall block model community structure.  In this paper, we establish general theory for checking consistency of community detection under the degree-corrected block model, and compare several community detection criteria under both the standard and the degree-corrected block models.  We show which criteria are consistent under which models and constraints, as well as compare their relative performance in practice.  We find that methods based on the degree-corrected block model, which includes the standard block model as a special case, are consistent under a wider class of models; and that modularity-type methods require parameter constraints for consistency, whereas likelihood-based methods do not.  On the other hand, in practice the degree correction involves estimating many more parameters, and empirically we find it is only worth doing if the node degrees within communities are indeed highly variable.  We illustrate the methods on simulated networks and on a network of political blogs.  This is joint work with Yunpeng Zhao and Elizaveta Levina. http:www.stat.brown.edu/Seminars.aspx 121 South Main, Room 245 Open to the Public, Audience, Dept: Applied Mathematics, Biology and Medicine, Lectures, Conferences, and Meetings, BioMed: Biostatistics, Departments, Lectures, Seminars
  • Brown Statistics C.M. Colver Lecture: “On Consistency of Community Detection in Networks” Download Brown Statistics C.M. Colver Lecture: “On Consistency of Community Detection in Networks” to my desktop calendar

    April 21, 2014 3:30 PM - 4:30 PM Brown Statistics C.M. Colver Lectureship Series “On Consistency of Community Detection in Networks” Community detection is a fundamental problem in network analysis, with applications in many diverse areas.  The stochastic block model is a common tool for model-based community detection, and asymptotic tools for checking consistency of community detection under the block model have been recently developed by Bickel and Chen (2009).  However, the block model is limited by its assumption that all nodes within a community are stochastically equivalent, and provides a poor fit to networks with hubs or highly varying node degrees within communities, which are common in practice.  The degree-corrected block model (Karrer and Newman 2010) was proposed to address this shortcoming, and allows variation in node degrees within a community while preserving the overall block model community structure.  In this paper, we establish general theory for checking consistency of community detection under the degree-corrected block model, and compare several community detection criteria under both the standard and the degree-corrected block models.  We show which criteria are consistent under which models and constraints, as well as compare their relative performance in practice.  We find that methods based on the degree-corrected block model, which includes the standard block model as a special case, are consistent under a wider class of models; and that modularity-type methods require parameter constraints for consistency, whereas likelihood-based methods do not.  On the other hand, in practice the degree correction involves estimating many more parameters, and empirically we find it is only worth doing if the node degrees within communities are indeed highly variable.  We illustrate the methods on simulated networks and on a network of political blogs.  This is joint work with Yunpeng Zhao and Elizaveta Levina. http:www.stat.brown.edu/Seminars.aspx 121 South Main, Room 245 Open to the Public, Audience, Dept: Applied Mathematics, Biology and Medicine, Lectures, Conferences, and Meetings, Departments, Lectures, Seminars
  • Fluids Seminar: Dynamic Wetting Failure and Air Entrainment in Coating Flows Download Fluids Seminar: Dynamic Wetting Failure and Air Entrainment in Coating Flows to my desktop calendar

    April 22, 2014 3:00 PM - 4:00 PM Professor Satish Kumar Chemical Engineering University of Minnesota Minneapolis, MN Dynamic Wetting Failure and Air Entrainment in Coating Flows Dynamic wetting is crucial to processes where liquid displaces another fluid (such as air) along a solid surface, an important example being the deposition of a coating liquid onto a moving substrate. Dynamic wetting failure occurs when the displacement happens too quickly, and this leads to entrainment of the receding fluid into the advancing liquid. In coating processes this entrainment compromises the quality of the final product, so it is desirable to develop a fundamental understanding of the factors that control the onset of dynamic wetting failure. In this talk, I will discuss how the interplay between experiments and modeling has enabled progress in this area. The experiments involve measurements of the critical speed at which wetting failure occurs and flow visualizations of air entrainment. The modeling involves a combination of asymptotic analysis and two-dimensional finite element calculations that link the onset of wetting failure to limit points in families of steady-state solutions. The results reveal the mechanisms responsible for wetting failure and suggest strategies for delaying the onset of air entrainment in coating flows. Barus & Holley, Room 190 Dept: Engineering, Dept: Applied Mathematics, Lectures, Conferences, and Meetings, Departments, Seminars
  • Providence Area Aging Research Forum Download Providence Area Aging Research Forum to my desktop calendar

    April 22, 2014 5:30 PM - 7:00 PM The next PAARF meeting of the semester will be held Tuesday, April 22, 2014, in the Alpert Medical School Education Building, 222 Richmond Street, Room 280. Food at 5:30, Presentations at 6:00 PM. Sara Ortega, of the Zhitkovich laboratory, and Kun Yang, of the Chen laboratory, will present. Alpert Medical Building, Case Study Room 280 Dept: MCB, Departments
  • MCB Graduate Program Seminar Download MCB Graduate Program Seminar to my desktop calendar

    April 23, 2014 12:00 PM - 1:00 PM Philip D. Zamore from the Universty of Massachusetts Medical School in Worcester will present a seminar. Title: "Mechanisms and Funcitons of RNA Silencing Pathways in Animals" Host: MCB Graduate Students Sidney Frank Hall, Room 220 (Nathan Marcuvitz Auditorium) NSGP (Neuroscience Graduate Program), Open to the Public, Graduate School, Audience, Biology and Medicine, Lectures, Conferences, and Meetings, MCB Graduate Program, Dept: MCB, MMI, BioMed: Office of Graduate and Postdoctoral Studies, Dept: MPPB, Dept: EEB, BioMed: PathoGrad, Departments, Seminars
  • Biology of Aging Seminar Series Download Biology of Aging Seminar Series to my desktop calendar

    April 24, 2014 12:00 PM - 1:00 PM The next seminar of the semester will be held Thursday,April 24, 2014, in the Eddy Auditorium, BioMed Center Room 291, at 12:00pm. Sandy Chang of the Yale University School of Medicine will present on "Genomic instability and premature aging in mouse models of telomere dysfunction." Biomed Center, Room 291 (Eddy Auditorium) Lectures, Conferences, and Meetings, Dept: MCB, Departments, Seminars
  • MCB Graduate Program Data Club Download MCB Graduate Program Data Club to my desktop calendar

    April 25, 2014 3:30 PM - 5:00 PM The MCB Data Club will be held at 70 Ship St., room 107. Akash Srivastava (Horb Lab)- "Differential roles of beta-catenin inhibitor Chibby1 in pancreas development and transdifferentiation of liver to pancreas", Abbie Frederick (Morrow Lab) and Arjun Ray (Kaun Lab)- "Investigating the role of Notch signaling in alcohol reward memory". Laboratories for Molecular Medicine NSGP (Neuroscience Graduate Program), Open to the Public, Graduate School, Audience, Biology and Medicine, MCB Graduate Program, Data Club, Dept: MCB, MMI, BioMed: Office of Graduate and Postdoctoral Studies, Dept: MPPB, Dept: EEB, BioMed: PathoGrad, Departments
  • Movie Night! - Screening of Good Will Hunting by AMDUG Download Movie Night! - Screening of Good Will Hunting by AMDUG to my desktop calendar

    April 25, 2014 5:00 PM - 8:00 PM Take a study break and come see a screening of Good Will Hunting sponsored by the Applied Math DUG! Free pizza, popcorn, and drinks will be served. This event will take place this Friday, April 25th, at 5PM in Smith-Buonanno Hall (Smitty B) Room 106. Smith-Buonanno, Room 106 Dept: Applied Mathematics, Departments, Films, Arts and Entertainment
  • Brown Statistics Seminar - “Convex Banding of High Dimensional Covariance Matrices" Download Brown Statistics Seminar - “Convex Banding of High Dimensional Covariance Matrices" to my desktop calendar

    April 28, 2014 3:30 PM - 4:30 PM Brown Statistics Seminar Series Florentina Bunea, PhD Professor, Department of Statistical Science Cornell University Title: “Convex Banding of High Dimensional Covariance Matrices" Estimation of large covariance matrices of a random vector with entries that are or can be ordered is an intensely studied problem in stochastic processes, spatial statistics and general high dimensional inference. When the popula­tion matrix is banded or approximately banded, a number of theoretically and practically optimal estimators have been proposed in the last five years. With very few exceptions, the theoretically optimal estimators are not adaptive, and the estimates that are practically performant do not have established theoret­ical properties. Moreover, most existing theoretical analyses are restricted to population covariance matrices with bounded operator norm. We introduce a new estimator, the hierarchically banded estimator, which is the solution of a computationally feasible convex optimization problem. Dur­ing this procedure, one successively penalizes nested triangular corners of the current candidate estimate. Since these ensembles are nested, the new penalty is not a variation on the group-type penalties, and poses new challenges. We show that the procedure can be implemented successfully and efficiently. The estimator, by construction, will be banded and positive definite. We introduce a class of semi-banded population covariance matrices, that generalizes both banded and approximately banded matrices. Members of this class are allowed to have diverging operator norm. We show that our estimator is minimax adaptive with respect to the Frobenius norm over the general class of semi-banded matrices, and with respect to the operator norm over the class of banded matrices. Extensive simulation studies show that our procedure is a strong competitor of all previously developed methods. An application to a classification problem shows the practical gain of employing a banded estimator in the construction of the classifier, for a concrete data set. http://www.stat.brown.edu/Seminars.aspx 121 South Main, Room 245 Open to the Public, Audience, Dept: Applied Mathematics, Biology and Medicine, Lectures, Conferences, and Meetings, BioMed: Biostatistics, Departments, Seminars
  • MCB Graduate Program Seminar Download MCB Graduate Program Seminar to my desktop calendar

    April 30, 2014 12:00 PM - 1:00 PM Dr. Holger Sonderman from Cornell University will present a seminar. Title: "The Ins and Outs of c-di-GMP Signaling in Bacterial Biofilm Formation" Host: Rebecca Page Laboratories for Molecular Medicine NSGP (Neuroscience Graduate Program), Open to the Public, Graduate School, Audience, Biology and Medicine, Lectures, Conferences, and Meetings, MCB Graduate Program, Dept: MCB, MMI, BioMed: Office of Graduate and Postdoctoral Studies, Dept: MPPB, Dept: EEB, BioMed: PathoGrad, Departments, Seminars
  • CCMB Seminar - Peter Park Download CCMB Seminar - Peter Park to my desktop calendar

    April 30, 2014 4:00 PM - 5:00 PM Wendesday, April 30, 2014 4:00 p.m. - Swig Boardroom - CIT 241 Peter Park Associate Professor of Pediatric Center for Biomedical Informatics Harvard Medical School "Discovering somatic variation in cancer genomes using whole-genome sequencing” Hosted by Erica Larschan http://brown.edu/research/projects/computational-molecular-biology/news-events/news-events Watson CIT - SWIG Boardroom (CIT241) Lectures, Conferences, and Meetings, CCMB, Departments, Seminars
  • Brown Statistics Seminar - “The Estimation of Spatially Varying Coefficients via a Spatial GLMM with Application to Multiple Sclerosis MRI Data” Download Brown Statistics Seminar - “The Estimation of Spatially Varying Coefficients via a Spatial GLMM with Application to Multiple Sclerosis MRI Data” to my desktop calendar

    May 2, 2014 3:30 PM - 4:30 PM Brown Statistics Seminar Series Timothy D. Johnson, PhD Professor, Department of Biostatistics University of Michigan School of Public Health “The Estimation of Spatially Varying Coefficients via a Spatial GLMM with Application to Multiple Sclerosis MRI Data” Multiple Sclerosis (MS) is an autoimmune disease that affects the central nervous system (CNS) by disrupting nerve transmission. This disruption is caused by damage to the myelin sheath surrounding nerves that acts as an insulator. Patients with MS have a multitude of symptoms that depend on where lesions occur in the brain and/or spinal cord. MS has no cure and in order to help manage the disease, physicians subtype MS patients into 4 categories that depend on the pattern of MS episodes. Patient symptoms are rated by the Kurtzke Functional Systems (FS) scores and the paced auditory serial addition test (PASAT)score. The eight functional systems (CNS areas or circuits that regulate body functions) are: 1) pyramidal; 2) cerebellar; 3) brainstem 4) sensory; 5) bowel and bladder; 6) visual; 7) cerebral; and 8) other. Of interest to neurologists is whether lesion locations can be predicted using these FS and PASAT scores and whether the data can help predict MS subtype in a newly diagnosed patient. To help answer these questions, we propose an autoprobit regression model with spatially varying random coeffcients. The data of interest are digitized binary images of the brain derived from high-resolution T2-weight MRI images encoded such that, at each voxel, 1 indicates the presence of a lesion and 0 denotes absence of a lesion. These binary lesion maps are taken as the dependent variables. In contrast to most spatial applications, in which only one realization of a process is observed, we have multiple, independent realizations, one from each patient. This allows the modeling and estimation of spatially varying parameters of patient level covariates such as age, gender, disease duration, FS and PASAT scores. Maps of these spatially varying parameters over the brain allow us to spatially predict lesion probabilities over the brain given covariates. Furthermore, we show that, via Bayes Theorem, the model can be used to accurately predict the MS subtype of a new subject. http://www.stat.brown.edu/Seminars.aspx 121 South Main, Room 245 Open to the Public, Audience, Dept: Applied Mathematics, Biology and Medicine, Lectures, Conferences, and Meetings, BioMed: Biostatistics, Departments, Seminars
  • Fluids Seminar: The Role of Vortex Lift on Flapping Wings Download Fluids Seminar: The Role of Vortex Lift on Flapping Wings to my desktop calendar

    May 6, 2014 3:00 PM - 4:00 PM Professor Anya Jones University of Maryland College Park, MD The Role of Vortex Lift on Flapping Wings The lift produced by an entomological flapping wing is investigated via simplified models of the wing kinematics, with a focus on near-impulsively started rectilinear and rotational motions. Force and velocity field measurements are examined in parallel with flow visualization to identify the sources of lift, the relative importance of these contributions, and the time-scales over which they persist. Experiments were performed in water tanks over a large parameter space, including variations in incidence angle, acceleration, flexibility and camber, and planform shape. Acceleration was found to affect the formation and trajectory of the leading edge vortex, but had little effect on the force history at long convective times. Classical aerodynamic theories were found to be a good approximation of the unsteady lift force near the start of a rectilinear surging wing motion at high incidence angle. However, after the initial lift transient, recovery to the classical results of thin airfoil theory required ~10+ convective times. Barus & Holley, Room 190 Dept: Engineering, Dept: Applied Mathematics, Lectures, Conferences, and Meetings, Departments, Seminars
  • MCB Graduate Program Seminar Download MCB Graduate Program Seminar to my desktop calendar

    May 7, 2014 12:00 PM - 1:00 PM Dr. Jason Sello, Department of Chemistry, Brown University will present a seminar: "Genetic Bases of Biological Chemistry and Ecology in Streptomyces" Host: Art Salomon Laboratories for Molecular Medicine NSGP (Neuroscience Graduate Program), Open to the Public, Graduate School, Audience, Biology and Medicine, Lectures, Conferences, and Meetings, MCB Graduate Program, Dept: MCB, MMI, BioMed: Office of Graduate and Postdoctoral Studies, Dept: MPPB, Dept: EEB, BioMed: PathoGrad, Departments, Seminars
  • Franziska Michor - CCMB Seminar May 7 Download Franziska Michor - CCMB Seminar May 7 to my desktop calendar

    May 7, 2014 4:00 PM - 5:00 PM Wednesday, May 7, 2014 4:00 p.m. - Swig Boardroom - CIT 241 Franziska Michor Associate Professor Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute Department of Biostatistics, Harvard School of Public Health Title & Abstract TBA Hosted by MCB/CCMB http://brown.edu/research/projects/computational-molecular-biology/news-events/news-events Watson CIT - SWIG Boardroom (CIT241) Lectures, Conferences, and Meetings, CCMB, Departments, Seminars
  • CCMB Symposium "Modern Genomic Approaches to Heritable Disease Download CCMB Symposium "Modern Genomic Approaches to Heritable Disease to my desktop calendar

    May 12, 2014 9:00 AM - May 13, 2014 9:00 AM *Save the Date* - UPDATES WITH TALK TITLES SOON CCMB Symposium - "Modern Genomic Approaches to Heritable Disease" Monday, May 12th 2014 in the Warren Alpert Medical School Building PRELIMINARY SCHEDULE: 9:00 -9:45 - Breakfast 9:45-10:00 - Introduction 10:00-12:00 - Speakers & Discussion 12:00 -1:15 - Lunch 1:15 - 2:45 - Speakers & Discussion 2:45 - 3:00 - Coffee Break 3:00 - 5:00 - Speakers & Discussion 5:00 - 6:00 - Reception and Poster Session (wine & cheese outside lecture hall) Confirmed Speakers include: Dr. Shamil Sunyaev Dr. Arthur Beaudet Dr. Constantin Polychronakos Dr. John Quackenbush Dr. Jun J. Yang Dr. William Fairbrother http://brown.edu/research/projects/computational-molecular-biology/news-events/events/upcoming-events/modern-genomic-approaches-heritable-disease Alpert Medical Building, Lecture Hall 170 Lectures, Conferences, and Meetings, Symposium, CCMB, Departments
  • MCB Graduate Program Seminar Download MCB Graduate Program Seminar to my desktop calendar

    May 14, 2014 12:00 PM - 1:00 PM Dr. Amanda Jamieson, Brown University, MMI, will present a seminar: Stress management: Tolerating polymicrobial infections of the lung. Host: Art Salomon Laboratories for Molecular Medicine NSGP (Neuroscience Graduate Program), Open to the Public, Graduate School, Audience, Biology and Medicine, Lectures, Conferences, and Meetings, MCB Graduate Program, Dept: MCB, MMI, BioMed: Office of Graduate and Postdoctoral Studies, Dept: MPPB, Dept: EEB, BioMed: PathoGrad, Departments, Seminars
  • CCMB Seminar - Anastasios Matzavinos Download CCMB Seminar - Anastasios Matzavinos to my desktop calendar

    May 14, 2014 4:00 PM - 5:00 PM Wednesday, May 14, 2014 4:00 p.m. - Swig Boardroom - CIT 241 Anastasios Matzavinos Assistant Professor of Applied Mathematics Brown University "Random walk distances in data clustering and applications" Hosted by Dan Weinreich http://brown.edu/research/projects/computational-molecular-biology/news-events/news-events Watson CIT - SWIG Boardroom (CIT241) Lectures, Conferences, and Meetings, CCMB, Departments, Seminars