Past Events

Diffusion-based Interactions in Noisy Single Cell Data

  • Where: Charles Commons conference center
  • When: November 14, 2016, 13:30
  • Smita Krishnaswamy
  • A Genomics@JHU Seminar

Abstract Recently, there have been significant advances in single-cell genomic and proteomic technologies that can measure the expression of thousands of mRNA transcripts and dozens of proteins. However, this data suffers from sparsity and noise. Furthermore, its high dimensionality makes interpreting the data difficult for biologists. Our aim is to facilitate interpretation by providing a … Continued

2016 IEEE 12th International Conference on eScience

  • Where: Baltimore Marriott Inner Harbor at Camden Yards
  • When: October 23, 2016 to October 26, 2016, 00:00

The IEEE 12th International Conference on eScience will explore the realms where big data and distributed computing fuse into Data Intensive Science. The objective of the eScience Conference is to promote and encourage all aspects of eScience and its associated technologies, applications, and tools. In short, eScience promotes innovation in collaborative, computationally- or data-intensive research … Continued

Tumor neoepitope selection for biomarker discovery and therapeutic vaccination

  • Where: Barber Conference Room at Charles Commons, 10 E 33rd St. Baltimore, MD
  • When: October 24, 2016, 13:30
  • Jeff Hammerbacher
  • A Genomics@JHU Seminar

Abstract We’ll review some open source software our lab has developed to facilitate a Phase I clinical trial of a personalized therapeutic vaccine targeting tumor neoepitopes. We’ll also present some results from our analysis of clinical trials of checkpoint blockade in 3 different cancer types and some open source software we’ve created to facilitate similar … Continued

IDIES Annual Symposium 2016

  • Where: Bloomberg School of Public Health, Sheldon Hall Auditorium
  • When: October 21, 2016, 08:30

Big Data in Healthcare The Institute for Data Intensive Engineering and Science will hold our 2016 Annual Symposium at Johns Hopkins University on Friday, October 21, 2016. This event will bring together experts in Big Data from all divisions of Johns Hopkins University, the government and industry to share their discoveries, practical ideas, and insights. … Continued

The Impact of Genetic Variation on Gene Regulation from RNA to Protein in Humans

  • Where: Barber Conference Room at Charles Commons, 10 E 33rd St. Baltimore, MD
  • When: October 17, 2016, 13:30
  • Zia Khan of UMCP
  • A Genomics@JHU Seminar

Abstract Understanding how genotype and environment interact to impact phenotypic variation is a central goal of genetics. Studies of important phenotypes in humans such as disease risk and drug toxicity have identified genomic regions and variants of interest. Yet, in many cases, the mechanisms by which these variants act are less clear. Gaining a better … Continued

Interactive Computing and Data Science with the Jupyter Platform

  • Where: Space Telescope Auditorium
  • When: October 07, 2016, 14:00
  • Dr. Fernando Pérez

Abstract Project Jupyter, evolved from the IPython environment, provides a platform for interactive computing that is widely used today in research, education, journalism and industry. The core premise of the Jupyter architecture is to design tools around the experience of interactive computing, building an environment, protocol, file format and libraries optimized for the computational process … Continued

Likelihood Approaches to Structural Variant Discovery: From Integrating Signals in Individual Genomes Towards Simultaneous Variant Discovery in Populations

  • Where: Bloomberg School of Public Health
  • When: April 26, 2016, 10:30
  • Suzanne Sindi
  • A Genomics@JHU Seminar

Abstract Structural variants (SVs) – such as deletions, insertions, copy-number gains and inversions – are rearrangements of a region of DNA relative to a reference. Until relatively recently, SVs were thought to be rare in genomes of healthy individuals, especially mammals. However, advances in high-throughput DNA sequencing, combined with the availability of high-quality reference genomes, … Continued

Fast Algorithms for Improved Transcriptome Analysis

  • Where: Bloomberg School of Public Health
  • When: April 05, 2016, 10:30
  • Rob Patro of Stony Brook University
  • A Genomics@JHU Seminar

Abstract Short read alignments are the lingua franca in much of computational genomics. Most analyses “begin with a bam”. This requires that the reads are aligned to the reference (genome or transcriptome) of interest. Given the tremendous speed of acquisition of sequencing data, the process of alignment can pose a significant computational burden. Crucially, this … Continued

Selecting genomics assays and making sense of the resulting data

  • Where: Welsh Library West Reading Room, 1900 E. Monument St
  • When: February 23, 2016, 10:00
  • William Noble of the University of Washington
  • A Genomics@JHU Seminar

Abstract Genomic sequencing assays such as ChIP-seq and DNase-seq can measure a wide variety of types of genomic activity, but the high cost of sequencing limits the number of these assays that are usually performed in a given experimental condition. I will discuss a principled method for selecting which genomics assays to perform, given a … Continued

(Data-driven) Strategies to Predict Intra- and Inter-cellular Signaling Dynamics and Function

  • Where: Barber Conference Room at Charles Commons, 10 E 33rd St. Baltimore, MD
  • When: December 08, 2015, 10:00
  • Neda Bagheri of Northwestern University
  • A Genomics@JHU Seminar

Abstract In the past decade, emerging technologies have offered increasingly high throughput data with greater resolution to investigate cellular responses. To gain insight from dynamic gene expression, transcription factor activity, phospho-signaling or other data, improved computational strategies to analyze, integrate, and predict complex biological function must be developed. We employ a variety of inference and … Continued