DNA sequences

Friday, April 9, 2010 - 3:00pm - 4:00pm
Lynn Zechiedrich (Baylor College of Medicine)
The long, rich history of topology in mathematics has proven
extremely useful for the study of DNA. DNA, the genetic
blueprint for life, undergoes tremendous flux as it is
packaged, replicated, segregated, transcribed, recombined and
repaired. Extremely long and skinny, DNA is prone to
entanglement. Every time it is copied, the two resulting
daughter chromosomes are entangled. And nearly all organisms
maintain duplex DNA in a slightly underwound state. Linking
number (Lk), the major descriptor for DNA apart from base pair
Monday, December 7, 2009 - 9:40am - 10:20am
Kevin Dorfman (University of Minnesota, Twin Cities)
Keywords: Brownian dynamics, microfabrication, boundary element method, DNA electrophoresis, separations
Tuesday, December 8, 2009 - 1:30pm - 2:10pm
Patrick Doyle (Massachusetts Institute of Technology)
Keywords: DNA, microfluidic, nanofluidic, electrophoresis
Monday, September 14, 2009 - 9:00am - 9:45am
Eric Shaqfeh (Stanford University)
Part 1: In this part of the talk we will discuss the coil-stretch hysteresis in dilute polymer solutions for extension dominated flows, including three-dimensional mixed flows. We will then turn to entangled systems and discuss the role of slip-link simulations in elucidating the extensional behavior in concentrated solutions and melts.
Wednesday, September 10, 2014 - 11:30am - 12:20pm
Jeff Kahn (Rutgers, The State University of New Jersey)
One of the more interesting of recent combinatorial directions
has been the attempt to understand the extent to which
various classical facts remain true in a random setting.
The present talk will mostly discuss what we know about this question
when the classical fact is the Erdos-Ko-Rado Theorem.
(Joint with Arran Hamm.)
Thursday, September 11, 2014 - 11:30am - 12:20pm
Jacques Verstraete (University of California, San Diego)
Let G be a graph of density p on n vertices. Erdös, Luczak and Spencer defined a subgraph H of G to be full if H has m vertices and every vertex of H has degree at least p(m - 1) in H. Let f(G) denote the largest number of vertices in a full subgraph of G and let fp(n) denote the smallest value of f(G) over all graphs G of density p with n vertices. Erdös, Luczak and Spencer proved √2n ≤ f0:5(n) ≤ 2n2/3 (log n)1/3 and also showed f(G) = (n) when G is the random graph Gn,p.
Wednesday, February 29, 2012 - 5:00pm - 5:15pm
Fabio Vandin (Brown University)
Cancer is a disease that is driven by somatic mutations that accumulate in the genome during an individual’s lifetime. Recent advances in DNA sequencing technology are enabling genome-wide measurements of these mutations in numerous cancers. A major challenge in analyzing this data is to distinguish functional mutations that drive cancer progression from “passenger” mutations not related to the disease. Recent cancer sequencing studies have shown that somatic mutations are distributed over a large number of genes.
Monday, February 13, 2012 - 3:15pm - 3:45pm
Dina Esposito (Whitehead Institute for Biomedical Research)
Finding rare genetic variations in large cohorts requires tedious preparation of large numbers of specimens for sequencing. We are developing a solution, called DNA Sudoku, to reduce prep time and increase the throughput of samples. By using a combinatorial pooling approach, we multiplex specimens and then barcode the pools, rather than individuals, for sequencing in a single lane on the Illumina platform.
Monday, February 13, 2012 - 2:00pm - 3:00pm
Noam Shental (Open University of Israel)
Identification of rare variants by resequencing is important both for detecting novel variations and for screening individuals for known disease alleles. New technologies enable low-cost resequencing of target regions, although it is still prohibitive to test more than a few individuals. We propose a novel pooling design that enables the recovery of novel or known rare alleles and their carriers in groups of individuals. The method is based on combining next-generation sequencing technology with a Compressed Sensing (CS) approach.
Monday, February 13, 2012 - 10:00am - 11:00am
Yaniv Erlich (Whitehead Institute for Biomedical Research)
In the past few years, we have experienced a paradigm shift in human genetics. Accumulating lines of evidence have highlighted the pivotal role of rare genetic variations in a wide variety of traits and diseases. Studying rare variations is a needle in a haystack problem, as large cohorts have to be assayed in order to trap the variations and gain statistical power. The performance of DNA sequencing is exponentially growing, providing sufficient capacity to profile an extensive number of specimens. However, sample preparation schemes do not scale as sequencing capacity.


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