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SUMMARY:PREMIER: PRobabilistic Error-correction using Markov Inference in 
 Errored Reads - Prof. Aditya Ramamoorthy\, Iowa State University
DTSTART:20150703T103000Z
DTEND:20150703T113000Z
UID:TALK59403@talks.cam.ac.uk
CONTACT:Prof. Ramji Venkataramanan
DESCRIPTION:Next generation DNA sequencing is a technology that is revolut
 ionizing research in biology and medicine. The sequencers operate by rando
 mly fragmenting a genome into reads (contiguous genome fragments) that are
  a few hundred of base pairs long. Reads are produced at a much higher thr
 oughput compared to classical techniques. However\, they are often corrupt
 ed by errors which pose a serious problem for downstream processes such as
  genome assembly. Correcting errors in reads is thus an important problem.
  The problem differs significantly from classical error correction since t
 here is a lack of alignment information between the different reads. \nWe 
 present a fully flexible\, probabilistic and reference-free method of erro
 r correction for high throughput DNA sequencing data. The outputs of a seq
 uencer are modeled as independent emissions of a Hidden Markov Model (HMM)
 \, where transition probabilities account for local dependence in the geno
 me and the emission distribution models the error properties of the sequen
 cer. We pose the problem of error correction of reads as one of maximum li
 kelihood sequence detection over this HMM. Exhaustive results on publicly 
 available datasets show that our algorithm consistently outperforms existi
 ng methods in terms of error correction performance.\n\n*BIO*: Aditya Rama
 moorthy is an Associate Professor of Electrical and Computer Engineering a
 t Iowa State University. He received his B. Tech. degree in Electrical Eng
 ineering from the Indian Institute of Technology\, Delhi in 1999 and the
  M.S. and Ph.D. degrees from the University of California\, Los Angele
 s (UCLA) in 2002 and 2005 respectively. From 2005 to 2006 he was with the 
 data storage signal processing group at Marvell Semiconductor Inc. His res
 earch interests are in the areas of network information theory\, channel c
 oding and signal processing for nanotechnology and bioinformatics. Dr. Ram
 amoorthy has been serving as an associate editor for the IEEE Transactions
  on Communications since 2011. He is the recipient of the 2012 Iowa State 
 University's Early Career Engineering Faculty Research Award\, the 2012 NS
 F CAREER award\, and the Harpole-Pentair professorship in 2009 and 2010.
LOCATION:CBL Meeting Room (BE4-38\, Dept. of Engineering)
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