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UID:0-5757@eng.ufl.edu
DTSTART;TZID=America/New_York:20230327T150000
DTEND;TZID=America/New_York:20230327T160000
DTSTAMP:20230330T123734Z
URL:https://www.eng.ufl.edu/news-events/events/bme-seminar-building-scalab
 le-indexes-that-can-be-efficiently-queried/
SUMMARY:BME Seminar: Building scalable indexes that can be efficiently quer
 ied.
DESCRIPTION:Dr. Boucher\,Associate Professor in the Department of Computer 
 and Information Science and Engineering at the University of Florida\nRece
 ntly\, Gagie et al. proposed a version of the FM-index\, called the r-inde
 x\, that can store thousands of human genomes on a commodity computer. We 
 later showed how to build the r-index efficiently via a technique called p
 refix-free parsing (PFP) and demonstrated its effectiveness for exact patt
 ern matching. Exact pattern matching can be leveraged to support approxima
 te pattern matching but the r-index itself cannot support efficiently popu
 lar and important queries such as finding maximal exact matches (MEMs). To
  address this shortcoming\, Bannai et al. introduced the concept of thresh
 olds\, and showed that storing them together with the r-index enables effi
 cient MEM finding --- but they did not say how to find those thresholds. W
 e present another novel algorithm that applies PFP to build the r-index an
 d find the thresholds simultaneously and in linear time and space with res
 pect to the size of the prefix-free parse. Our implementation can rapidly 
 find MEMs between reads and large sequence collections of highly repetitiv
 e sequences. Compared to existing methods\, ours used 2 to 11 times less m
 emory and was 2 to 32 times faster for index construction. Moreover\, our 
 method was less than one thousandth the size of competing indexes for larg
 e collections of human chromosomes.\nDr. Boucher is an Associate Professor
  in the Department of Computer and Information Science and Engineering at 
 the University of Florida. She has over 125 publications in bioinformatics
 \, with over several dozens of them in succinct data structures and/or ali
 gnment. She has given keynote addresses at 2022 WABI Pangenomics workshop\
 , HICOMB 2022. IGGSY 2022\, SPIRE 2021\, RECOMB-SEQ 2016 and the ECCB 2016
  Workshop on Pan-Genomics. She is a recipient of an ESA 2016 Best Paper Aw
 ard. She oversees the development and maintenance of several software meth
 ods\, including Moni\, MEGARes and AMRPlusPlus\, METAMarc\, Kohdista\, Var
 i\, VariMerge — and most recently\, Moni. In addition\, she has built a 
 team of collaborators in various biomedical sciences including microbiolog
 y\, veterinarian medicine\, epidemiology\, public health\, and clinical sc
 iences. Her lab receives funding from NIH\, NSF\, and USDA.\nIn addition\,
  she actively works on increasing the diversity in bioinformatics educatio
 n. Her efforts include being a member of the University of Florida’s Imp
 licit Bias committee\, being a panellist for the NSF-funded ACM BCB 2015 W
 omen in Bioinformatics meeting\, serving as a faculty advisor for an ACM-W
  chapter\, and being an active member of the Diversity Committee for over 
 three years. She also received a fellowship from The Institute for Learnin
 g and Teaching (TILT) for her course redevelopment and served on the advis
 ory committee for an NSF Research Traineeships Program.\nShe was the PC ch
 air for several conferences\, including WABI 2022\, SPIRE 2020\, RECOMB-SE
 Q 2019\, and ACM-BCB 2018. Most recently\, she was nominated to serve on t
 he NIH BDMA Study Section as a Standing Member\, and a member of the Execu
 tive Board of ACM SIG BIO.
CATEGORIES:Seminars
LOCATION:Communicore Room C1-17\, 1249 Center Dr.\, Gainesville\, FL\, 3261
 0\, United States
GEO:29.640849;-82.34479
X-APPLE-STRUCTURED-LOCATION;VALUE=URI;X-ADDRESS=1249 Center Dr.\, Gainesvil
 le\, FL\, 32610\, United States;X-APPLE-RADIUS=100;X-TITLE=Communicore Roo
 m C1-17:geo:29.640849,-82.34479
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