- Seminarleiter: Francois Nicolas
- Termin: Do 10-12h, SR 021 AB4
Here is the list of papers for the seminar:
Paolo Ferragina, Giovanni Manzini, Veli Mäkinen, Gonzalo Navarro
An Alphabet-Friendly FM-Index
dx.doi.org/10.1007/978-3-540-30213-1_23
Michael Beckstette, Robert Homann, Robert Giegerich, Stefan Kurtz
Significant speedup of database searches with HMMs by search space reduction with PSSM family models
bioinformatics.oxfordjournals.org/content/25/24/3251
Ben Langmead, Cole Trapnell, Mihai Pop, Steven L. Salzberg
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
genomebiology.com/content/10/3/R25
Thomas Schnattinger, Enno Ohlebusch, Simon Gog
Bidirectional Search in a String with Wavelet Trees
dx.doi.org/10.1007/978-3-642-13509-5_5
Dirk Strothmann
The affix array data structure and its applications to RNA secondary structure analysis
http://dx.doi.org/10.1016/j.tcs.2007.09.029
Thomas P. Niedringhaus, Denitsa Milanova, Matthew B. Kerby, Michael P. Snyder, Annelise E. Barron
Landscape of Next-Generation Sequencing Technologies
pubs.acs.org/doi/abs/10.1021/ac2010857
Cole Trapnell, Lior Pachter, Steven L. Salzberg
TopHat: discovering splice junctions with RNA-Seq
bioinformatics.oxfordjournals.org/content/25/9/1105
Paolo Ferragina, Giovanni Manzini
Indexing compressed text
dx.doi.org/10.1145/1082036.1082039
Michael Beckstette, Robert Homann, Robert Giegerich, Stefan Kurtz
Fast index based algorithms and software for matching position specific scoring matrices
www.biomedcentral.com/1471-2105/7/389/
Mohamed Ibrahim Abouelhoda, Stefan Kurtz, Enno Ohlebusch
Replacing suffix trees with enhanced suffix arrays
dx.doi.org/10.1016/S1570-8667(03)00065-0
Fernando Meyer, Stefan Kurtz, Rolf Backofen, Sebastian Will, Michael Beckstette
Structator: fast index-based search for RNA sequence-structure patterns
www.biomedcentral.com/1471-2105/12/214
Heng Li, Richard Durbin
Fast and accurate short read alignment with Burrows–Wheeler transform
dx.doi.org/10.1093/bioinformatics/btp324
Heng Li, Richard Durbin
Fast and accurate long-read alignment with Burrows-Wheeler transform
dx.doi.org/10.1093/bioinformatics/btp698
Jonathan M. Rothberg, Wolfgang Hinz, Todd M. Rearick, Jonathan Schultz, William Mileski, Mel Davey, John H. Leamon, Kim Johnson, Mark J. Milgrew, Matthew Edwards, Jeremy Hoon, Jan F. Simons, David Marran, Jason W. Myers, John F. Davidson, Annika Branting, John R. Nobile, Bernard P. Puc, David Light, Travis A. Clark, Martin Huber, Jeffrey T. Branciforte, Isaac B. Stoner, Simon E. Cawley, Michael Lyons, Yutao Fu, Nils Homer, Marina Sedova, Xin Miao, Brian Reed, Jeffrey Sabina, Erika Feierstein, Michelle Schorn, Mohammad Alanjary, Eileen Dimalanta, Devin Dressman, Rachel Kasinskas, Tanya Sokolsky, Jacqueline A. Fidanza, Eugeni Namsaraev, Kevin J. McKernan, Alan Williams, G. Thomas Roth, James Bustillo
An integrated semiconductor device enabling non-optical genome sequencing
www.nature.com/nature/journal/v475/n7356/full/nature10242.html