Fakultät für Informatik
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Technische Universität München
Lehrstuhl für Effiziente Algorithmen
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SMURFLite: Combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone
Noah M. Daniels
,
Raghavendra Hosur
,
Bonnie Berger
,
Lenore J. Cowen
Bioinformatics
28
(9), 2012, pp. 1216-1222
Structure-based whole genome realignment reveals many novel non-coding RNAs
Sebastian Will
,
Michael Yu
,
Bonnie Berger
Lecture Notes in Computer Science
7262
, 2012, pp. 341-341
Metabolic network analysis demystified
Leonid Chindelevitch
,
Aviv Regev
,
Bonnie Berger
LNCS/LNBI
6577
, 2011, pp. 31-33
A method for probing the mutational landscape of amyloid structure
Charles W. O'Donnell
,
Jérôme Waldispühl
,
Mieszko Lis
,
Randal Halfmann
,
Srinivas Devadas
,
Susan Lindquist
,
Bonnie Berger
Bioinformatics
27
(13), 2011, pp. 34-42
Efficient traversal of beta-sheet protein folding pathways using ensemble models
Solomon Shenker
,
Charles W. O'Donnell
,
Srinivas Devadas
,
Bonnie Berger
,
Jérôme Waldispühl
LNCS/LNBI
6577
, 2011, pp. 408-423
An algorithmic framework for predicting side-effects of drugs
Nir Atias
,
Roded Sharan
LNCS/LNBI
6044
, 2010, pp. 1-14
SubMAP: Aligning metabolic pathways with subnetwork mappings
Ferhat Ay
,
Tamer Kahveci
LNCS/LNBI
6044
, 2010, pp. 15-30
A self-regulatory system of interlinked signaling feedback loops controls mouse limb patterning
Jean-Denis Benazet
,
Mirko Bischofberger
,
Eva Tiecke
,
Alexandre Gonalves
,
James F. Martin
,
Zuniga
,
Aime
,
Felix Naef
,
Rolf Zeller
LNCS/LNBI
6044
, 2010, pp. 575-576
Admixture aberration analysis: Application to mapping in admixed population using pooled DNA
Sivan Bercovici
,
Dan Geiger
LNCS/LNBI
6044
, 2010, pp. 31-49
Pathway-based functional analysis of metagenomes
Sivan Bercovici
,
Itai Sharon
,
Ron Y. Pinter
,
Tomer Shlomi
LNCS/LNBI
6044
, 2010, pp. 50-64
Hierarchical generative biclustering for microRNA expression analysis
José Caldas
,
Samuel Kaski
LNCS/LNBI
6044
, 2010, pp. 65-79
Genomic DNA
k
-mer spectra: Models and modalities
Benny Chor
,
David Horn
,
Nick Goldman
,
Yaron Levy
,
Tim Massingham
LNCS/LNBI
6044
, 2010, pp. 571-571
Subnetwork state functions define dysregulated subnetworks in cancer
Salim A. Chowdhury
,
Rod K. Nibbe
,
Mark R. Chance
,
Mehmet Koyutürk
LNCS/LNBI
6044
, 2010, pp. 80-95
Proteome coverage prediction for integrated proteomics datasets
Manfred Claassen
,
Ruedi Aebersold
,
Joachim M. Buhmann
LNCS/LNBI
6044
, 2010, pp. 96-109
Discovering regulatory overlapping RNA transcripts
Timothy Danford
,
Robin Dowell
,
Sudeep Agarwala
,
Paula Grisafi
,
Gerald Fink
,
David Gifford
LNCS/LNBI
6044
, 2010, pp. 110-122
Alignment-free phylogenetic reconstruction
Constantinos Daskalakis
,
Sebastien Roch
LNCS/LNBI
6044
, 2010, pp. 123-137
Inference of isoforms from short sequence reads
Jianxing Feng
,
Wei Li
,
Tao Jiang
LNCS/LNBI
6044
, 2010, pp. 138-157
Deciphering the swine-flu pandemics of 1918 and 2009
Richard Goldstein
,
Mario dos Reis
,
Asif Tamuri
,
Alan Hay
LNCS/LNBI
6044
, 2010, pp. 572-573
Distinguishing direct versus indirect transcription factor-DNA interactions
Raluca Gordân
,
Alexander J. Hartemink
,
Martha L. Bulyk
LNCS/LNBI
6044
, 2010, pp. 574-574
The Clark phase-able sample size problem: Long-range phasing and loss of heterozygosity in GWAS
Bjarni V. Halldórsson
,
Derek Aguiar
,
Ryan Tarpine
,
Sorin Istrail
LNCS/LNBI
6044
, 2010, pp. 158-173
Discovering transcriptional modules by combined analysis of expression profiles and regulatory sequences
Yonit Halperin
,
Chaim Linhart
,
Igor Ulitsky
,
Ron Shamir
LNCS/LNBI
6044
, 2010, pp. 578-579
A new algorithm for improving the resolution of cryo-EM density maps
Michael Hirsch
,
Bernhard Schölkopf
,
Michael Habeck
LNCS/LNBI
6044
, 2010, pp. 174-188
Towards automated structure-based NMR resonance assignment
Richard Jang
,
Xin Gao
,
Ming Li
LNCS/LNBI
6044
, 2010, pp. 189-207
Gapped Spectral Dictionaries and their applications for database searches of tandem mass spectra
Kyowon Jeong
,
Sangtae Kim
,
Nuno Bandeira
,
Pavel A. Pevzner
LNCS/LNBI
6044
, 2010, pp. 208-232
naiveBayesCall: An efficient model-based base-calling algorithm for high-throughput sequencing
Wei-Chun Kao
,
Yun S. Song
LNCS/LNBI
6044
, 2010, pp. 233-247
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