Publications & Patents
This is a selection of our own papers as well as
several publications from our customers. You can learn how to apply
our tools, read about successful collaborative research efforts,
get a general overview from one of our reviews or dig into the
details of our algorithms. There is also a list of patents where
our methods or publications have been cited or our tools have
been used for the application.
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- Cartharius K, Frech K, Grote K, Klocke B, Haltmeier
M, Klingenhoff A, Frisch M, Bayerlein M, Werner T
(2005)
MatInspector and beyond: promoter analysis based
on transcription factor binding sites
Bioinformatics 21, 2933-42
(http://bioinformatics.oxfordjournals.org/cgi/content/full/bti473?ijkey=3QavQ7RzEIqzCfS)
[PUBMED: 15860560]
- Cartharius K (2005)
MatInspector: Analysing Promoters for Transcription
Factor Binding Sites
in "Analytical tools for DNA, genes and genomes:
nuts & bolts", by Arseni Markoff ed., The
nuts & bolts series, DNA Press, 2005,
ISBN 0-9748765-1-8.
- Quandt K, Frech K, Karas H, Wingender E, Werner
T (1995)
MatInd and MatInspector: new fast and versatile
tools for detection of consensus matches in nucleotide
sequence data.
Nucleic Acids Res. 23, 4878-84
[PUBMED: 8532532]
BiblioSphere
- Scherf M, Epple A, Werner T (2005)
The next generation of literature analysis: integration of genomic analysis into
text mining.
Brief Bioinform. 6, 287-97
[PUBMED: 16212776]
- Frisch M, Frech K, Klingenhoff A, Cartharius K,
Liebich I, Werner T (2002)
In Silico Prediction of Scaffold/Matrix Attachment
Regions in Large Genomic Sequences.
Genome Research 12, 349-54
[PUBMED: 11827955]
- Liebich I, Bode J, Frisch M, Wingender E (2002)
S/MARt DB: a database on scaffold/matrix attached
regions.
Nucleic Acids Res. 30, 372-74
[PUBMED: 11752340]
- Frisch M, Frech K, Klingenhoff A, Quandt K, Liebich
I, Werner T (2000)
A new tool for the in silico prediction of matrix
attachment regions in large genomic sequences.
in Proceedings of the German Conference on Bioinformatics,
GCB 2000 (Eds. Bornberg-Bauer E, Rost U, Stoye J,
Vingron, M.), 27-34, Logos Verlag, Berlin.
- Scherf M, Klingenhoff A, Werner T (2000)
Highly Specific Localization of Promoter Regions
in Large Genomic Sequences by PromoterInspector:
A Novel Context Analysis Approach.
J. Mol. Biol. 297 (3), 599-606
[PUBMED: 10731414]
- Klingenhoff A, Frech K, Quandt K, Werner T (1999)
Functional promoter modules can be detected by
formal models independent of overall nucleotide sequence
similarity.
Bioinformatics 15, 180-6
[PUBMED: 10222404]
- Lavorgna G, Boncinelli E, Wagner A, Werner T (1998)
Detection of potential target genes in silico?
Trends Genet. 14, 375-6
[PUBMED: 9841458]
- Frech K, Danescu-Mayer
J, Werner T (1997)
A novel method to develop highly specific models
for regulatory units detects a new LTR in GenBank
which contains a functional promoter.
J. Mol. Biol. 270 (5), 674-87
[PUBMED: 9245596]
- Frech K, Quandt K, Werner T (1997)
A new method to develop highly specific models
for regulatory DNA regions.
in Lecture Notes in Computer Science Vol. 1278:
Bioinformatics, German Conference on Bioinformatics,
GCB'96 (Eds. R. Hofestädt, T. Lengauer, M. Löffler,
D. Schomburg), 79-87, Springer Verlag, Berlin Heidelberg
(Download as PDF)
- Frech K, Werner T (1996)
Specific modelling of regulatory units in DNA
sequences.
in Pacific Symposium on Biocomputing 1997 (Eds.
R.B. Altman, A.K. Dunker, L. Hunter, T.E. Klein),
151-162, World Scientific Publishing Co. Pte. Ltd,
Singapore (Download as PDF)
- Morgenstern
B, Dress A, Werner T (1996)
Multiple DNA and protein sequence alignment based
on segment-to-segment comparison.
Proc. Natl. Acad. Sci. USA 93, 12098-103
[PUBMED: 8901539]
- Morgenstern
B, Frech K, Dress A, Werner T (1998)
DIALIGN : Finding local similarities by multiple
sequence alignment.
Bioinformatics 14, 290-4
[PUBMED: 9614273]
- Wolfertstetter F, Frech K, Herrmann G, Werner T
(1996)
Identification of functional elements in unaligned
nucleic acid sequences by a novel tuple search algorithm.
Comp. Appl. Biosci. 12, 71-80
[PUBMED: 8670622]
GenomeInspector
- Quandt K, Grote K, Werner T (1996)
GenomeInspector: Basic software tools for analysis
of spatial correlations between genomic structures
within megabase sequences.
Genomics 33, 301-4
[PUBMED: 8660981]
- Quandt K, Grote K, Werner T (1996)
GenomeInspector: A new approach to detect correlation
patterns of elements on genomic sequences.
Comp. Appl. Biosci. 12, 405-13
[PUBMED: 8996789]
- Quandt K, Frech K, Werner T (1997)
Analysis of transcription control regions by detecting
individual transcription factor binding sites and
assessing their spatial organization.
Mol. Biol (Engl. Tr.) 31, 638-46
ConsInspector
- Frech K, Herrmann G, Werner T (1993)
Computer-assisted prediction, classification,
and delimitation of protein binding sites in nucleic
acids.
Nucleic Acids Res. 21, 1655-64
[PUBMED: 8479918]
- Frech K, Dietze P, Werner T (1997)
ConsInspector 3.0: new library and enhanced functionality.
Comp. Appl. Biosci. 13, 109-10
[PUBMED: 9088717]
- Quandt K, Frech K, Herrmann G, Werner T (1995)
A consensus match scoring system that is correlated
with biological functionality.
in Bioinformatics: From Nucleic Acids and Proteins
to Cell Metabolism (Eds. D. Schomburg, U. Lessel),
47-57, GBF Monographs Volume 18, VCH Publishers,
Inc, NewYork, NY.
- Wingender E, Knüppel R, Dietze P, Karas H,
Frech K, Quandt K, Werner T (1995)
The TRANSFAC database and ConsInd program as tools
for describing and understanding regulatory functions
of the genome.
SAMS, 18-19, 823-6
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