cs236818 refs 2005

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Oct 1, 2013 (3 years and 9 months ago)

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Seminar in Bioinformatics


Spring 2005

(236818)


Topics and References


1.

Genome Rearrangements

a)

Background

1.

Pevzner, P. A.:
"Computational Molecular Biology
-

an Algorithmic Approach",

MIT
Press (2000), Chapter 10.

2.

Jones, N. C. and Pevzner, P. A.:
"An Introdu
ction to Bioinformatics Algorithms",

MIT
Press (2004), Chapter 5.

3.

Selected articles from Sankoff, D. and Nadeau, J. H. (eds.):
Comparative Genomics,
Kluwer Academic Publishers, 2000.

b)

Sorting signed permutations

1.

Hannenhalli, S. and Pevzner, P. A.: "Transfor
ming cabbage into turnip: Polynomial
algorithm for sorting signed permutations by reversals",
Journal of the Association for
Computing Machinery (ACM),
Vol. 46, No. 1, pp. 1
-
27 (1999).

2.

Bergeron, A.: “A very elementary presentation of the Hannenhalli
-
Pevzne
r theory”,
Proceedings of the 12
th

Symposium on Combinatorial Pattern Matching (CPM),

Springer
-
Verlag Lecture Notes in Computer Science, Vol. 2089, pp. 106
-
117 (2001).

3.

Bader, D.A., Moret, B.M.E., and Yan, M.: "A linear
-
time algorithm for computing
inversio
n distances between signed permutations with an experimental study,''
J
ournal
of
Computational Biology,

Vol. 8, No. 5, pp. 483
-
491 (2001).

4.

Tannier, E., and Sagot
,

M.
-
F.:

"Sorting by reversals in subquadratic time
,"
Proceedings
of the 15th Annual Symposium
on Combinatorial Pattern Matching (CPM),

Lecture
Notes in Computer Science (LNCS), Vol. 3109, July 2004, pp.

1
-
13.

5.

El
-
Mabrouk, N.: “Sorting Signed Permutations by Reversals and Insertions/Deletions
of Contiguous Segments”;
Journal of Discrete Algorithms.

V
ol. 1, No. 1, pp. 105
-
122
(2000).

c)

Sorting unsigned permutations

1.

Caprara, A.: "Sorting by Reversals is Difficult",
Proceedings of the First Annual
International Conference on Computational Molecular Biology (RECOMB),

ACM
Press, pp. 75
-
83 (1997).

2.

Berman, P.,

Hannenhalli, S. and Karpinski, M.: “1.375
-
approximation Algorithm for
Sorting by Reversals”,
Proceedings of the 10th European Symposium on Algorithms
(ESA),

Springer
-
Verlag Lecture Notes in Computer Science, Vol. 2461, pp. 200
-
210
(2002).

d)

Length
-
weighted
sorting of permutations

1.

Pinter, R.Y., and
Skiena
, S.: "Sorting with length
-
weighted reversals",
Proceedings of
the 13th International Conference on Genome Informatics (GIW),

pp. 103
-
111, (2002).

2.

Bender,
M. A.,
Ge,
D.
He,
S.,
Hu,
H.,
Pinter,
R. Y.,
Skiena,
S.,
and Swidan
, F.
:
"Improved Bounds on Sorting with Length
-
Weighted Reversals",
Proceedings of the
15th Annual ACM
-
SIAM Symposium on Discrete Algorithms (SODA),

pp. 912
-
921
(2004).

3.

Swidan, F., Bender, M.

A. Ge, D.


He, S.


Hu, H.

and Pinter R.

Y.

: "Sorti
ng by length
-
weighted reversals: Dealing with signs and circularity",
Proceedings of the 15th Annual
Symposium on Combinatorial Pattern Matching (CPM),

Lecture Notes in Computer
Science (LNCS), Vol. 3109, July 2004, pp. 32
-
46.

e)

Multichromosomal rearrangemen
t

1.

Tesler, G.: "Efficient algorithms for multichromosomal genome rearrangements",
Journal of Computer and System Sciences,

Vol. 65,

No. 3, pp. 587
-
609 (2002).


f)

Fixed
-
length rearrangement

1.

Chen, T. and Skiena, S.: "Sorting with fixed
-
length reversals",
Discre
te Applied
Mathematics,
Vol. 71, pp. 269
-

295 (1996).

g)

Combining with phylogeny

1.

Wang, L.: “Genome Rearrangement Phylogeny Using Weighbor”,
Proceedings of the
2
nd

International Workshop on Algorithms in Bioinformatics (WABI),

Springer
-
Verlag
Lecture Notes in

Computer Science, Vol. 2452, pp. 112
-
125 (2002).

2.

Earnest
-
DeYoung, J.V., Lerat, E., and Moret, B.M.E., "Reversing gene erosion:
Reconstructing ancestral bacterial genomes from gene
-
content and order data,"
Proceedings of the 4
th

International Workshop on A
lgorithms in Bioinformatics
(WABI),

Springer
-
Verlag Lecture Notes in Computer Science, Vol. 3240, pp. 1
-
13
(2004).

h)

Related papers

1.

Siepel, A.: "An Algorithm to Find All Sorting Reversals",
Proceedings of the Sixth
Annual International Conference on Computat
ional Molecular Biology (RECOMB),

ACM Press, pp. 281
-
290 (2002).

2.

Hartman, T. and Shamir, R.: "A
Simpler

1.5
-
Approximation Algorithm for Sorting by
Transpositions",
Proceedings of the 14
th

Symposium on Combinatorial Pattern
Matching (CPM),

Springer
-
Verlag L
ecture Notes in Computer Science, Vol. 2089, pp.

156
-
169 (2003).

3.

Hartman, T. and Sharan, R.: "A 1.5
-
Approximation Algorithm for Sorting by
Transpositions and Transreversals",
Proceedings of the 4
th

International Workshop on
Algorithms in Bioinformatics (WA
BI),

Springer
-
Verlag Lecture Notes in Computer
Science, Vol. 3240, pp.
50
-
61

(2004)
.

4.

Ozery
-
Flato, M. Shamir, R.: "Two notes on genome rearragnements'', the
Journal of
Bioinformatics

and

Computational Biology
.

Vol. 1, No. 1, pp. 71
-
94 (2003).


2.

Pathway and N
etwork Analysis

a)

Clustering

of protein f
amilies

1.

Linial, N., London, E. and Rabinovich, Y.: "The Geometry of Graphs and Some of its
Algorithmic Applications",
Combinatorica,

Vol. 15, No. 2, pp. 215
-
245 (1995).

2.

Golan Yona, Nathan Linial, Michal Linial: “Proto
Map: Automatic classification of
protein sequences, a hierarchy of protein families, and local maps of the protein space”;
Proteins: Structure, Function and Genetics

37, 360
-
378 (1999).

3.

Sasson O, Linial N, Linial M. “The metric space of proteins
-
comparativ
e study of
clustering algorithms”;
Bioinformatics

18, Suppl 1: S14
-
21 (2002)
.

Also:
http://www.protonet.cs.huji.ac.il/protonet/


4.

Bader, G. D., Betel, D., Hogue, C.W.: “BIND: the Biomolecular Inte
raction Network
Database”;
Nucleic Acids Res
. 31(1): 248
-
50 (2003).

Also:
http://www.bind.ca


b)

Analysis of
m
etabolic
p
athways

1.

Pinter, R. Y., Rokhlenko, O., Tsur, D., and Ziv
-
Ukelson, M.: "Approximate Labelled
Subtree Hom
eomorphism";
Proceedings of the 15th Annual Symposium on
Combinatorial Pattern Matching (CPM),

Lecture Notes in Computer Science (LNCS),
Vol. 3109, July 2004, pp. 59
-
73.

2.

Pinter, R. Y., Rokhlenko, O., Yeger
-
Lotem, E., Ziv
-
Ukelson, M.: "Alignment of
Metaboli
c Pathways"; to appear in
Bioinformatics
, 2005.

3.

Koyuturk M., Grama A., Szpankowski W
.:
"An efficient algorithm for detecting
frequent subgraphs in biological networks",
Bioinformatics

20, Suppl 1: I200
-
I207
(2004).

c)

Flux

balance

a
nalysis of
m
etabolic
p
athwa
ys

1.

Papin, J.A., Price, N.D., and Palsson, B.O.; "Extreme Pathway Lengths and Reaction
Participation in Genome
-
Scale Metabolic Networks,"
Genome Research

12: pp. 1889
-
1900 (2002).

2.

Ibarra, R.U., Edwards, J.S., and Palsson, B.O.; "Escherichia coli K
-
12 underg
oes
adaptive evolution to achieve in silico predicted optimal growth,"
Nature
, 420: pp. 186
-
189 (2002).

3.

Forster J, Famili I, Fu P, Palsson BO, Nielsen J
: "Genome
-
Scale Reconstruction of the
Saccharomyces cerevisiae Metabolic Network,"
Genome Research
, 13(2
): pp. 244
-
253
(2003).

4.

Schuster S, Fell DA, Dandekar T.
:

“A general definition of metabolic pathways useful
for systematic organization and analysis of complex metabolic networks”.
Nature
Biotechnology

18(3): 326
-
32 (2000).

5.

Stelling J, Klamt S, Bettenbrock

K, Schuster S, Gilles ED
: “Metabolic network
structure determines key aspects o
f functionality and regulation”,

Nature

420

(6912):190
-
3 (2002).

d)

Analysis of genomewide networks

1.

Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y, Barkai N
.: “Revealing modu
lar
organization in the yeast transcriptional network”.
Nature Genetics

31(4): 370
-
7
(August 2002).

2.

Tanay A, Sharan R, Kupiec M, Shamir R.
: "
Revealing modularity and organization in
the yeast molecular network by integrated analysis of highly heterogeneous

genomewide data."
Proc Natl Acad Sci

(PNAS
)

101

(9)
, pp.
2981
-
6 (2004).

e)

Dynamic analysis of metabolic pathways

1.

Guet CC, Elowitz MB, Hsing W, Leibler S.
:
“Combinatorial synthesis of genetic
networks”;
Science

296(5572): 1466
-
70 (May 2002).

2.

Vilar JM, Kueh H
Y, Barkai N, Leibler S.
: "
Mechanisms of noise
-
resistance in genetic
oscillators”;
Proc Natl Acad Sci
(PNAS
)

99

(9): 5988
-
92 (April 2002).

3.

Houchmandzadeh B, Wieschaus E, Leibler S.
:

“Establishment of developmental
precision and proportions in the early Dros
ophila embryo”;
Nature

415(6873):798
-
802
(2002).

4.

Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R,
Goodlett DR, Aebersold R, Hood L.
:

“Integrated genomic and proteomic analyses of a
systematically perturbed metabolic network”;
Sc
ience
. 292(5518):

929
-
34 (2001).

f)

Network motifs: discovery and applications

1.

Ideker T, Ozier O, Schwikowski B, Siegel A
.: “Discovering regulatory and signaling
circuits in molecular interaction networks”;
Bioinformatics

18, Suppl 1: S233
-
40

(
2002).

2.

Milo,

R.
,
Shen
-
Orr,

S.,

Itzkovitz,

S.,

Kashtan,

N.,

Chklovskii,

D.,

Alon
, U.
: "Network
Motifs: Simple Building Blocks of Complex Networks",
Science
, Vol
. 298, Issue 5594,
824
-
827 (
October 2002
).

3.

Yeger
-
Lotem,
E.,
Sattath,

S.,
Kashtan,
N.,
Itzkovitz,
S.,
Milo
, R.
, P
inter,
R. Y.,
Alon
,
U.
, and Margalit
, H.
: "Network Motifs in Integrated Cellular Networks of Transcription
Regulation and Protein
-
protein Interaction",
Proceedings of the National Academy of
Sciences (PNAS),

Vol. 101, No. 16
,

pp. 5934
-
5939

(
2004),

4.

Hershber
g, R., Yeger
-
Lotem, E., Margalit, H.
:

"
Chromosomal organization is shaped
by the transcription regulatory network"
,

Trends
in
Genetics
,

Vol. 21, No. 3, pp. 138
-
142 (March

2005
)
.