%%% -*-BibTeX-*-
%%% ====================================================================
%%% BibTeX-file{
%%% author = "Nelson H. F. Beebe",
%%% version = "1.12",
%%% date = "04 July 2008",
%%% time = "09:05:17 MDT",
%%% filename = "tcbb.bib",
%%% address = "University of Utah
%%% Department of Mathematics, 110 LCB
%%% 155 S 1400 E RM 233
%%% Salt Lake City, UT 84112-0090
%%% USA",
%%% telephone = "+1 801 581 5254",
%%% FAX = "+1 801 581 4148",
%%% URL = "http://www.math.utah.edu/~beebe",
%%% checksum = "53443 5842 29346 264976",
%%% email = "beebe at math.utah.edu, beebe at acm.org,
%%% beebe at computer.org (Internet)",
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%%% on Computational Biology and
%%% Bioinformatics; TCBB",
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%%% docstring = "This is a COMPLETE BibTeX bibliography for
%%% IEEE/ACM Transactions on Computational
%%% Biology and Bioinformatics (CODEN ITCBCY,
%%% ISSN 1545-5963), covering all journal issues
%%% from 2004 to date.
%%%
%%% At version 1.12, the COMPLETE journal
%%% coverage looked like this:
%%%
%%% 2004 ( 23) 2006 ( 41) 2008 ( 30)
%%% 2005 ( 37) 2007 ( 69)
%%%
%%% Article: 200
%%%
%%% Total entries: 200
%%%
%%% The journal Web pages can be found at:
%%%
%%% http://www.acm.org/pubs/tcbb/
%%% http://portal.acm.org/browse_dl.cfm?idx=J954
%%%
%%% Qualified subscribers can retrieve the full
%%% text of recent articles in PDF form.
%%%
%%% The initial draft was extracted from the ACM
%%% Web pages.
%%%
%%% ACM copyrights explicitly permit abstracting
%%% with credit, so article abstracts, keywords,
%%% and subject classifications have been
%%% included in this bibliography wherever
%%% available. Article reviews have been
%%% omitted, until their copyright status has
%%% been clarified.
%%%
%%% bibsource keys in the bibliography entries
%%% below indicate the entry originally came
%%% from the computer science bibliography
%%% archive, even though it has likely since
%%% been corrected and updated.
%%%
%%% URL keys in the bibliography point to
%%% World Wide Web locations of additional
%%% information about the entry.
%%%
%%% BibTeX citation tags are uniformly chosen
%%% as name:year:abbrev, where name is the
%%% family name of the first author or editor,
%%% year is a 4-digit number, and abbrev is a
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%%% ====================================================================
%%% Acknowledgement abbreviations:
@String{ack-nhfb = "Nelson H. F. Beebe,
University of Utah,
Department of Mathematics, 110 LCB,
155 S 1400 E RM 233,
Salt Lake City, UT 84112-0090, USA,
Tel: +1 801 581 5254,
FAX: +1 801 581 4148,
e-mail: \path|beebe@math.utah.edu|,
\path|beebe@acm.org|,
\path|beebe@computer.org| (Internet),
URL: \path|http://www.math.utah.edu/~beebe/|"}
%%% ====================================================================
%%% Journal abbreviations:
@String{j-TCBB = "IEEE/ACM Transactions on Computational
Biology and Bioinformatics"}
%%% ====================================================================
%%% Bibliography entries:
@Article{Williams:2004:WM,
author = "Michael R. Williams",
title = "Welcome Message",
journal = j-TCBB,
volume = "1",
number = "1",
pages = "1--1",
month = jan,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Nov 22 06:42:56 MST 2004",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Gusfield:2004:IIA,
author = "Dan Gusfield",
title = "Introduction to the {IEEE\slash ACM Transactions on
Computational Biology and Bioinformatics}",
journal = j-TCBB,
volume = "1",
number = "1",
pages = "2--3",
month = jan,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Nov 22 06:42:56 MST 2004",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Williams:2004:INA,
author = "Michael R. Williams",
title = "Introduction of New {Associate Editors}",
journal = j-TCBB,
volume = "1",
number = "1",
pages = "4--12",
month = jan,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Nov 22 06:42:56 MST 2004",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Moret:2004:PNM,
author = "Bernard M. E. Moret and Luay Nakhleh and Tandy Warnow
and C. Randal Linder and Anna Tholse and Anneke
Padolina and Jerry Sun and Ruth Timme",
title = "Phylogenetic Networks: Modeling, Reconstructibility,
and Accuracy",
journal = j-TCBB,
volume = "1",
number = "1",
pages = "13--23",
month = jan,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Nov 22 06:42:56 MST 2004",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Madeira:2004:BAB,
author = "Sara C. Madeira and Arlindo L. Oliveira",
title = "Biclustering Algorithms for Biological Data Analysis:
{A} Survey",
journal = j-TCBB,
volume = "1",
number = "1",
pages = "24--45",
month = jan,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Nov 22 06:42:56 MST 2004",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Preparata:2004:SHR,
author = "Franco P. Preparata",
title = "Sequencing-by-Hybridization Revisited: The
Analog-Spectrum Proposal",
journal = j-TCBB,
volume = "1",
number = "1",
pages = "46--52",
month = jan,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Nov 22 06:42:56 MST 2004",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Hochsmann:2004:PMR,
author = "Matthias H{\"o}chsmann and Bj{\"o}rn Voss and Robert
Giegerich",
title = "Pure Multiple {RNA} Secondary Structure Alignments:
{A} Progressive Profile Approach",
journal = j-TCBB,
volume = "1",
number = "1",
pages = "53--62",
month = jan,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Nov 22 06:42:56 MST 2004",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Anonymous:2004:INA,
author = "Anonymous",
title = "Introduction of New {Associate Editor}",
journal = j-TCBB,
volume = "1",
number = "2",
pages = "65--65",
month = apr,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Nov 22 06:42:56 MST 2004",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Witwer:2004:PCR,
author = "Christina Witwer and Ivo L. Hofacker and Peter F.
Stadler",
title = "Prediction of Consensus {RNA} Secondary Structures
Including Pseudoknots",
journal = j-TCBB,
volume = "1",
number = "2",
pages = "66--77",
month = apr,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Nov 22 06:42:56 MST 2004",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Bafna:2004:NRE,
author = "Vineet Bafna and Vikas Bansal",
title = "The Number of Recombination Events in a Sample
History: Conflict Graph and Lower Bounds",
journal = j-TCBB,
volume = "1",
number = "2",
pages = "78--90",
month = apr,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Nov 22 06:42:56 MST 2004",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Raphael:2004:UPM,
author = "Benjamin Raphael and Lung-Tien Liu and George
Varghese",
title = "A Uniform Projection Method for Motif Discovery in
{DNA} Sequences",
journal = j-TCBB,
volume = "1",
number = "2",
pages = "91--94",
month = apr,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Nov 22 06:42:56 MST 2004",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Gusfield:2004:INA,
author = "Dan Gusfield",
title = "Introduction of New {Associate Editors}",
journal = j-TCBB,
volume = "1",
number = "3",
pages = "97--97",
month = jul,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Jan 24 14:15:55 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Scheid:2004:SDS,
author = "Stefanie Scheid and Rainer Spang",
title = "A Stochastic Downhill Search Algorithm for Estimating
the Local False Discovery Rate",
journal = j-TCBB,
volume = "1",
number = "3",
pages = "98--108",
month = jul,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Jan 24 14:15:55 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Dress:2004:CSG,
author = "Andreas W. M. Dress and Daniel H. Huson",
title = "Constructing Splits Graphs",
journal = j-TCBB,
volume = "1",
number = "3",
pages = "109--115",
month = jul,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Jan 24 14:15:55 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Cameron:2004:IGA,
author = "Michael Cameron and Hugh E. Williams and Adam
Cannane",
title = "Improved Gapped Alignment in {BLAST}",
journal = j-TCBB,
volume = "1",
number = "3",
pages = "116--129",
month = jul,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Jan 24 14:15:55 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Evans:2004:UDT,
author = "Steven N. Evans and Tandy Warnow",
title = "Unidentifiable Divergence Times in Rates-across-Sites
Models",
journal = j-TCBB,
volume = "1",
number = "3",
pages = "130--134",
month = jul,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Jan 24 14:15:55 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Kim:2004:GEW,
author = "Junhyong Kim and Inge Jonassen",
title = "Guest Editorial: {WABI} Special Section Part 1",
journal = j-TCBB,
volume = "1",
number = "4",
pages = "137--138",
month = oct,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Jan 24 14:15:55 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Csuros:2004:MSS,
author = "Miklos Csuros",
title = "Maximum-Scoring Segment Sets",
journal = j-TCBB,
volume = "1",
number = "4",
pages = "139--150",
month = oct,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Jan 24 14:15:55 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Huson:2004:PSN,
author = "Daniel H. Huson and Tobias Dezulian and Tobias Klopper
and Mike A. Steel",
title = "Phylogenetic Super-Networks from Partial Trees",
journal = j-TCBB,
volume = "1",
number = "4",
pages = "151--158",
month = oct,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Jan 24 14:15:55 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Bannai:2004:ADO,
author = "Hideo Bannai and Heikki Hyyro and Ayumi Shinohara and
Masayuki Takeda and Kenta Nakai and Satoru Miyano",
title = "An {$O(N^2)$} Algorithm for Discovering Optimal
{Boolean} Pattern Pairs",
journal = j-TCBB,
volume = "1",
number = "4",
pages = "159--170",
month = oct,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Jan 24 14:15:55 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Gramm:2004:PTA,
author = "Jens Gramm",
title = "A Polynomial-Time Algorithm for the Matching of
Crossing Contact-Map Patterns",
journal = j-TCBB,
volume = "1",
number = "4",
pages = "171--180",
month = oct,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Jan 24 14:15:55 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Ye:2004:UUD,
author = "Jieping Ye and Tao Li and Tao Xiong and Ravi
Janardan",
title = "Using Uncorrelated Discriminant Analysis for Tissue
Classification with Gene Expression Data",
journal = j-TCBB,
volume = "1",
number = "4",
pages = "181--190",
month = oct,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Jan 24 14:15:55 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Anonymous:2004:AI,
author = "Anonymous",
title = "Annual Index",
journal = j-TCBB,
volume = "1",
number = "4",
pages = "191--192",
month = oct,
year = "2004",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Jan 24 14:15:55 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Kim:2005:GEW,
author = "Junhyong Kim and Inge Jonassen",
title = "Guest Editorial: {WABI} Special Section Part {II}",
journal = j-TCBB,
volume = "2",
number = "1",
pages = "1--2",
month = jan,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Tue Apr 12 07:11:54 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Allali:2005:NDH,
author = "Julien Allali and Marie-France Sagot",
title = "A New Distance for High Level {RNA} Secondary
Structure Comparison",
journal = j-TCBB,
volume = "2",
number = "1",
pages = "3--14",
month = jan,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Tue Apr 12 07:11:54 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Bertrand:2005:TRL,
author = "Denis Bertrand and Olivier Gascuel",
title = "Topological Rearrangements and Local Search Method for
Tandem Duplication Trees",
journal = j-TCBB,
volume = "2",
number = "1",
pages = "15--28",
month = jan,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Tue Apr 12 07:11:54 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Brown:2005:OMS,
author = "Daniel G. Brown",
title = "Optimizing Multiple Seeds for Protein Homology
Search",
journal = j-TCBB,
volume = "2",
number = "1",
pages = "29--38",
month = jan,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Tue Apr 12 07:11:54 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Gusfield:2005:EST,
author = "Dan Gusfield",
title = "Editorial-State of the Transaction",
journal = j-TCBB,
volume = "2",
number = "1",
pages = "39--39",
month = jan,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Tue Apr 12 07:11:54 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Pisanti:2005:BMG,
author = "Nadia Pisanti and Maxime Crochemore and Roberto Grossi
and Marie-France Sagot",
title = "Bases of Motifs for Generating Repeated Patterns with
Wild Cards",
journal = j-TCBB,
volume = "2",
number = "1",
pages = "40--50",
month = jan,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Tue Apr 12 07:11:54 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Kucherov:2005:MLF,
author = "Gregory Kucherov and Laurent Noe and Mikhail
Roytberg",
title = "Multiseed Lossless Filtration",
journal = j-TCBB,
volume = "2",
number = "1",
pages = "51--61",
month = jan,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Tue Apr 12 07:11:54 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Liu:2005:TMB,
author = "Ying Liu and Shamkant B. Navathe and Jorge Civera and
Venu Dasigi and Ashwin Ram and Brian J. Ciliax and Ray
Dingledine",
title = "Text Mining Biomedical Literature for Discovering
Gene-to-Gene Relationships: {A} Comparative Study of
Algorithms",
journal = j-TCBB,
volume = "2",
number = "1",
pages = "62--76",
month = jan,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Tue Apr 12 07:11:54 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Staff:2005:RL,
author = "{IEEE/ACM Transactions on Computational Biology and
Bioinformatics staff}",
title = "2004 Reviewers List",
journal = j-TCBB,
volume = "2",
number = "1",
pages = "77--77",
month = jan,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Tue Apr 12 07:11:54 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Ling:2005:GEIa,
author = "Charles X. Ling and William Stafford Noble and Qiang
Yang",
title = "{Guest Editors}' Introduction to the {Special Issue:
Machine Learning for Bioinformatics---Part 1}",
journal = j-TCBB,
volume = "2",
number = "2",
pages = "81--82",
month = apr,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Wed Jun 22 17:33:35 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Au:2005:ACG,
author = "Wai-Ho Au and Keith C. C. Chan and Andrew K. C. Wong
and Yang Wang",
title = "Attribute Clustering for Grouping, Selection, and
Classification of Gene Expression Data",
journal = j-TCBB,
volume = "2",
number = "2",
pages = "83--101",
month = apr,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Wed Jun 22 17:33:35 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Biyani:2005:JCP,
author = "Pravesh Biyani and Xiaolin Wu and Abhijit Sinha",
title = "Joint Classification and Pairing of Human
Chromosomes",
journal = j-TCBB,
volume = "2",
number = "2",
pages = "102--109",
month = apr,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Wed Jun 22 17:33:35 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Furlanello:2005:SLM,
author = "Cesare Furlanello and Maria Serafini and Stefano
Merler and Giuseppe Jurman",
title = "Semisupervised Learning for Molecular Profiling",
journal = j-TCBB,
volume = "2",
number = "2",
pages = "110--118",
month = apr,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Wed Jun 22 17:33:35 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Mamitsuka:2005:ELK,
author = "Hiroshi Mamitsuka",
title = "Essential Latent Knowledge for Protein-Protein
Interactions: Analysis by an Unsupervised Learning
Approach",
journal = j-TCBB,
volume = "2",
number = "2",
pages = "119--130",
month = apr,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Wed Jun 22 17:33:35 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Rajapakse:2005:MED,
author = "Jagath C. Rajapakse and Loi Sy Ho",
title = "{Markov} Encoding for Detecting Signals in Genomic
Sequences",
journal = j-TCBB,
volume = "2",
number = "2",
pages = "131--142",
month = apr,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Wed Jun 22 17:33:35 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Rogers:2005:LPD,
author = "Simon Rogers and Mark Girolami and Colin Campbell and
Rainer Breitling",
title = "The Latent Process Decomposition of {cDNA} Microarray
Data Sets",
journal = j-TCBB,
volume = "2",
number = "2",
pages = "143--156",
month = apr,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Wed Jun 22 17:33:35 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Xu:2005:FRP,
author = "Jinbo Xu",
title = "Fold Recognition by Predicted Alignment Accuracy",
journal = j-TCBB,
volume = "2",
number = "2",
pages = "157--165",
month = apr,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Wed Jun 22 17:33:35 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Shen:2005:DRB,
author = "Li Shen and Eng Chong Tan",
title = "Dimension Reduction-Based Penalized Logistic
Regression for Cancer Classification Using Microarray
Data",
journal = j-TCBB,
volume = "2",
number = "2",
pages = "166--175",
month = apr,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Wed Jun 22 17:33:35 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Ling:2005:GEIb,
author = "C. X. Ling and W. S. Noble and Q. Yang",
title = "{Guest Editor}'s Introduction to the {Special Issue:
Machine Learning for Bioinformatics---Part 2}",
journal = j-TCBB,
volume = "2",
number = "3",
pages = "177--178",
month = jul,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Tue Sep 20 06:11:25 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Schliep:2005:AGE,
author = "Alexander Schliep and Ivan G. Costa and Christine
Steinhoff and Alexander Schonhuth",
title = "Analyzing Gene Expression Time-Courses",
journal = j-TCBB,
volume = "2",
number = "3",
pages = "179--193",
month = jul,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Tue Sep 20 06:11:25 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Kundaje:2005:CST,
author = "Anshul Kundaje and Manuel Middendorf and Feng Gao and
Chris Wiggins and Christina Leslie",
title = "Combining Sequence and Time Series Expression Data to
Learn Transcriptional Modules",
journal = j-TCBB,
volume = "2",
number = "3",
pages = "194--202",
month = jul,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Tue Sep 20 06:11:25 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Kaski:2005:ACE,
author = "Samuel Kaski and Janne Nikkila and Janne Sinkkonen and
Leo Lahti and Juha E. A. Knuuttila and Christophe
Roos",
title = "Associative Clustering for Exploring Dependencies
between Functional Genomics Data Sets",
journal = j-TCBB,
volume = "2",
number = "3",
pages = "203--216",
month = jul,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Tue Sep 20 06:11:25 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Zhang:2005:PMF,
author = "Jingfen Zhang and Wen Gao and Jinjin Cai and Simin He
and Rong Zeng and Runsheng Chen",
title = "Predicting Molecular Formulas of Fragment Ions with
Isotope Patterns in Tandem Mass Spectra",
journal = j-TCBB,
volume = "2",
number = "3",
pages = "217--230",
month = jul,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Tue Sep 20 06:11:25 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Keedwell:2005:DGN,
author = "Edward Keedwell and Ajit Narayanan",
title = "Discovering Gene Networks with a Neural-Genetic
Hybrid",
journal = j-TCBB,
volume = "2",
number = "3",
pages = "231--242",
month = jul,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Tue Sep 20 06:11:25 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Hawkins:2005:ARN,
author = "John Hawkins and Mikael Boden",
title = "The Applicability of Recurrent Neural Networks for
Biological Sequence Analysis",
journal = j-TCBB,
volume = "2",
number = "3",
pages = "243--253",
month = jul,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Tue Sep 20 06:11:25 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Gustafsson:2005:CAL,
author = "Mika Gustafsson and Michael Hornquist and Anna
Lombardi",
title = "Constructing and Analyzing a Large-Scale Gene-to-Gene
Regulatory Network-Lasso-Constrained Inference and
Biological Validation",
journal = j-TCBB,
volume = "2",
number = "3",
pages = "254--261",
month = jul,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Tue Sep 20 06:11:25 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Demir:2005:LTP,
author = "Cigdem Demir and S. Humayun Gultekin and Bulent
Yener",
title = "Learning the Topological Properties of Brain Tumors",
journal = j-TCBB,
volume = "2",
number = "3",
pages = "262--270",
month = jul,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Tue Sep 20 06:11:25 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Anonymous:2005:CPS,
author = "Anonymous",
title = "Call for Papers for {Special Issue on Computational
Intelligence Approaches in Computational Biology and
Bioinformatics}",
journal = j-TCBB,
volume = "2",
number = "3",
pages = "271--271",
month = jul,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Tue Sep 20 06:11:25 MDT 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Cickovski:2005:FTD,
author = "Trevor M. Cickovski and Chengbang Huang and Rajiv
Chaturvedi and Tilmann Glimm and H. George E. Hentschel
and Mark S. Alber and James A. Glazier and Stuart A.
Newman and Jesus A. Izaguirre",
title = "A Framework for Three-Dimensional Simulation of
Morphogenesis",
journal = j-TCBB,
volume = "2",
number = "4",
pages = "273--288",
month = oct,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Fri Nov 18 05:22:15 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Boscolo:2005:GFN,
author = "Riccardo Boscolo and Chiara Sabatti and James C. Liao
and Vwani P. Roychowdhury",
title = "A Generalized Framework for Network Component
Analysis",
journal = j-TCBB,
volume = "2",
number = "4",
pages = "289--301",
month = oct,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Fri Nov 18 05:22:15 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Chen:2005:AOG,
author = "Xin Chen and Jie Zheng and Zheng Fu and Peng Nan and
Yang Zhong and Stefano Lonardi and Tao Jiang",
title = "Assignment of Orthologous Genes via Genome
Rearrangement",
journal = j-TCBB,
volume = "2",
number = "4",
pages = "302--315",
month = oct,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Fri Nov 18 05:22:15 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Turner:2005:BMS,
author = "Heather L. Turner and Trevor C. Bailey and Wojtek J.
Krzanowski and Cheryl A. Hemingway",
title = "Biclustering Models for Structured Microarray Data",
journal = j-TCBB,
volume = "2",
number = "4",
pages = "316--329",
month = oct,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Fri Nov 18 05:22:15 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Sevilla:2005:CBG,
author = "Jose L. Sevilla and Victor Segura and Adam Podhorski
and Elizabeth Guruceaga and Jose M. Mato and Luis A.
Martinez-Cruz and Fernando J. Corrales and Angel
Rubio",
title = "Correlation between Gene Expression and {GO} Semantic
Similarity",
journal = j-TCBB,
volume = "2",
number = "4",
pages = "330--338",
month = oct,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Fri Nov 18 05:22:15 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Yoon:2005:DCB,
author = "Sungroh Yoon and Christine Nardini and Luca Benini and
Giovanni De Micheli",
title = "Discovering Coherent Biclusters from Gene Expression
Data Using Zero-Suppressed Binary Decision Diagrams",
journal = j-TCBB,
volume = "2",
number = "4",
pages = "339--354",
month = oct,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Fri Nov 18 05:22:15 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Tseng:2005:EMG,
author = "Vincent S. Tseng and Ching-Pin Kao",
title = "Efficiently Mining Gene Expression Data via a Novel
Parameterless Clustering Method",
journal = j-TCBB,
volume = "2",
number = "4",
pages = "355--365",
month = oct,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Fri Nov 18 05:22:15 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Zhang:2005:SGN,
author = "Shaojie Zhang and Brian Haas and Eleazar Eskin and
Vineet Bafna",
title = "Searching Genomes for Noncoding {RNA} Using {FastR}",
journal = j-TCBB,
volume = "2",
number = "4",
pages = "366--379",
month = oct,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Fri Nov 18 05:22:15 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Anonymous:2005:AI,
author = "Anonymous",
title = "2005 Annual Index",
journal = j-TCBB,
volume = "2",
number = "4",
pages = "380--384",
month = oct,
year = "2005",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Fri Nov 18 05:22:15 MST 2005",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Gusfield:2006:SJ,
author = "Dan Gusfield",
title = "State of the Journal",
journal = j-TCBB,
volume = "3",
number = "1",
pages = "1--1",
month = jan,
year = "2006",
CODEN = "ITCBCY",
DOI = "http://dx.doi.org/10.1109/TCBB.2006.12",
ISSN = "1545-5963",
bibdate = "Thu Feb 16 11:06:15 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Berger:2006:JAG,
author = "John A. Berger and Sampsa Hautaniemi and Sanjit K.
Mitra and Jaakko Astola",
title = "Jointly Analyzing Gene Expression and Copy Number Data
in Breast Cancer Using Data Reduction Models",
journal = j-TCBB,
volume = "3",
number = "1",
pages = "2--16",
month = jan,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Feb 16 11:06:15 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Sebastian:2006:STA,
author = "Rafael Sebastian and Maria-Elena Diaz and Guillermo
Ayala and Kresimir Letinic and Jose Moncho-Bogani and
Derek Toomre",
title = "Spatio-Temporal Analysis of Constitutive Exocytosis in
Epithelial Cells",
journal = j-TCBB,
volume = "3",
number = "1",
pages = "17--32",
month = jan,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Feb 16 11:06:15 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Hershkovitz:2006:SAR,
author = "Eli Hershkovitz and Guillermo Sapiro and Allen
Tannenbaum and Loren Dean Williams",
title = "Statistical Analysis of {RNA} Backbone",
journal = j-TCBB,
volume = "3",
number = "1",
pages = "33--46",
month = jan,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Feb 16 11:06:15 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Dawy:2006:GMM,
author = "Zaher Dawy and Bernhard Goebel and Joachim Hagenauer
and Christophe Andreoli and Thomas Meitinger and Jakob
C. Mueller",
title = "Gene Mapping and Marker Clustering Using {Shannon}'s
Mutual Information",
journal = j-TCBB,
volume = "3",
number = "1",
pages = "47--56",
month = jan,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Feb 16 11:06:15 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Goutsias:2006:HMM,
author = "John Goutsias",
title = "A Hidden {Markov} Model for Transcriptional Regulation
in Single Cells",
journal = j-TCBB,
volume = "3",
number = "1",
pages = "57--71",
month = jan,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Feb 16 11:06:15 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Rueda:2006:HCA,
author = "Luis Rueda and Vidya Vidyadharan",
title = "A Hill-Climbing Approach for Automatic Gridding of
{cDNA} Microarray Images",
journal = j-TCBB,
volume = "3",
number = "1",
pages = "72--83",
month = jan,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Feb 16 11:06:15 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Semple:2006:UNC,
author = "Charles Semple and Mike Steel",
title = "Unicyclic Networks: Compatibility and Enumeration",
journal = j-TCBB,
volume = "3",
number = "1",
pages = "84--91",
month = jan,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Feb 16 11:06:15 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Roch:2006:SPP,
author = "Sebastien Roch",
title = "A Short Proof that Phylogenetic Tree Reconstruction by
Maximum Likelihood Is Hard",
journal = j-TCBB,
volume = "3",
number = "1",
pages = "92--94",
month = jan,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Feb 16 11:06:15 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Anonymous:2006:RL,
author = "Anonymous",
title = "2005 Reviewers List",
journal = j-TCBB,
volume = "3",
number = "1",
pages = "95--96",
month = jan,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Feb 16 11:06:15 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Gusfield:2006:INA,
author = "Dan Gusfield",
title = "Introduction of New {Associate Editors}",
journal = j-TCBB,
volume = "3",
number = "2",
pages = "97--97",
month = apr,
year = "2006",
CODEN = "ITCBCY",
DOI = "http://dx.doi.org/10.1109/TCBB.2006.25",
ISSN = "1545-5963",
bibdate = "Wed Jun 7 06:38:18 MDT 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Chu:2006:BSM,
author = "Wei Chu and Zoubin Ghahramani and Alexei
Podtelezhnikov and David L. Wild",
title = "{Bayesian} Segmental Models with Multiple Sequence
Alignment Profiles for Protein Secondary Structure and
Contact Map Prediction",
journal = j-TCBB,
volume = "3",
number = "2",
pages = "98--113",
month = apr,
year = "2006",
CODEN = "ITCBCY",
DOI = "http://dx.doi.org/10.1109/TCBB.2006.17",
ISSN = "1545-5963",
bibdate = "Wed Jun 7 06:38:18 MDT 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Danziger:2006:FCM,
author = "Samuel A. Danziger and S. Joshua Swamidass and Jue
Zeng and Lawrence R. Dearth and Qiang Lu and Jonathan
H. Chen and Jianlin Cheng and Vinh P. Hoang and Hiroto
Saigo and Ray Luo and Pierre Baldi and Rainer K.
Brachmann and Richard H. Lathrop",
title = "Functional Census of Mutation Sequence Spaces: The
Example of p53 Cancer Rescue Mutants",
journal = j-TCBB,
volume = "3",
number = "2",
pages = "114--125",
month = apr,
year = "2006",
CODEN = "ITCBCY",
DOI = "http://dx.doi.org/10.1109/TCBB.2006.22",
ISSN = "1545-5963",
bibdate = "Wed Jun 7 06:38:18 MDT 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Carvalho:2006:EAI,
author = "Alexandra M. Carvalho and Ana T. Freitas and Arlindo
L. Oliveira and Marie-France Sagot",
title = "An Efficient Algorithm for the Identification of
Structured Motifs in {DNA} Promoter Sequences",
journal = j-TCBB,
volume = "3",
number = "2",
pages = "126--140",
month = apr,
year = "2006",
CODEN = "ITCBCY",
DOI = "http://dx.doi.org/10.1109/TCBB.2006.16",
ISSN = "1545-5963",
bibdate = "Wed Jun 7 06:38:18 MDT 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Brown:2006:IPA,
author = "Daniel G. Brown and Ian M. Harrower",
title = "Integer Programming Approaches to Haplotype Inference
by Pure Parsimony",
journal = j-TCBB,
volume = "3",
number = "2",
pages = "141--154",
month = apr,
year = "2006",
CODEN = "ITCBCY",
DOI = "http://dx.doi.org/10.1109/TCBB.2006.24",
ISSN = "1545-5963",
bibdate = "Wed Jun 7 06:38:18 MDT 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Vass:2006:JMB,
author = "Marc T. Vass and Clifford A. Shaffer and Naren
Ramakrishnan and Layne T. Watson and John J. Tyson",
title = "The {JigCell} Model Builder: {A} Spreadsheet Interface
for Creating Biochemical Reaction Network Models",
journal = j-TCBB,
volume = "3",
number = "2",
pages = "155--164",
month = apr,
year = "2006",
CODEN = "ITCBCY",
DOI = "http://dx.doi.org/10.1109/TCBB.2006.27",
ISSN = "1545-5963",
bibdate = "Wed Jun 7 06:38:18 MDT 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Chen:2006:MFS,
author = "Duhong Chen and Oliver Eulenstein and David
Fernandez-Baca and Michael Sanderson",
title = "Minimum-Flip Supertrees: Complexity and Algorithms",
journal = j-TCBB,
volume = "3",
number = "2",
pages = "165--173",
month = apr,
year = "2006",
CODEN = "ITCBCY",
DOI = "http://dx.doi.org/10.1109/TCBB.2006.26",
ISSN = "1545-5963",
bibdate = "Wed Jun 7 06:38:18 MDT 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Sevon:2006:TTP,
author = "Petteri Sevon and Hannu Toivonen and Vesa Ollikainen",
title = "{TreeDT}: Tree Pattern Mining for Gene Mapping",
journal = j-TCBB,
volume = "3",
number = "2",
pages = "174--185",
month = apr,
year = "2006",
CODEN = "ITCBCY",
DOI = "http://dx.doi.org/10.1109/TCBB.2006.28",
ISSN = "1545-5963",
bibdate = "Wed Jun 7 06:38:18 MDT 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Song:2006:CNS,
author = "Yun S. Song",
title = "A Concise Necessary and Sufficient Condition for the
Existence of a Galled-Tree",
journal = j-TCBB,
volume = "3",
number = "2",
pages = "186--191",
month = apr,
year = "2006",
CODEN = "ITCBCY",
DOI = "http://dx.doi.org/10.1109/TCBB.2006.15",
ISSN = "1545-5963",
bibdate = "Wed Jun 7 06:38:18 MDT 2006",
bibsource = "http://portal.acm.org/",
abstract = "Galled-trees are a special class of graphical
representation of evolutionary history that has proven
amenable to efficient, polynomial-time algorithms. The
goal of this paper is to construct a concise necessary
and sufficient condition for the existence of a
galled-tree for $M$, a set of binary sequences that
purportedly have evolved in the presence of
recombination. Both root-known and root-unknown cases
are considered here.",
acknowledgement = ack-nhfb,
}
@Article{Daras:2006:TDS,
author = "Petros Daras and Dimitrios Zarpalas and Apostolos
Axenopoulos and Dimitrios Tzovaras and Michael
Gerassimos Strintzis",
title = "Three-Dimensional Shape-Structure Comparison Method
for Protein Classification",
journal = j-TCBB,
volume = "3",
number = "3",
pages = "193--207",
month = jul,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Sep 11 07:36:29 MDT 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Yu:2006:MPA,
author = "Weichuan Yu and Xiaoye Li and Junfeng Liu and Baolin
Wu and Kenneth R. Williams and Hongyu Zhao",
title = "Multiple Peak Alignment in Sequential Data Analysis:
{A} Scale-Space-Based Approach",
journal = j-TCBB,
volume = "3",
number = "3",
pages = "208--219",
month = jul,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Sep 11 07:36:29 MDT 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Abul:2006:PAE,
author = "Osman Abul and Reda Alhajj and Faruk Polat",
title = "A Powerful Approach for Effective Finding of
Significantly Differentially Expressed Genes",
journal = j-TCBB,
volume = "3",
number = "3",
pages = "220--231",
month = jul,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Sep 11 07:36:29 MDT 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Nagarajan:2006:CSC,
author = "Radhakrishnan Nagarajan and Meenakshi Upreti",
title = "Correlation Statistics for {cDNA} Microarray Image
Analysis",
journal = j-TCBB,
volume = "3",
number = "3",
pages = "232--238",
month = jul,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Sep 11 07:36:29 MDT 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Song:2006:CAP,
author = "Yun S. Song and Rune Lyngso and Jotun Hein",
title = "Counting All Possible Ancestral Configurations of
Sample Sequences in Population Genetics",
journal = j-TCBB,
volume = "3",
number = "3",
pages = "239--251",
month = jul,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Sep 11 07:36:29 MDT 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Pirinen:2006:FCG,
author = "Matti Pirinen and Dario Gasbarra",
title = "Finding Consistent Gene Transmission Patterns on Large
and Complex Pedigrees",
journal = j-TCBB,
volume = "3",
number = "3",
pages = "252--262",
month = jul,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Sep 11 07:36:29 MDT 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Popescu:2006:FMG,
author = "Mihail Popescu and James M. Keller and Joyce A.
Mitchell",
title = "Fuzzy Measures on the Gene Ontology for Gene Product
Similarity",
journal = j-TCBB,
volume = "3",
number = "3",
pages = "263--274",
month = jul,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Sep 11 07:36:29 MDT 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Bernt:2006:GRB,
author = "Matthias Bernt and Daniel Merkle and Martin
Middendorf",
title = "Genome Rearrangement Based on Reversals that Preserve
Conserved Intervals",
journal = j-TCBB,
volume = "3",
number = "3",
pages = "275--288",
month = jul,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Sep 11 07:36:29 MDT 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Berry:2006:IPC,
author = "Vincent Berry and Fran{\c{c}}ois Nicolas",
title = "Improved Parameterized Complexity of the Maximum
Agreement Subtree and Maximum Compatible Tree
Problems",
journal = j-TCBB,
volume = "3",
number = "3",
pages = "289--302",
month = jul,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Sep 11 07:36:29 MDT 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Sharan:2006:ITP,
author = "Roded Sharan and Bjarni V. Halldorsson and Sorin
Istrail",
title = "Islands of Tractability for Parsimony Haplotyping",
journal = j-TCBB,
volume = "3",
number = "3",
pages = "303--311",
month = jul,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Sep 11 07:36:29 MDT 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Zhang:2006:SGR,
author = "Chaolin Zhang and Xuesong Lu and Xuegong Zhang",
title = "Significance of Gene Ranking for Classification of
Microarray Samples",
journal = j-TCBB,
volume = "3",
number = "3",
pages = "312--320",
month = jul,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Mon Sep 11 07:36:29 MDT 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Casadio:2006:GEI,
author = "Rita Casadio",
title = "{Guest Editor}'s Introduction to the Special Issue on
Computational Biology and Bioinformatics -- Part 1",
journal = j-TCBB,
volume = "3",
number = "4",
pages = "321--322",
month = oct,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Nov 30 19:05:58 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Snir:2006:UMC,
author = "Sagi Snir and Satish Rao",
title = "Using Max Cut to Enhance Rooted Trees Consistency",
journal = j-TCBB,
volume = "3",
number = "4",
pages = "323--333",
month = oct,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Nov 30 19:05:58 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Ganapathy:2006:PIB,
author = "Ganeshkumar Ganapathy and Barbara Goodson and Robert
Jansen and Hai-son Le and Vijaya Ramachandran and Tandy
Warnow",
title = "Pattern Identification in Biogeography",
journal = j-TCBB,
volume = "3",
number = "4",
pages = "334--346",
month = oct,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Nov 30 19:05:58 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Wernicke:2006:EDN,
author = "Sebastian Wernicke",
title = "Efficient Detection of Network Motifs",
journal = j-TCBB,
volume = "3",
number = "4",
pages = "347--359",
month = oct,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Nov 30 19:05:58 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Lacroix:2006:MSG,
author = "Vincent Lacroix and Cristina G. Fernandes and
Marie-France Sagot",
title = "Motif Search in Graphs: Application to Metabolic
Networks",
journal = j-TCBB,
volume = "3",
number = "4",
pages = "360--368",
month = oct,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Nov 30 19:05:58 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Elias:2006:AAS,
author = "Isaac Elias and Tzvika Hartman",
title = "A $1.375$-Approximation Algorithm for Sorting by
Transpositions",
journal = j-TCBB,
volume = "3",
number = "4",
pages = "369--379",
month = oct,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Nov 30 19:05:58 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Labarre:2006:NBT,
author = "Anthony Labarre",
title = "New Bounds and Tractable Instances for the
Transposition Distance",
journal = j-TCBB,
volume = "3",
number = "4",
pages = "380--394",
month = oct,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Nov 30 19:05:58 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Sammeth:2006:CTR,
author = "Michael Sammeth and Jens Stoye",
title = "Comparing Tandem Repeats with Duplications and
Excisions of Variable Degree",
journal = j-TCBB,
volume = "3",
number = "4",
pages = "395--407",
month = oct,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Nov 30 19:05:58 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Bilu:2006:FAO,
author = "Yonatan Bilu and Pankaj K. Agarwal and Rachel
Kolodny",
title = "Faster Algorithms for Optimal Multiple Sequence
Alignment Based on Pairwise Comparisons",
journal = j-TCBB,
volume = "3",
number = "4",
pages = "408--422",
month = oct,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Nov 30 19:05:58 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Song:2006:EPA,
author = "Yinglei Song and Chunmei Liu and Xiuzhen Huang and
Russell L. Malmberg and Ying Xu and Liming Cai",
title = "Efficient Parameterized Algorithms for Biopolymer
Structure-Sequence Alignment",
journal = j-TCBB,
volume = "3",
number = "4",
pages = "423--432",
month = oct,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Nov 30 19:05:58 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Anonymous:2006:AI,
author = "Anonymous",
title = "Annual Index",
journal = j-TCBB,
volume = "3",
number = "4",
pages = "??--??",
month = oct,
year = "2006",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Nov 30 19:05:58 MST 2006",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Gusfield:2007:SJ,
author = "Dan Gusfield",
title = "State of the {Journal}",
journal = j-TCBB,
volume = "4",
number = "1",
pages = "1--1",
month = jan,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:20 MDT 2008",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Gusfield:2007:AEAa,
author = "Dan Gusfield",
title = "{Associate Editor} Appreciation and Welcome",
journal = j-TCBB,
volume = "4",
number = "1",
pages = "2--2",
month = jan,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:20 MDT 2008",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Casadio:2007:GEI,
author = "Rita Casadio",
title = "{Guest Editor}'s Introduction to the {Special Section
on Computational Biology and Bioinformatics (WABI)} --
Part 2",
journal = j-TCBB,
volume = "4",
number = "1",
pages = "3--3",
month = jan,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:20 MDT 2008",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Berard:2007:PSR,
author = "Severine B{\'e}rard and Anne Bergeron and Cedric
Chauve and Christophe Paul",
title = "Perfect Sorting by Reversals Is Not Always Difficult",
journal = j-TCBB,
volume = "4",
number = "1",
pages = "4--16",
month = jan,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:20 MDT 2008",
bibsource = "http://portal.acm.org/",
abstract = "We propose new algorithms for computing pairwise
rearrangement scenarios that conserve the combinatorial
structure of genomes. More precisely, we investigate
the problem of sorting signed permutations by reversals
without breaking common intervals. We describe a
combinatorial framework for this problem that allows us
to characterize classes of signed permutations for
which one can compute, in polynomial time, a shortest
reversal scenario that conserves all common intervals.
In particular, we define a class of permutations for
which this computation can be done in linear time with
a very simple algorithm that does not rely on the
classical Hannenhalli-Pevzner theory for sorting by
reversals. We apply these methods to the computation of
rearrangement scenarios between permutations obtained
from 16 synteny blocks of the X chromosomes of the
human, mouse, and rat.",
acknowledgement = ack-nhfb,
keywords = "common intervals; evolution scenarios; reversals",
}
@Article{Vashist:2007:OCM,
author = "Akshay Vashist and Casimir A. Kulikowski and Ilya
Muchnik",
title = "Ortholog Clustering on a Multipartite Graph",
journal = j-TCBB,
volume = "4",
number = "1",
pages = "17--27",
month = jan,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:20 MDT 2008",
bibsource = "http://portal.acm.org/",
abstract = "We present a method for automatically extracting
groups of orthologous genes from a large set of genomes
by a new clustering algorithm on a weighted
multipartite graph. The method assigns a score to an
arbitrary subset of genes from multiple genomes to
assess the orthologous relationships between genes in
the subset. This score is computed using sequence
similarities between the member genes and the
phylogenetic relationship between the corresponding
genomes. An ortholog cluster is found as the subset
with the highest score, so ortholog clustering is
formulated as a combinatorial optimization problem. The
algorithm for finding an ortholog cluster runs in time
O(|E|+|V| log|V|), where V and E are the sets of
vertices and edges, respectively, in the graph.
However, if we discretize the similarity scores into a
constant number of bins, the runtime improves to
O(|E|+|V|). The proposed method was applied to seven
complete eukaryote genomes on which the manually
curated database of eukaryotic ortholog clusters, KOG,
is constructed. A comparison of our results with the
manually curated ortholog clusters shows that our
clusters are well correlated with the existing
clusters.",
acknowledgement = ack-nhfb,
keywords = "biology; clustering algorithms; genetics;
Graph-theoretic methods",
}
@Article{Lasker:2007:EDH,
author = "Keren Lasker and Oranit Dror and Maxim Shatsky and
Ruth Nussinov and Haim J. Wolfson",
title = "{EMatch}: Discovery of High Resolution Structural
Homologues of Protein Domains in Intermediate
Resolution Cryo-{EM} Maps",
journal = j-TCBB,
volume = "4",
number = "1",
pages = "28--39",
month = jan,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:20 MDT 2008",
bibsource = "http://portal.acm.org/",
abstract = "Cryo-EM has become an increasingly powerful technique
for elucidating the structure, dynamics, and function
of large flexible macromolecule assemblies that cannot
be determined at atomic resolution. However, due to the
relatively low resolution of cryo-EM data, a major
challenge is to identify components of complexes
appearing in cryo-EM maps. Here, we describe EMatch, a
novel integrated approach for recognizing structural
homologues of protein domains present in a 6-10{\AA}
resolution cryo-EM map and constructing a quasi-atomic
structural model of their assembly. The method is
highly efficient and has been successfully validated on
various simulated data. The strength of the method is
demonstrated by a domain assembly of an experimental
cryo-EM map of native GroEL at 6{\AA} resolution.",
acknowledgement = ack-nhfb,
keywords = "3D alignment of secondary structures; cyclic symmetry;
intermediate resolution cryo-EM maps; macromolecular
assemblies; structural bioinformatics",
}
@Article{Wang:2007:ACC,
author = "Lipo Wang and Feng Chu and Wei Xie",
title = "Accurate Cancer Classification Using Expressions of
Very Few Genes",
journal = j-TCBB,
volume = "4",
number = "1",
pages = "40--53",
month = jan,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:20 MDT 2008",
bibsource = "http://portal.acm.org/",
abstract = "We aim at finding the smallest set of genes that can
ensure highly accurate classification of cancers from
microarray data by using supervised machine learning
algorithms. The significance of finding the minimum
gene subsets is three-fold: 1) It greatly reduces the
computational burden and `noise' arising from
irrelevant genes. In the examples studied in this
paper, finding the minimum gene subsets even allows for
extraction of simple diagnostic rules which lead to
accurate diagnosis without the need for any
classifiers. 2) It simplifies gene expression tests to
include only a very small number of genes rather than
thousands of genes, which can bring down the cost for
cancer testing significantly. 3) It calls for further
investigation into the possible biological relationship
between these small numbers of genes and cancer
development and treatment. Our simple yet very
effective method involves two steps. In the first step,
we choose some important genes using a feature
importance ranking scheme. In the second step, we test
the classification capability of all simple
combinations of those important genes by using a good
classifier. For three `small' and `simple' data sets
with two, three, and four cancer (sub)types, our
approach obtained very high accuracy with only two or
three genes. For a `large' and `complex' data set with
14 cancer types, we divided the whole problem into a
group of binary classification problems and applied the
2--step approach to each of these binary classification
problems. Through this `divide-and-conquer' approach,
we obtained accuracy comparable to previously reported
results but with only 28 genes rather than 16,063
genes. In general, our method can significantly reduce
the number of genes required for highly reliable
diagnosis.",
acknowledgement = ack-nhfb,
keywords = "cancer classification; fuzzy; gene expression; neural
networks; support vector machines.",
}
@Article{Zhi:2007:CBA,
author = "Degui Zhi and Uri Keich and Pavel Pevzner and Steffen
Heber and Haixu Tang",
title = "Correcting Base-Assignment Errors in Repeat Regions of
Shotgun Assembly",
journal = j-TCBB,
volume = "4",
number = "1",
pages = "54--64",
month = jan,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:20 MDT 2008",
bibsource = "http://portal.acm.org/",
abstract = "Accurate base-assignment in repeat regions of a whole
genome shotgun assembly is an unsolved problem. Since
reads in repeat regions cannot be easily attributed to
a unique location in the genome, current assemblers may
place these reads arbitrarily. As a result, the
base-assignment error rate in repeats is likely to be
much higher than that in the rest of the genome. We
developed an iterative algorithm, EULER-AIR, that is
able to correct base-assignment errors in finished
genome sequences in public databases. The Wolbachia
genome is among the best finished genomes. Using this
genome project as an example, we demonstrated that
EULER-AIR can 1) discover and correct base-assignment
errors, 2) provide accurate read assignments, 3)
utilize finishing reads for accurate base-assignment,
and 4) provide guidance for designing finishing
experiments. In the genome of Wolbachia, EULER-AIR
found 16 positions with ambiguous base-assignment and
two positions with erroneous bases. Besides Wolbachia,
many other genome sequencing projects have
significantly fewer finishing reads and, hence, are
likely to contain more base-assignment errors in
repeats. We demonstrate that EULER-AIR is a software
tool that can be used to find and correct
base-assignment errors in a genome assembly project.",
acknowledgement = ack-nhfb,
keywords = "expectation maximization; finishing; fragment
assembly",
}
@Article{Xu:2007:MCC,
author = "Rui Xu and Georgios C. Anagnostopoulos and Donald C.
Wunsch",
title = "Multiclass Cancer Classification Using Semisupervised
Ellipsoid {ARTMAP} and Particle Swarm Optimization with
Gene Expression Data",
journal = j-TCBB,
volume = "4",
number = "1",
pages = "65--77",
month = jan,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:20 MDT 2008",
bibsource = "http://portal.acm.org/",
abstract = "It is crucial for cancer diagnosis and treatment to
accurately identify the site of origin of a tumor. With
the emergence and rapid advancement of DNA microarray
technologies, constructing gene expression profiles for
different cancer types has already become a promising
means for cancer classification. In addition to
research on binary classification such as normal versus
tumor samples, which attracts numerous efforts from a
variety of disciplines, the discrimination of multiple
tumor types is also important. Meanwhile, the selection
of genes which are relevant to a certain cancer type
not only improves the performance of the classifiers,
but also provides molecular insights for treatment and
drug development. Here, we use Semisupervised Ellipsoid
ARTMAP (ssEAM) for multiclass cancer discrimination and
particle swarm optimization for informative gene
selection. ssEAM is a neural network architecture
rooted in Adaptive Resonance Theory and suitable for
classification tasks. ssEAM features fast, stable, and
finite learning and creates hyperellipsoidal clusters,
inducing complex nonlinear decision boundaries. PSO is
an evolutionary algorithm-based technique for global
optimization. A discrete binary version of PSO is
employed to indicate whether genes are chosen or not.
The effectiveness of ssEAM/PSO for multiclass cancer
diagnosis is demonstrated by testing it on three
publicly available multiple-class cancer data sets.
ssEAM/PSO achieves competitive performance on all these
data sets, with results comparable to or better than
those obtained by other classifiers.",
acknowledgement = ack-nhfb,
keywords = "cancer classification; gene expression profile;
particle swarm optimization; semisupervised ellipsoid
ARTMAP",
}
@Article{Huang:2007:PPP,
author = "Chengbang Huang and Faruck Morcos and Simon P. Kanaan
and Stefan Wuchty and Danny Z. Chen and Jesus A.
Izaguirre",
title = "Predicting Protein-Protein Interactions from Protein
Domains Using a Set Cover Approach",
journal = j-TCBB,
volume = "4",
number = "1",
pages = "78--87",
month = jan,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:20 MDT 2008",
bibsource = "http://portal.acm.org/",
abstract = "One goal of contemporary proteome research is the
elucidation of cellular protein interactions. Based on
currently available protein-protein interaction and
domain data, we introduce a novel method, Maximum
Specificity Set Cover (MSSC), for the prediction of
protein-protein interactions. In our approach, we map
the relationship between interactions of proteins and
their corresponding domain architectures to a
generalized weighted set cover problem. The application
of a greedy algorithm provides sets of domain
interactions which explain the presence of protein
interactions to the largest degree of specificity.
Utilizing domain and protein interaction data of S.
cerevisiae, MSSC enables prediction of previously
unknown protein interactions, links that are well
supported by a high tendency of coexpression and
functional homogeneity of the corresponding proteins.
Focusing on concrete examples, we show that MSSC
reliably predicts protein interactions in well-studied
molecular systems, such as the 26S proteasome and RNA
polymerase II of S. cerevisiae. We also show that the
quality of the predictions is comparable to the Maximum
Likelihood Estimation while MSSC is faster. This new
algorithm and all data sets used are accessible through
a Web portal at http://ppi.cse.nd.edu.",
acknowledgement = ack-nhfb,
keywords = "bioinformatics (genome or protein) databases; biology;
Computations on discrete structures; genetics; graph
algorithms",
}
@Article{Kim:2007:AAD,
author = "Jong Hyun Kim and Michael S. Waterman and Lei M. Li",
title = "Accuracy Assessment of Diploid Consensus Sequences",
journal = j-TCBB,
volume = "4",
number = "1",
pages = "88--97",
month = jan,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:20 MDT 2008",
bibsource = "http://portal.acm.org/",
abstract = "If the origins of fragments are known in genome
sequencing projects, it is straightforward to
reconstruct diploid consensus sequences. In reality,
however, this is not true. Although there are proposed
methods to reconstruct haplotypes from genome
sequencing projects, an accuracy assessment is required
to evaluate the confidence of the estimated diploid
consensus sequences. In this paper, we define the
confidence score of diploid consensus sequences. It
requires the calculation of the likelihood of an
assembly. To calculate the likelihood, we propose a
linear time algorithm with respect to the number of
polymorphic sites. The likelihood calculation and
confidence score are used for further improvements of
haplotype estimation in two directions. One direction
is that low-scored phases are disconnected. The other
direction is that, instead of using nominal frequency
1/2, the haplotype frequency is estimated to reflect
the actual contribution of each haplotype. Our method
was evaluated on the simulated data whose polymorphism
rate (1.2 percent) was based on Ciona intestinalis. As
a result, the high accuracy of our algorithm was
indicated: The true positive rate of the haplotype
estimation was greater than 97 percent.",
acknowledgement = ack-nhfb,
keywords = "diploid; haplotype; polymorphism; shotgun sequencing",
}
@Article{Alekseyev:2007:CBG,
author = "Max A. Alekseyev and Pavel A. Pevzner",
title = "Colored de Bruijn Graphs and the Genome Halving
Problem",
journal = j-TCBB,
volume = "4",
number = "1",
pages = "98--107",
month = jan,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:20 MDT 2008",
bibsource = "http://portal.acm.org/",
abstract = "Breakpoint graph analysis is a key algorithmic
technique in studies of genome rearrangements. However,
breakpoint graphs are defined only for genomes without
duplicated genes, thus limiting their applications in
rearrangement analysis. We discuss a connection between
the breakpoint graphs and de Bruijn graphs that leads
to a generalization of the notion of breakpoint graph
for genomes with duplicated genes. We further use the
generalized breakpoint graphs to study the Genome
Halving Problem (first introduced and solved by Nadia
El-Mabrouk and David Sankoff). The El-Mabrouk-Sankoff
algorithm is rather complex, and, in this paper, we
present an alternative approach that is based on
generalized breakpoint graphs. The generalized
breakpoint graphs make the El-Mabrouk-Sankoff result
more transparent and promise to be useful in future
studies of genome rearrangements.",
acknowledgement = ack-nhfb,
keywords = "breakpoint graph; de Bruijn graph; genome duplication;
genome halving; genome rearrangement; reversal",
}
@Article{Mossel:2007:DMT,
author = "Elchanan Mossel",
title = "Distorted Metrics on Trees and Phylogenetic Forests",
journal = j-TCBB,
volume = "4",
number = "1",
pages = "108--116",
month = jan,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:20 MDT 2008",
bibsource = "http://portal.acm.org/",
abstract = "We study distorted metrics on binary trees in the
context of phylogenetic reconstruction. Given a binary
tree $T$ on $n$ leaves with a path metric $d$, consider
the pairwise distances $d(u,v)$ between leaves. It is
well known that these determine the tree and the
$d$-length of all edges. Here, we consider distortions
$\hat{d}$ of $d$ such that, for all leaves $u$ and $v$,
it holds that $|d(u,v) - \hat{d}(u,v)| < f/2$ if either
$d(u,v) < M + f/2$ or $\hat{d}(u,v) < M + f/2$, where
$d$ satisfies $f \leq d(e) \leq g$ for all edges $e$.
Given such distortions, we show how to reconstruct in
polynomial time a forest $T_1, \ldots{}, T_\alpha$ such
that the true tree $T$ may be obtained from that forest
by adding $\alpha-1$ edges and $\alpha-1 \leq
2-\Omega(M/g) n$. Our distorted metric result implies a
reconstruction algorithm of phylogenetic forests with a
small number of trees from sequences of length
logarithmic in the number of species. The
reconstruction algorithm is applicable for the general
Markov model. Both the distorted metric result and its
applications to phylogeny are almost tight.",
acknowledgement = ack-nhfb,
keywords = "CFN; distortion; forest; Jukes--Cantor; metric;
phylogenetics; tree",
}
@Article{Aeling:2007:DDE,
author = "Kimberly A. Aeling and Nicholas R. Steffen and Matthew
Johnson and G. Wesley Hatfield and Richard H. Lathrop
and Donald F. Senear",
title = "{DNA} Deformation Energy as an Indirect Recognition
Mechanism in Protein-{DNA} Interactions",
journal = j-TCBB,
volume = "4",
number = "1",
pages = "117--125",
month = jan,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:20 MDT 2008",
bibsource = "http://portal.acm.org/",
abstract = "Proteins that bind to specific locations in genomic
DNA control many basic cellular functions. Proteins
detect their binding sites using both direct and
indirect recognition mechanisms. Deformation energy,
which models the energy required to bend DNA from its
native shape to its shape when bound to a protein, has
been shown to be an indirect recognition mechanism for
one particular protein, Integration Host Factor (IHF).
This work extends the analysis of deformation to two
other DNA-binding proteins, CRP and SRF, and two
endonucleases, I-CreI and I-PpoI. Known binding sites
for all five proteins showed statistically significant
differences in mean deformation energy as compared to
random sequences. Binding sites for the three
DNA-binding proteins and one of the endonucleases had
mean deformation energies lower than random sequences.
Binding sites for I-PpoI had mean deformation energy
higher than random sequences. Classifiers that were
trained using the deformation energy at each base pair
step showed good cross-validated accuracy when
classifying unseen sequences as binders or nonbinders.
These results support DNA deformation energy as an
indirect recognition mechanism across a wider range of
DNA-binding proteins. Deformation energy may also have
a predictive capacity for the underlying catalytic
mechanism of DNA-binding enzymes.",
acknowledgement = ack-nhfb,
keywords = "deformation energy; DNA bending; DNA-protein binding;
indirect readout; indirect recognition; perceptron
learning",
}
@Article{Yang:2007:MFE,
author = "Jing Yang and Sarawan Wongsa and Visakan
Kadirkamanathan and Stephen A. Billings and Phillip C.
Wright",
title = "Metabolic Flux Estimation-{A} Self-Adaptive
Evolutionary Algorithm with Singular Value
Decomposition",
journal = j-TCBB,
volume = "4",
number = "1",
pages = "126--138",
month = jan,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:20 MDT 2008",
bibsource = "http://portal.acm.org/",
abstract = "Metabolic flux analysis is important for metabolic
system regulation and intracellular pathway
identification. A popular approach for intracellular
flux estimation involves using ^{13}{\rm C} tracer
experiments to label states that can be measured by
nuclear magnetic resonance spectrometry or gas
chromatography mass spectrometry. However, the bilinear
balance equations derived from ^{13}{\rm C} tracer
experiments and the noisy measurements require a
nonlinear optimization approach to obtain the optimal
solution. In this paper, the flux quantification
problem is formulated as an error-minimization problem
with equality and inequality constraints through the
^{13}{\rm C} balance and stoichiometric equations. The
stoichiometric constraints are transformed to a null
space by singular value decomposition. Self-adaptive
evolutionary algorithms are then introduced for flux
quantification. The performance of the evolutionary
algorithm is compared with ordinary least squares
estimation by the simulation of the central pentose
phosphate pathway. The proposed algorithm is also
applied to the central metabolism of Corynebacterium
glutamicum under lysine-producing conditions. A
comparison between the results from the proposed
algorithm and data from the literature is given. The
complexity of a metabolic system with bidirectional
reactions is also investigated by analyzing the
fluctuations in the flux estimates when available
measurements are varied.",
acknowledgement = ack-nhfb,
keywords = "evolutionary computing; least squares method;
metabolic flux analysis; singular value
decomposition.",
}
@Article{Wu:2007:QBP,
author = "Gang Wu and Jia-Huai You and Guohui Lin",
title = "Quartet-Based Phylogeny Reconstruction with Answer Set
Programming",
journal = j-TCBB,
volume = "4",
number = "1",
pages = "139--152",
month = jan,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:20 MDT 2008",
bibsource = "http://portal.acm.org/",
abstract = "In this paper, a new representation is presented for
the Maximum Quartet Consistency (MQC) problem, where
solving the MQC problem becomes searching for an
ultrametric matrix that satisfies a maximum number of
given quartet topologies. A number of structural
properties of the MQC problem in this new
representation are characterized through formulating
into answer set programming, a recent powerful logic
programming tool for modeling and solving search
problems. Using these properties, a number of
optimization techniques are proposed to speed up the
search process. The experimental results on a number of
simulated data sets suggest that the new
representation, combined with answer set programming,
presents a unique perspective to the MQC problem.",
acknowledgement = ack-nhfb,
keywords = "Answer Set Programming (ASP); Maximum Quartet
Consistency (MQC); phylogeny; quartet; ultrametric
matrix.",
}
@Article{Reinert:2007:LLE,
author = "Gesine Reinert and Michael S. Waterman",
title = "On the Length of the Longest Exact Position Match in a
Random Sequence",
journal = j-TCBB,
volume = "4",
number = "1",
pages = "153--156",
month = jan,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:20 MDT 2008",
bibsource = "http://portal.acm.org/",
abstract = "A mixed Poisson approximation and a Poisson
approximation for the length of the longest exact match
of a random sequence across another sequence are
provided, where the match is required to start at
position 1 in the first sequence. This problem arises
when looking for suitable anchors in whole genome
alignments.",
acknowledgement = ack-nhfb,
keywords = "Chen-Stein method; length of longest match; mixed
Poisson approximation; Poisson approximation",
}
@Article{Au:2007:CAC,
author = "Wai-Ho Au and Keith C. C. Chan and Andrew K. C. Wong
and Yang Wang",
title = "Correction to {``Attribute Clustering for Grouping,
Selection, and Classification of Gene Expression
Data''}",
journal = j-TCBB,
volume = "4",
number = "1",
pages = "157--157",
month = jan,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:20 MDT 2008",
bibsource = "http://portal.acm.org/",
abstract = "This is a correction to a typographical error in (11)
in [1] which present the calculation of the sum of the
multiple significant interdependence redundancy
measure. Equation (11) in [1] should be:
$$k=\arg\max\nolimits_{k\in\{2,\ldots,p\}}\sum_{r=1}^k
\sum_{A_i\in\{C_r-\eta_r\}}R(A_i:\eta_r).$$(11)We
remark that the experimental results reported in [1]
are based on (11) above not (11) in [1].",
acknowledgement = ack-nhfb,
}
@Article{Biology:2007:RL,
author = "IEEE/ACM Transactions on Computational Biology and
Bioinformatics staff",
title = "2006 Reviewers List",
journal = j-TCBB,
volume = "4",
number = "1",
pages = "158--160",
month = jan,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:20 MDT 2008",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Rajapakse:2007:GEI,
author = "Jagath C. Rajapakse and Yan-Qing Zhang and Gary B.
Fogel",
title = "{Guest Editors}' Introduction to the {Special Section:
Computational Intelligence Approaches in Computational
Biology and Bioinformatics}",
journal = j-TCBB,
volume = "4",
number = "2",
pages = "161--162",
month = apr,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:55 MDT 2008",
bibsource = "http://portal.acm.org/",
acknowledgement = ack-nhfb,
}
@Article{Wang:2007:PBS,
author = "Haiying Wang and Huiru Zheng and Francisco Azuaje",
title = "{Poisson}-Based Self-Organizing Feature Maps and
Hierarchical Clustering for Serial Analysis of Gene
Expression Data",
journal = j-TCBB,
volume = "4",
number = "2",
pages = "163--175",
month = apr,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:55 MDT 2008",
bibsource = "http://portal.acm.org/",
abstract = "Serial analysis of gene expression (SAGE) is a
powerful technique for global gene expression
profiling, allowing simultaneous analysis of thousands
of transcripts without prior structural and functional
knowledge. Pattern discovery and visualization have
become fundamental approaches to analyzing such
large-scale gene expression data. From the pattern
discovery perspective, clustering techniques have
received great attention. However, due to the
statistical nature of SAGE data (i.e., underlying
distribution), traditional clustering techniques may
not be suitable for SAGE data analysis. Based on the
adaptation and improvement of Self-Organizing Maps and
hierarchical clustering techniques, this paper presents
two new clustering algorithms, namely, PoissonS and
PoissonHC, for SAGE data analysis. Tested on synthetic
and experimental SAGE data, these algorithms
demonstrate several advantages over traditional pattern
discovery techniques. The results indicate that, by
incorporating statistical properties of SAGE data,
PoissonS and PoissonHC, as well as a hybrid approach
(neuro-hierarchical approach) based on the combination
of PoissonS and PoissonHC, offer significant
improvements in pattern discovery and visualization for
SAGE data. Moreover, a user-friendly platform, which
may improve and accelerate SAGE data mining, was
implemented. The system is freely available on request
from the authors for nonprofit use.",
acknowledgement = ack-nhfb,
keywords = "hybrid machine learning; Pattern discovery and
visualization; Poisson distribution; self-organizing
maps; serial analysis of gene expression.",
}
@Article{Sjahputera:2007:RAC,
author = "Ozy Sjahputera and James M. Keller and J. Wade Davis
and Kristen H. Taylor and Farahnaz Rahmatpanah and
Huidong Shi and Derek T. Anderson and Samuel N. Blisard
and Robert H. Luke and Mihail Popescu and Gerald C.
Arthur and Charles W. Caldwell",
title = "Relational Analysis of {CpG} Islands Methylation and
Gene Expression in Human Lymphomas Using Possibilistic
{C}-Means Clustering and Modified Cluster Fuzzy
Density",
journal = j-TCBB,
volume = "4",
number = "2",
pages = "176--189",
month = apr,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:55 MDT 2008",
bibsource = "http://portal.acm.org/",
abstract = "Heterogeneous genetic and epigenetic alterations are
commonly found in human non-Hodgkin's lymphomas (NHL).
One such epigenetic alteration is aberrant methylation
of gene promoter-related CpG islands, where
hypermethylation frequently results in transcriptional
inactivation of target genes, while a decrease or loss
of promoter methylation (hypomethylation) is frequently
associated with transcriptional activation. Discovering
genes with these relationships in NHL or other types of
cancers could lead to a better understanding of the
pathobiology of these diseases. The simultaneous
analysis of promoter methylation using Differential
Methylation Hybridization (DMH) and its associated gene
expression using Expressed CpG Island Sequence Tag
(ECIST) microarrays generates a large volume of
methylation-expression relational data. To analyze this
data, we propose a set of algorithms based on fuzzy
sets theory, in particular Possibilistic c-Means (PCM)
and cluster fuzzy density. For each gene, these
algorithms calculate measures of confidence of various
methylation-expression relationships in each NHL
subclass. Thus, these tools can be used as a means of
high volume data exploration to better guide biological
confirmation using independent molecular biology
methods.",
acknowledgement = ack-nhfb,
keywords = "cluster density; clustering; expression; fuzzy sets;
Methylation; microarray",
}
@Article{Lu:2007:ISL,
author = "Yijuan Lu and Qi Tian and Feng Liu and Maribel Sanchez
and Yufeng Wang",
title = "Interactive Semisupervised Learning for Microarray
Analysis",
journal = j-TCBB,
volume = "4",
number = "2",
pages = "190--203",
month = apr,
year = "2007",
CODEN = "ITCBCY",
ISSN = "1545-5963",
bibdate = "Thu Jun 12 16:57:55 MDT 2008",
bibsource = "http://portal.acm.org/",
abstract = "Microarray technology has generated vast amounts of
gene expression data with distinct patterns. Based on
the premise that genes of correlated functions tend to
exhibit similar expression patterns, various machine
learning methods have been applied to capture these
specific patterns in microarray data. However, the
discrepancy between the rich expression profiles and
the limited knowledge of gene functions has been a
major hurdle to the understanding of cellular networks.
To bridge this gap so as to properly comprehend and
interpret expression data, we introduce Relevance
Feedback to microarray analysis and propose an
interactive learning framework to incorporate the
expert knowledge into the decision module. In order to
find a good learning method and solve two intrinsic
problems in microarray data, high dimensionality and
small sample size, we also propose a semisupervised
learning algorithm: Kerne