bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic reconstruction from non-genomic data
Authors: Clemente José C. , Satou Kenji , Valiente Gabriel 
Published: January 2007

AbstractMotivation: Recent results related to horizontal gene transfer suggest that phylogenetic reconstruction cannot be determined conclusively from sequence data, resulting in a shift from approaches based on polymorphism information in DNA or protein sequence to studies aimed at understanding the evolution of complete biological processes. The increasing amount of available information on metabolic pathways for several species makes it of greater relevance to understand the similarities and differences among such pathways. These similarities can then be used to infer phylogenetic trees not based exclusively in sequence data, therefore avoiding the previously mentioned problems.Results: In this article, we present a method to assess the structural similarity of metabolic pathways for several organisms. Our algorithms work by using one of the three possible enzyme similarity measures (hierarchical, information content, gene ontology), and one of the two clustering methods (neighbor-joining, unweighted pair group method with arithmetic mean), to produce a phylogenetic tree both in Newick and graphic format. The web server implementing our algorithms is optimized to answer queries in linear time.Availability: The software is available for free public use on a web server, at the address . It is available on demand in source code form for research use to educational institutions, non-profit research institutes, government research laboratories and individuals, for non-exclusive use, without the right of the licensee to further redistribute the source code.Contact: valiente@lsi.upc.edu; clemente@jaist.ac.jp
Using an alignment of fragment strings for comparing protein structures
Authors: Friedberg Iddo , Harder Tim , Kolodny Rachel , Sitbon Einat , Li Zhanwen , Godzik Adam 
Published: January 2007

AbstractMotivation: Most methods that are used to compare protein structures use three-dimensional (3D) structural information. At the same time, it has been shown that a 1D string representation of local protein structure retains a degree of structural information. This type of representation can be a powerful tool for protein structure comparison and classification, given the arsenal of sequence comparison tools developed by computational biology. However, in order to do so, there is a need to first understand how much information is contained in various possible 1D representations of protein structure.Results: Here we describe the use of a particular structure fragment library, denoted here as KL-strings, for the 1D representation of protein structure. Using KL-strings, we develop an infrastructure for comparing protein structures with a 1D representation. This study focuses on the added value gained from such a description. We show the new local structure language adds resolution to the traditional three-state (helix, strand and coil) secondary structure description, and provides a high degree of accuracy in recognizing structural similarities when used with a pairwise alignment benchmark. The results of this study have immediate applications towards fast structure recognition, and for fold prediction and classification.Contact: idoerg@burnham.orgSupplementary information: ECCB06-supplement
Multiple alignment by sequence annealing
Authors: S. Schwartz Ariel , Pachter Lior 
Published: January 2007

AbstractMotivation: We introduce a novel approach to multiple alignment that is based on an algorithm for rapidly checking whether single matches are consistent with a partial multiple alignment. This leads to a sequence annealing algorithm, which is an incremental method for building multiple sequence alignments one match at a time. Our approach improves significantly on the standard progressive alignment approach to multiple alignment.Results: The sequence annealing algorithm performs well on benchmark test sets of protein sequences. It is not only sensitive, but also specific, drastically reducing the number of incorrectly aligned residues in comparison to other programs. The method allows for adjustment of the sensitivity/specificity tradeoff and can be used to reliably identify homologous regions among protein sequences.Availability: An implementation of the sequence annealing algorithm is available atContact: sariel@cs.berkeley.edu
Electrostatic potentials of proteins in water: a structured continuum approach
Authors: Hildebrandt Andreas , Blossey Ralf , Rjasanow Sergej , Kohlbacher Oliver , Lenhof Hans-Peter 
Published: January 2007

AbstractElectrostatic interactions play a crucial role in many biomolecular processes, including molecular recognition and binding. Biomolecular electrostatics is modulated to a large extent by the water surrounding the molecules. Here, we present a novel approach to the computation of electrostatic potentials which allows the inclusion of water structure into the classical theory of continuum electrostatics. Based on our recent purely differential formulation of nonlocal electrostatics [Hildebrandt, et al. (2004)Phys. Rev. Lett., 93, 108104] we have developed a new algorithm for its efficient numerical solution. The key component of this algorithm is a boundary element solver, having the same computational complexity as established boundary element methods for local continuum electrostatics. This allows, for the first time, the computation of electrostatic potentials and interactions of large biomolecular systems immersed in water including effects of the solvent's structure in a continuum description. We illustrate the applicability of our approach with two examples, the enzymes trypsin and acetylcholinesterase. The approach is applicable to all problems requiring precise prediction of electrostatic interactions in water, such as protein–ligand and protein–protein docking, folding and chromatin regulation. Initial results indicate that this approach may shed new light on biomolecular electrostatics and on aspects of molecular recognition that classical local electrostatics cannot reveal.Contact: anhi@bioinf.uni-sb.de
Optimization of probe coverage for high-resolution oligonucleotide aCGH
Authors: Lipson Doron , Yakhini Zohar , Aumann Yonatan 
Published: January 2007

AbstractMotivation: The resolution at which genomic alterations can be mapped by means of oligonucleotide aCGH (array-based comparative genomic hybridization) is limited by two factors: the availability of high-quality probes for the target genomic sequence and the array real-estate. Optimization of the probe selection process is required for arrays that are designed to probe specific genomic regions in very high resolution without compromising probe quality constraints.Results: In this paper we describe a well-defined optimization problem associated with the problem of probe selection for high-resolution aCGH arrays. We propose the whenever possible ∈-cover as a formulation that faithfully captures the requirement of probe selection problem, and provide a fast randomized algorithm that solves the optimization problem in O(n logn) time, as well as a deterministic algorithm with the same asymptotic performance. We apply the method in a typical high-definition array design scenario and demonstrate its superiority with respect to alternative approaches.Availability: Address requests to the authors.Contact: dlipson@cs.technion.ac.il
Genetic code symmetry and efficient design of GC-constrained coding sequences
Authors: Gavish Matan , Peled Amnon , Chor Benny 
Published: January 2007

AbstractMotivation: Cloning of long DNA sequences (40–60 bases) into phage display libraries using polymerase chain reaction (PCR) is a low efficiency process, in which PCR is used to incorporate a DNA insert, coding for a certain peptide, into the amplified sequence. The PCR efficiency in this process is strongly affected by the distribution of G–C bases in the amplified sequence. As any DNA insert coding for the target peptide may be attempted, there is a flexibility in choosing part of the amplified sequence. Since the number of inserts coding for the same peptide is exponential in the peptide length, a computational problem naturally arises—that of efficiently finding an insert, whose parameters are optimal for PCR cloning.Results: The GC distribution requirements are formulated as a search problem. We developed an efficient, linear time ‘one pass’ algorithm for this problem. Interestingly, our algorithm strongly relies on an interesting symmetry, which we observed in the standard genetic code. Most non-standard genetic codes examined possess this symmetry as well, yet some do not. We generalize the search problem and consider the case of a non-standard, or arbitrary, genetic code where this symmetry does not necessary hold. We solve the generalized problem in polynomial, but nonlinear, time.Availability: An implementation of the proposed algorithm is available upon request from the authors.Contact: benny@cs.tau.ac.il
A tale of two tails: why are terminal residues of proteins exposed?
Authors: Jacob Etai , Unger Ron 
Published: January 2007

AbstractMotivation: It is widely known that terminal residues of proteins (i.e. the N- and C-termini) are predominantly located on the surface of proteins and exposed to the solvent. However, there is no good explanation as to the forces driving this phenomenon. The common explanation that terminal residues are charged, and charged residues prefer to be on the surface, cannot explain the magnitude of the phenomenon. Here, we survey a large number of proteins from the PDB in order to explore, quantitatively, this phenomenon, and then we use a lattice model to study the mechanisms involved.Results: The location of the termini was examined for 425 small monomeric proteins (50–200 amino acids) and it was found that the average solvent accessibility of termini residues is 87.1% compared with 49.2% of charged residues and 35.9% of all residues. Using a cutoff of 50% of the maximal possible exposure, 80.3% of the N-terminal and 86.1% of the C-terminal residues are exposed compared to 32% for all residues. In addition, terminal residues are much more distant from the center of mass of their proteins than other residues. Using a 2D lattice, a large population of model proteins was studied on three levels: structural selection of compact structures, thermodynamic selection of conformations with a pronounced energy gap and kinetic selection of fast folding proteins using Monte-Carlo simulations. Progressively, each selection raises the proportion of proteins with termini on the surface, resulting in similar proportions to those observed for real proteins.Contact: ron@biocom1.ls.biu.ac.il
Learning probabilistic models ofcis-regulatory modules that represent logical and spatial aspects
Authors: Noto Keith , Craven Mark 
Published: January 2007

AbstractMotivation: The process of transcription is controlled by systems of factors which bind in specific arrangements, called cis-regulatory modules (CRMs), in promoter regions. We present a discriminative learning algorithm which simultaneously learns the DNA binding site motifs as well as the logical structure and spatial aspects of CRMs.Results: Our results on yeast datasets show better predictive accuracy than a current state-of-the-art approach on the same datasets. Our results on yeast, fly and human datasets show that the inclusion of logical and spatial aspects improves the predictive accuracy of our learned models.Availability: Source code is available atContact: noto@cs.wisc.edu
Designing patterns for profile HMM search
Authors: Sun Yanni , Buhler Jeremy 
Published: January 2007

AbstractMotivation: Profile HMMs are a powerful tool for modeling conserved motifs in proteins. These models are widely used by search tools to classify new protein sequences into families based on domain architecture. However, the proliferation of known motifs and new proteomic sequence data poses a computational challenge for search, requiring days of CPU time to annotate an organism's proteome.Results: We use PROSITE-like patterns as a filter to speed up the comparison between protein sequence and profile HMM. A set of patterns is designed starting from the HMM, and only sequences matching one of these patterns are compared to the HMM by full dynamic programming. We give an algorithm to design patterns with maximal sensitivity subject to a bound on the false positive rate. Experiments show that our patterns typically retain at least 90% of the sensitivity of the source HMM while accelerating search by an order of magnitude.Availability: Contact the first author at the address below.Contact: yanni@cse.wustl.edu
Identifying HLA supertypes by learning distance functions
Authors: Hertz Tomer , Yanover Chen 
Published: January 2007

AbstractMotivation: The development of epitope-based vaccines crucially relies on the ability to classify Human Leukocyte Antigen (HLA) molecules into sets that have similar peptide binding specificities, termed supertypes. In their seminal work, Sette and Sidney defined nine HLA class I supertypes and claimed that these provide an almost perfect coverage of the entire repertoire of HLA class I molecules.HLA alleles are highly polymorphic and polygenic and therefore experimentally classifying each of these molecules to supertypes is at present an impossible task. Recently, a number of computational methods have been proposed for this task. These methods are based on defining protein similarity measures, derived from analysis of binding peptides or from analysis of the proteins themselves.Results: In this paper we define both peptide derived and protein derived similarity measures, which are based on learning distance functions. The peptide derived measure is defined using a peptide–peptide distance function, which is learned using information about known binding and non-binding peptides. The protein derived similarity measure is defined using a protein–protein distance function, which is learned using information about alleles previously classified to supertypes by Sette and Sidney (1999). We compare the classification obtained by these two complimentary methods to previously suggested classification methods. In general, our results are in excellent agreement with the classifications suggested by Sette and Sidney (1999) and with those reported by Buus et al. (2004).The main important advantage of our proposed distance-based approach is that it makes use of two different and important immunological sources of information—HLA alleles and peptides that are known to bind or not bind to these alleles. Since each of our distance measures is trained using a different source of information, their combination can provide a more confident classification of alleles to supertypes.Contact: tomboy@cs.huji.ac.il; cheny@cs.huji.ac.il
CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data
Authors: Girardot Charles , Sklyar Oleg , Grosz Sophie , Huber Wolfgang , Furlong Eileen E. M. 
Published: January 2007

AbstractMotivation: CoCo, ChIP-on-Chip online, is an open-source web application that supports the annotation and curation of regulatory regions and associated target genes discovered in ChIP-on-chip experiments. CoCo integrates ChIP-on-chip results with diverse types of gene expression data (expression profiling, in situ hybridization) and displays them within a genomic context. Regulatory relationships between the transcription factor-bound regions and putative target genes can be stored and expanded throughout different sessions.Availability: http://furlonglab.embl.de/methods/tools/cocoContact: charles.girardot@embl.de
snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package
Authors: Luna Augustin , Nicodemus Kristin K. 
Published: January 2007

Abstract
Summary: snp.plotter is a newly developed R package which produces high-quality plots of results from genetic association studies. The main features of the package include options to display a linkage disequilibrium (LD) plot below the P-value plot using either the r2 or D′ LD metric, to set the X-axis to equal spacing or to use the physical map of markers, and to specify plot labels, colors, symbols and LD heatmap color scheme. snp.plotter can plot single SNP and/or haplotype data and simultaneously plot multiple sets of results. R is a free software environment for statistical computing and graphics available for most platforms. The proposed package provides a simple way to convey both association and LD information in a single appealing graphic for genetic association studies.
Availability: Downloadable R package and example datasets are available at http://cbdb.nimh.nih.gov/~kristin/snp.plotter.html and http://www.r-project.org
Contact: nicodemusk@mail.nih.gov
Protein–protein interaction site prediction based on conditional random fields
Authors: Li Ming-Hui , Lin Lei , Wang Xiao-Long , Liu Tao 
Published: January 2007

AbstractMotivation: We are motivated by the fast-growing number of protein structures in the Protein Data Bank with necessary information for prediction of protein–protein interaction sites to develop methods for identification of residues participating in protein–protein interactions. We would like to compare conditional random fields (CRFs)-based method with conventional classification-based methods that omit the relation between two labels of neighboring residues to show the advantages of CRFs-based method in predicting protein–protein interaction sites.Results: The prediction of protein–protein interaction sites is solved as a sequential labeling problem by applying CRFs with features including protein sequence profile and residue accessible surface area. The CRFs-based method can achieve a comparable performance with state-of-the-art methods, when 1276 nonredundant hetero-complex protein chains are used as training and test set. Experimental result shows that CRFs-based method is a powerful and robust protein–protein interaction site prediction method and can be used to guide biologists to make specific experiments on proteins.Availability: http://www.insun.hit.edu.cn/~mhli/site_CRFs/index.htmlContact: mhli@insun.hit.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online.
Critical threshold effects of benthiscape structure on stream herbivore movement
Authors: Olden Julian D 
Published: January 2007

Abstract

In landscape ecology, substantial theoretical progress has been made in understanding how critical threshold levels of habitat loss may result in sudden changes in landscape connectivity to animal movement. Empirical evidence for such thresholds in real systems, however, remains scarce. Streambed landscapes provide a strong testing ground for studying critical thresholds because organisms are faced with substantial environmental heterogeneity while attempting to overcome the physical force of water. In this study, I report on the results from a series of experiments investigating the influence of habitat abundance and current velocity on the movement dynamics of two stream herbivores (caddisfly larva
Agapetus boulderensis
and snail
Physa
sp.) that differ substantially in how they perceive landscape structure. Specifically, I ask whether critical thresholds to herbivore movement exist in streambed landscapes. By exploiting the pattern recognition capabilities of artificial neural networks, I found that the rate, sinuosity and directionality of movement by
Agapetus
and
Physa
varied nonlinearly according to the abundance of habitat patches, current velocity and habitat–current interaction. Both the study organisms exhibited threshold responses to habitat abundance, yet the location and slope of these thresholds differed between species and with respect to different current velocities. These results suggest that a critical threshold in functional connectivity (i.e. the connection of habitat patches by dispersal) is not an inherent property of the landscape, but in fact emerges from the interplay of species' interactions with landscape structure. Moreover, current velocity interacted with habitat abundance to elicit strong upstream-oriented movement for both the species. This suggests that dispersing individuals may be polarized in the upstream direction and therefore functional connectivity is not equal in all directions. Such results highlight the need for future research addressing the sources of variability of critical threshold effects in ecological phenomena.
ON CENTRAL BANK INDEPENDENCE, WAGE INDEXING AND A MONOPOLY UNION
Authors: Efthimiadis Tilemahos 
Published: January 2007

ABSTRACTThe Rogoff proposition (Quarterly Journal of Economics, 100 (1985), pp. 1169–90) that it is socially optimal to delegate monetary policy to a central banker that is more inflation‐averse than society has been widely accepted and implemented in practice. However, there is a literature that argues that, if there is an inflation‐averse monopoly union in the economy, it is optimal to delegate monetary policy to an ‘ultra‐liberal’ central banker, i.e., a central banker that is interested only in output. In this paper, we examine whether introducing wage indexing into the latter models has any effect on the optimal degree of central bank conservativeness and find that, once a monopoly‐type labour union is introduced, wage indexing does not matter for the determination of the optimal degree of conservativeness of the monetary authority.
Viral vector vaccines make memory T cells against malaria
Authors: Reyes‐Sandoval Arturo , Harty John T. , Todryk Stephen M. 
Published: January 2007

SummaryVaccines that comprise attenuated viral vectors encoding antigens from target pathogens generate potent T‐cell responses. One such pathogen is malaria, and in particular the liver stage of its life cycle. Immunogenicity and efficacy studies in animals and humans have revealed the generation of memory T cells of both the central and effector phenotypes, depending on the viral vectors used in the malaria vaccination regime (viral species and serotype, combination and sequence for prime–boost) and suggest a divergence in their protective role. Being able to influence the memory T‐cell make‐up in a rational manner may allow us to develop more efficacious vaccines.