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A consensus sequence of the euchromatic portion of human genome has been generated by the whole genome shot-gun sequencing method that was developed while sequencing the genomes of Haemophilus influenzae and Drosophila melanogaster. The 2.9 billion bp ...

The Smith-Waterman algorithm for local sequence alignment is one of the most important techniques in computational molecular biology. This ingenious dynamic programming approach was designed to reveal the highly conserved fragments by discarding poorly ...

The recent growth in genomic data and measurement of genome-wide expression patterns allows to examine gene regulation by transcription factors using computational tools. In this work, we present a class of mathematical models that help in understanding ...

Tettelin et. al. proposed a new method for closing the gaps in whole genome shotgun sequencing projects. The method uses a multiplex PCR strategy in order to minimize the time and effort required to sequence the DNA in the missing gaps. This procedure ...

Recent studies (Alizadeh et al, [1]; Bittner et al,[5]; Golub et al, [11]) demonstrate the discovery of putative disease subtypes from gene expression data. The underlying computational problem is to partition the set of sample tissues into ...

Perhaps the most direct way to infer functional linkage of proteins is through structural similarity. However, structure determination lags behind DNA sequencing. Here we show that sequence similarity based on nucleotide sequences alone between ORFs in ...

Phylogenetic footprinting is a technique that identifies regulatory elements by finding unusually well conserved regions in a set of orthologous non-coding DNA sequences from multiple species. In an earlier paper, we presented an exact algorithm that ...

A method is presented that uses β-strand interactions to predict the right-handed β-helix super-secondary structural motif in protein sequences. A program called BetaWrap implements this method, and is shown to score known β-helices above non-β-helices ...

The core agenda of post-WWII molecular biology has been defined as the molecular understanding of how genetic information was transmitted and read out (see for example Stent 1968), and, by the 1950's, the analogy between the tape in a Turing machine and ...

Pevzner and Sze [23] considered a precise version of the motif discovery problem and simultaneously issued an algorithmic challenge: find a motif M of length 15, where each planted instance differs from M in 4 positions. Whereas previous algorithms all ...

In order to assess the significance of sequence alignments it is crucial to know the distribution of alignment scores of pairs of random sequences. For gapped local alignment it is empirically known that the shape of this distribution is of the Gumbel ...

We present a new computational method for discovering cis- regulatory elements which circumvents the need to cluster genes based on their expression profiles. Based on a model in which upstream motifs contribute additively to the expression level of a ...

We propose a new gene-finding methodology that combines high performance liquid chromatograph (HPLC)-tandem mass spectrometry experiments with a fast computer algorithm to locate coding regions and introns. Proteins are first extracted from cells and ...

Cross-linking technology combined with tandem mass spectrometry (MS-MS) is a powerful method that provides a rapid solution to the discovery of protein-protein interactions and protein structures. We studied the problem of detecting cross-linked ...

Functional genomics, as a field, is applying genomic self-improvement protocols (cost-effective, comprehensive, precise, accurate, and useful) to the kinetics of complex cellular systems. Radical surgery in functional biology aims to mimic the success ...

We present a novel distance-based algorithm for evolutionary tree reconstruction. Our algorithm reconstructs the topology of a tree with n leaves in O(n²) time using O(n) working space. In the general Markov model of evolution the algorithm recovers the ...

In proteomics 2-dimensional gel electrophoresis (2-DE) is a separation technique for proteins. The resulting protein spots can be identified by either using picking robots and subsequent mass spectrometry or by visual cross inspection of a new gel image ...

We introduce new methods for the analysis of short-term time-series data, and apply them to gene expression data in yeast. These include (1) methods for automated period detection in a predominately cycling data set and (2) phase detection between phase-...

A central task in the study of evolution is the reconstruction of a phylogenetic tree from sequences of current-day taxa. A well supported approach to tree reconstruction performs maximum likelihood (ML) analysis. Unfortunately, searching for the ...

Sequencing by hybridization (SBH) is a method for reconstructing a sequence over a small finite alphabet from a collection of probes (substrings). Substring queries can be arranged on an array (SBH chip) and then a combinatorial method is used to ...

This paper develops a model for lateral gene transfer events (a.k.a. horizontal gene transfer events) between a set of gene trees T₁, T₂, …, T_k and a species tree S. To the best of our knowledge, this model possesses a higher degree of biological and ...

Two different approaches to determining the human genome are currently being pursued: one is the “clone-by-clone” approach, employed by the publicly-funded. Human Genome Project, and the other is the “whole genome shotgun” approach, favored by ...

High-throughput, data-directed computational protocols for Structural Genomics (or Proteomics) are required in order to evaluate the protein products of genes for structure and function at rates comparable to current gene-sequencing technology. To ...

One of the key open problems in large-scale DNA sequence assembly is the correct reconstruction of sequences that contain repeats. A long repeat can confound a sequence assembler into falsely overlaying fragments that sample its copies, effectively ...

A well studied problem in the area of Computational Molecular Biology is the so-called Protein-Protein Docking problem (PPD) that can be formulated as follows: Given two proteins A and B that form a protein complex, compute the 3D-structure of the ...

Structure comparison is a fundamental problem for structural genomics. A variety of structure comparison methods were proposed and several protein structure classification servers e.g., SCOP, DALI, CATH, were designed based on them, and are extensively ...

With genomic data (generated by classical, functional, structural, proteo- and other `omic' approaches) accumulating at a stupendous rate, there is an ever increasing need for the development of new, more efficient and more sensitive computational ...

Previous divide-and-conquer segmentation analyses of DNA sequences do not provide a satisfactory stopping criterion for the recursion. This paper proposes that segmentation be considered as a model selection process. Using the tools in model selection, ...

Arc-annotated sequences are useful in representiug the structural information of RNA sequences. Typically, RNA secondary and tertiary structures could be represented by a set of nested arcs and a set of crossing arcs, respectively. As the specified RNA ...

complex diseases is limited by a still rudimentary understanding of the molecular basis of disease as well as of drug action. At the heart of this is our current inability to account for inter-individual differences in disease etiology and drug ...