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- 1. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com IEEE FINAL YEAR PROJECTS 2012 – 2013 BIO- INFORMATICSCorporate Office: Madurai 227-230, Church road, Anna nagar, Madurai – 625 020. 0452 – 4390702, 4392702, +9199447933980 Email: info@elysiumtechnologies.com, elysiumtechnologies@gmail.com Website: www.elysiumtechnologies.comBranch Office: Trichy 15, III Floor, SI Towers, Melapudur main road, Trichy – 620 001. 0431 – 4002234, +919790464324. Email: trichy@elysiumtechnologies.com, elysium.trichy@gmail.com. Website: www.elysiumtechnologies.comBranch Office: Coimbatore 577/4, DB Road, RS Puram, Opp to KFC, Coimbatore – 641 002. +919677751577 Website: Elysiumtechnologies.com, Email: info@elysiumtechnologies.comBranch Office: Kollam Surya Complex, Vendor junction, Kollam – 691 010, Kerala. 0474 – 2723622, +919446505482. Email: kerala@elysiumtechnologies.com. Website: www.elysiumtechnologies.comBranch Office: Cochin 4th Floor, Anjali Complex, near south over bridge, Valanjampalam, Cochin – 682 016, Kerala. 0484 – 6006002, +917736004002. Email: kerala@elysiumtechnologies.com, Website: www.elysiumtechnologies.com IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 2. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com BIO - INFORMATICS 2012 - 2013EGC A Biologically Inspired Validity Measure for Comparison of Clustering Methods over8201 Metabolic Data Sets In the biological domain, clustering is based on the assumption that genes or metabolites involved in a common biological process are coexpressed/coaccumulated under the control of the same regulatory network. Thus, a detailed inspection of the grouped patterns to verify their memberships to well-known metabolic pathways could be very useful for the evaluation of clusters from a biological perspective. The aim of this work is to propose a novel approach for the comparison of clustering methods over metabolic data sets, including prior biological knowledge about the relation among elements that constitute the clusters. A way of measuring the biological significance of clustering solutions is proposed. This is addressed from the perspective of the usefulness of the clusters to identify those patterns that change in coordination and belong to common pathways of metabolic regulation. The measure summarizes in a compact way the objective analysis of clustering methods, which respects coherence and clusters distribution. It also evaluates the biological internal connections of such clusters considering common pathways. The proposed measure was tested in two biological databases using three clustering methods. EGC A Co-Clustering Approach for Mining Large Protein-Protein Interaction Networks 8202 Several approaches have been presented in the literature to cluster Protein-Protein Interaction (PPI) networks. They can be grouped in two main categories: those allowing a protein to participate in different clusters and those generating only nonoverlapping clusters. In both cases, a challenging task is to find a suitable compromise between the biological relevance of the results and a comprehensive coverage of the analyzed networks. Indeed, methods returning high accurate results are often able to cover only small parts of the input PPI network, especially when low-characterized networks are considered. We present a coclustering-based technique able to generate both overlapping and nonoverlapping clusters. The density of the clusters to search for can also be set by the user. We tested our method on the two networks of yeast and human, and compared it to other five well-known techniques on the same interaction data sets. The results showed that, for all the examples considered, our approach always reaches a good compromise between accuracy and network coverage. Furthermore, the behavior of our algorithm is not influenced by the structure of the input network, different from all the techniques considered in the comparison, which returned very good results on the yeast network, while on the human network their outcomes are rather poor.EGC A Comparative Study on Filtering Protein Secondary Structure Prediction8203 IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 3. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com Filtering of Protein Secondary Structure Prediction (PSSP) aims to provide physicochemically realistic results, while it usually improves the predictive performance. We performed a comparative study on this challenging problem, utilizing both machine learning techniques and empirical rules and we found that combinations of the two lead to the highest improvement.EGC A Computational Model for Predicting Protein Interactions Based on Multidomain8204 Collaboration Recently, several domain-based computational models for predicting protein-protein interactions (PPIs) have been proposed. The conventional methods usually infer domain or domain combination (DC) interactions from already known interacting sets of proteins, and then predict PPIs using the information. However, the majority of these models often have limitations in providing detailed information on which domain pair (single domain interaction) or DC pair (multidomain interaction) will actually interact for the predicted protein interaction. Therefore, a more comprehensive and concrete computational model for the prediction of PPIs is needed. We developed a computational model to predict PPIs using the information of intraprotein domain cohesion and interprotein DC coupling interaction. A method of identifying the primary interacting DC pair was also incorporated into the model in order to infer actual participants in a predicted interaction. Our method made an apparent improvement in the PPI prediction accuracy, and the primary interacting DC pair identification was valid specifically in predicting multidomain protein interactions. In this paper, we demonstrate that 1) the intraprotein domain cohesion is meaningful in improving the accuracy of domain-based PPI prediction, 2) a prediction model incorporating the intradomain cohesion enables us to identify the primary interacting DC pair, and 3) a hybrid approach using the intra/interdomain interaction information can lead to a more accurate prediction.EGC8205 A Framework for Incorporating Functional Interrelationships into Protein Function Prediction Algorithms The functional annotation of proteins is one of the most important tasks in the post-genomic era. Although many computational approaches have been developed in recent years to predict protein function, most of these traditional algorithms do not take interrelationships among functional terms into account, such as different GO terms usually coannotate with some common proteins. In this study, we propose a new functional similarity measure in the form of Jaccard coefficient to quantify these interrelationships and also develop a framework for incorporating GO term similarity into protein function prediction process. The experimental results of cross-validation on S. cerevisiae and Homo sapiens data sets demonstrate that our method is able to improve the performance of protein function prediction. In addition, we find that small size terms associated with a few of proteins obtain more benefit than the large size ones when considering functional interrelationships. We also compare our similarity measure with other two widely used measures, and results indicate that when incorporated into function prediction algorithms, our proposed measure is more effective. Experiment results also illustrate that our algorithms outperform two previous competing IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 4. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com algorithms, which also take functional interrelationships into account, in prediction accuracy. Finally, we show that our method is robust to annotations in the database which are not complete at present. These results give new insights about the importance of functional interrelationships in protein function prediction.EGC A Hybrid Approach to Survival Model Building Using Integration of Clinical and Molecular8206 Information in Censored Data In medical society, the prognostic models, which use clinicopathologic features and predict prognosis after a certain treatment, have been externally validated and used in practice. In recent years, most research has focused on high dimensional genomic data and small sample sizes. Since clinically similar but molecularly heterogeneous tumors may produce different clinical outcomes, the combination of clinical and genomic information, which may be complementary, is crucial to improve the quality of prognostic predictions. However, there is a lack of an integrating scheme for clinic- genomic models due to the {rm P}gg{rm N} problem, in particular, for a parsimonious model. We propose a methodology to build a reduced yet accurate integrative model using a hybrid approach based on the Cox regression model, which uses several dimension reduction techniques, {rm L}_{2} penalized maximum likelihood estimation (PMLE), and resampling methods to tackle the problem. The predictive accuracy of the modeling approach is assessed by several metrics via an independent and thorough scheme to compare competing methods. In breast cancer data studies on a metastasis and death event, we show that the proposed methodology can improve prediction accuracy and build a final model with a hybrid signature that is parsimonious when integrating both types of variables.EGC A Hybrid EKF and Switching PSO Algorithm for Joint State and Parameter Estimation of8207 Lateral Flow Immunoassay Models In this paper, a hybrid extended Kalman filter (EKF) and switching particle swarm optimization (SPSO) algorithm is proposed for jointly estimating both the parameters and states of the lateral flow immunoassay model through available short time-series measurement. Our proposed method generalizes the well-known EKF algorithm by imposing physical constraints on the system states. Note that the state constraints are encountered very often in practice that give rise to considerable difficulties in system analysis and design. The main purpose of this paper is to handle the dynamic modeling problem with state constraints by combining the extended Kalman filtering and constrained optimization algorithms via the maximization probability method. More specifically, a recently developed SPSO algorithm is used to cope with the constrained optimization problem by converting it into an unconstrained optimization one through adding a penalty term to the objective function. The proposed algorithm is then employed to simultaneously identify the parameters and states of a lateral flow immunoassay model. It is shown that the proposed algorithm gives much improved performance over the traditional EKF method.EGC A Memory Efficient Method for Structure-Based RNA Multiple Alignment8208 IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 5. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com Structure-based RNA multiple alignment is particularly challenging because covarying mutations make sequence information alone insufficient. Existing tools for RNA multiple alignment first generate pairwise RNA structure alignments and then build the multiple alignment using only sequence information. Here we present PMFastR, an algorithm which iteratively uses a sequence-structure alignment procedure to build a structure-based RNA multiple alignment from one sequence with known structure and a database of sequences from the same family. PMFastR also has low memory consumption allowing for the alignment of large sequences such as 16S and 23S rRNA. The algorithm also provides a method to utilize a multicore environment. We present results on benchmark data sets from BRAliBase, which shows PMFastR performs comparably to other state-of-the-art programs. Finally, we regenerate 607 Rfam seed alignments and show that our automated process creates multiple alignments similar to the manually curated Rfam seed alignments. Thus, the techniques presented in this paper allow for the generation of multiple alignments using sequence-structure guidance, while limiting memory consumption. As a result, multiple alignments of long RNA sequences, such as 16S and 23S rRNAs, can easily be generated locally on a personal computer. The software and supplementary data are available at http://genome.ucf.edu/PMFastR.EGC8209 A Metric for Phylogenetic Trees Based on Matching Comparing two or more phylogenetic trees is a fundamental task in computational biology. The simplest outcome of such a comparison is a pairwise measure of similarity, dissimilarity, or distance. A large number of such measures have been proposed, but so far all suffer from problems varying from computational cost to lack of robustness; many can be shown to behave unexpectedly under certain plausible inputs. For instance, the widely used Robinson-Foulds distance is poorly distributed and thus affords little discrimination, while also lacking robustness in the face of very small changes—reattaching a single leaf elsewhere in a tree of any size can instantly maximize the distance. In this paper, we introduce a new pairwise distance measure, based on matching, for phylogenetic trees. We prove that our measure induces a metric on the space of trees, show how to compute it in low polynomial time, verify through statistical testing that it is robust, and finally note that it does not exhibit unexpected behavior under the same inputs that cause problems with other measures. We also illustrate its usefulness in clustering trees, demonstrating significant improvements in the quality of hierarchical clustering as compared to the same collections of trees clustered using the Robinson-Foulds distance.EGC8210 A New Efficient Algorithm for the Gene-Team Problem on General Sequences Identifying conserved gene clusters is an important step toward understanding the evolution of genomes and predicting the functions of genes. A famous model to capture the essential biological features of a conserved gene cluster is called the gene-team model. The problem of finding the gene teams of two general sequences is the focus of this paper. For this problem, He and Goldwasser had an efficient algorithm that requires O(mn) time using O(m + n) working space, where m and n are, respectively, the numbers of genes in the two given sequences. In this paper, a new efficient IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 6. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com algorithm is presented. Assume m ≤ n. Let C = ΣαϵΣ o1(α)o2(α), where Σ is the set of distinct genes, and o1(α) and o2(a) are, respectively, the numbers of copies of a in the two given sequences. Our new algorithm requires O(min{C lg n,mn}) time using O(m + n) working space. As compared with He and Goldwassers algorithm, our new algorithm is more practical, as C is likely to be much smaller than mn in practice. In addition, our new algorithm is output sensitive. Its running time is O(lg n) times the size of the output. Moreover, our new algorithm can be efficiently extended to find the gene teams of k general sequences in O(k C Ig (n1n2...nk)) time, where ni is the number of genes in the ith input sequence.EGC A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences8211 Todays genome analysis applications require sequence representations allowing for fast access to their contents while also being memory-efficient enough to facilitate analyses of large-scale data. While a wide variety of sequence representations exist, lack of a generic implementation of efficient sequence storage has led to a plethora of poorly reusable or programming language- specific implementations. We present a novel, space-efficient data structure (GtEncseq) for storing multiple biological sequences of variable alphabet size, with customizable character transformations, wildcard support, and an assortment of internal representations optimized for different distributions of wildcards and sequence lengths. For the human genome (3.1 gigabases, including 237 million wildcard characters) our representation requires only 2 + 8 · 10-6 bits per character. Implemented in C, our portable software implementation provides a variety of methods for random and sequential access to characters and substrings (including different reading directions) using an object-oriented interface. In addition, it includes access to metadata like sequence descriptions or character distributions. The library is extensible to be used from various scripting languages. GtEncseq is much more versatile than previous solutions, adding features that were previously unavailable. Benchmarks show that it is competitive with respect to space and time requirementsEGC A New Unsupervised Feature Ranking Method for Gene Expression Data Based on8212 Consensus Affinity Feature selection is widely established as one of the fundamental computational techniques in mining microarray data. Due to the lack of categorized information in practice, unsupervised feature selection is more practically important but correspondingly more difficult. Motivated by the cluster ensemble techniques, which combine multiple clustering solutions into a consensus solution of higher accuracy and stability, recent efforts in unsupervised feature selection proposed to use these consensus solutions as oracles. However, these methods are dependent on both the particular cluster ensemble algorithm used and the knowledge of the true cluster number. These methods will be unsuitable when the true cluster number is not available, which is common in practice. In view of the above problems, a new unsupervised feature ranking method is proposed to evaluate the importance of the features based on consensus affinity. Different from previous works, our method compares the corresponding affinity of each feature between a pair of instances based on the consensus matrix of clustering solutions. As a result, our method alleviates the need to know the true number of clusters and the dependence on particular cluster ensemble approaches as in previous works. IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 7. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com Experiments on real gene expression data sets demonstrate significant improvement of the feature ranking results when compared to several state-of-the-art techniques.EGC A Sparse Regulatory Network of Copy-Number Driven Gene Expression Reveals8213 Putative Breast Cancer Oncogenes The influence of DNA cis-regulatory elements on a genes expression has been intensively studied. However, little is known about expressions driven by trans-acting DNA hotspots. DNA hotspots harboring copy number aberrations are recognized to be important in cancer as they influence multiple genes on a global scale. The challenge in detecting trans-effects is mainly due to the computational difficulty in detecting weak and sparse trans-acting signals amidst co- occuring passenger events. We propose an integrative approach to learn a sparse interaction network of DNA copy- number regions with their downstream targets in a breast cancer dataset. Information from this network helps distinguish copy-number driven from copy-number independent expression changes on a global scale. Our result further delineates cis- and trans-effects in a breast cancer dataset, for which important oncogenes such as ESR1 and ERBB2 appear to be highly copy-number dependent. Further, our model is shown to be efficient and in terms of goodness of fit no worse than other state-of the art predictors and network reconstruction models using both simulated and real data.EGC A Survey on Filter Techniques for Feature Selection in Gene Expression Microarray8214 Analysis Despite years of research, the name ambiguity problem remains largely unresolved. Outstanding issues include how to A plenitude of feature selection (FS) methods is available in the literature, most of them rising as a need to analyze data of very high dimension, usually hundreds or thousands of variables. Such data sets are now available in various application areas like combinatorial chemistry, text mining, multivariate imaging, or bioinformatics. As a general accepted rule, these methods are grouped in filters, wrappers, and embedded methods. More recently, a new group of methods has been added in the general framework of FS: ensemble techniques. The focus in this survey is on filter feature selection methods for informative feature discovery in gene expression microarray (GEM) analysis, which is also known as differentially expressed genes (DEGs) discovery, gene prioritization, or biomarker discovery. We present them in a unified framework, using standardized notations in order to reveal their technical details and to highlight their common characteristics as well as their particularities. EGC A Swarm Intelligence Framework for Reconstructing Gene Networks: Searching for 8215 Biologically Plausible Architectures In this paper, we investigate the problem of reverse engineering the topology of gene regulatory networks from temporal gene expression data. We adopt a computational intelligence approach comprising swarm intelligence techniques, namely particle swarm optimization (PSO) and ant colony optimization (ACO). In addition, the recurrent neural network IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 8. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com (RNN) formalism is employed for modeling the dynamical behavior of gene regulatory systems. More specifically, ACO is used for searching the discrete space of network architectures and PSO for searching the corresponding continuous space of RNN model parameters. We propose a novel solution construction process in the context of ACO for generating biologically plausible candidate architectures. The objective is to concentrate the search effort into areas of the structure space that contain architectures which are feasible in terms of their topological resemblance to real-world networks. The proposed framework is initially applied to the reconstruction of a small artificial network that has previously been studied in the context of gene network reverse engineering. Subsequently, we consider an artificial data set with added noise for reconstructing a subnetwork of the genetic interaction network of S. cerevisiae (yeast). Finally, the framework is applied to a real-world data set for reverse engineering the SOS response system of the bacterium Escherichia coli. Results demonstrate the relative advantage of utilizing problem-specific knowledge regarding biologically plausible structural properties of gene networks over conducting a problem-agnostic search in the vast space of network architectures.EGC A Top-r Feature Selection Algorithm for Microarray Gene Expression Data8216 Most of the conventional feature selection algorithms have a drawback whereby a weakly ranked gene that could perform well in terms of classification accuracy with an appropriate subset of genes will be left out of the selection. Considering this shortcoming, we propose a feature selection algorithm in gene expression data analysis of sample classifications. The proposed algorithm first divides genes into subsets, the sizes of which are relatively small (roughly of size h), then selects informative smaller subsets of genes (of size r <; h) from a subset and merges the chosen genes with another gene subset (of size r) to update the gene subset. We repeat this process until all subsets are merged into one informative subset. We illustrate the effectiveness of the proposed algorithm by analyzing three distinct gene expression data sets. Our method shows promising classification accuracy for all the test data sets. We also show the relevance of the selected genes in terms of their biological functions.EGC Algorithms for Reticulate Networks of Multiple Phylogenetic Trees8217 A reticulate network N of multiple phylogenetic trees may have nodes with two or more parents (called reticulation nodes). There are two ways to define the reticulation number of N. One way is to define it as the number of reticulation nodes in N in this case, a reticulate network with the smallest reticulation number is called an optimal type-I reticulate network of the trees. The better way is to define it as the total number of parents of reticulation nodes in N minus the number of reticulation nodes in N ; in this case, a reticulate network with the smallest reticulation number is called an optimal type-II reticulate network of the trees. In this paper, we first present a fast fixed-parameter algorithm for constructing one or all optimal type-I reticulate networks of multiple phylogenetic trees. We then use the algorithm together with other ideas to obtain an algorithm for estimating a lower bound on the reticulation number of an optimal type-II reticulate network of the input trees. To our knowledge, these are the first fixed-parameter algorithms for the IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 9. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com problems. We have implemented the algorithms in ANSI C, obtaining programs CMPT and MaafB. Our experimental data show that CMPT can construct optimal type-I reticulate networks rapidly and MaafB can compute better lower bounds for optimal type-II reticulate networks within shorter time than the previously best program PIRN designed by Wu.EGC Algorithms to Detect Multi-protein Modularity Conserved during Evolution8218 Detecting essential multiprotein modules that change infrequently during evolution is a challenging algorithmic task that is important for understanding the structure, function, and evolution of the biological cell. In this paper, we define a measure of modularity for interactomes and present a linear-time algorithm, Produles, for detecting multiprotein modularity conserved during evolution that improves on the running time of previous algorithms for related problems and offers desirable theoretical guarantees. We present a biologically motivated graph theoretic set of evaluation measures complementary to previous evaluation measures, demonstrate that Produles exhibits good performance by all measures, and describe certain recurrent anomalies in the performance of previous algorithms that are not detected by previous measures. Consideration of the newly defined measures and algorithm performance on these measures leads to useful insights on the nature of interactomics data and the goals of previous and current algorithms. Through randomization experiments, we demonstrate that conserved modularity is a defining characteristic of interactomes. Computational experiments on current experimentally derived interactomes for Homo sapiens and Drosophila melanogaster, combining results across algorithms, show that nearly 10 percent of current interactome proteins participate in multiprotein modules with good evidence in the protein interaction data of being conserved between human and Drosophila.EGC An Efficient Algorithm for Haplotype Inferenceon Pedigrees with Recombinations and8219 Mutations Haplotype Inference (HI) is a computational challenge of crucial importance in a range of genetic studies. Pedigrees allow to infer haplotypes from genotypes more accurately than population data, since Mendelian inheritance restricts the set of possible solutions. In this work, we define a new HI problem on pedigrees, called Minimum-Change Haplotype Configuration (MCHC) problem, that allows two types of genetic variation events: recombinations and mutations. Our new formulation extends the Minimum-Recombinant Haplotype Configuration (MRHC) problem, that has been proposed in the literature to overcome the limitations of classic statistical haplotyping methods. Our contribution is twofold. First, we prove that the MCHC problem is APX-hard under several restrictions. Second, we propose an efficient and accurate heuristic algorithm for MCHC based on an L-reduction to a well-known coding problem. Our heuristic can also be used to solve the original MRHC problem and can take advantage of additional knowledge about the input genotypes. Moreover, the L-reduction proves for the first time that MCHC and MRHC are O(nm/log nm)-approximable on general pedigrees, where n is the pedigree size and m is the genotype length. Finally, we present an extensive experimental evaluation and comparison of our heuristic algorithm with several other state-of-the-art methods for HI on pedigrees. IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 10. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.comEGC An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a8220 Probabilistic Framework Background. Inferring an evolutionary scenario for a gene family is a fundamental problem with applications both in functional and evolutionary genomics. The gene tree/species tree reconciliation approach has been widely used to address this problem, but mostly in a discrete parsimony framework that aims at minimizing the number of gene duplications and/or gene losses. Recently, a probabilistic approach has been developed, based on the classical birth- and-death process, including efficient algorithms for computing posterior probabilities of reconciliations and orthology prediction. Results. In previous work, we described an algorithm for exploring the whole space of gene tree/species tree reconciliations, that we adapt here to compute efficiently the posterior probability of such reconciliations. These posterior probabilities can be either computed exactly or approximated, depending on the reconciliation space size. We use this algorithm to analyze the probabilistic landscape of the space of reconciliations for a real data set of fungal gene families and several data sets of synthetic gene trees. Conclusion. The results of our simulations suggest that, with exact gene trees obtained by a simple birth-and-death process and realistic gene duplication/loss rates, a very small subset of all reconciliations needs to be explored in order to approximate very closely the posterior probability of the most likely reconciliations. For cases where the posterior probability mass is more evenly dispersed, our method allows to explore efficiently the required subspace of reconciliations.EGC8221 An Efficient Method for Modeling Kinetic Behavior of Channel Proteins in Cardiomyocytes Characterization of the kinetic and conformational properties of channel proteins is a crucial element in the integrative study of congenital cardiac diseases. The proteins of the ion channels of cardiomyocytes represent an important family of biological components determining the physiology of the heart. Some computational studies aiming to understand the mechanisms of the ion channels of cardiomyocytes have concentrated on Markovian stochastic approaches. Mathematically, these approaches employ Chapman-Kolmogorov equations coupled with partial differential equations. As the scale and complexity of such subcellular and cellular models increases, the balance between efficiency and accuracy of algorithms becomes critical. We have developed a novel two-stage splitting algorithm to address efficiency and accuracy issues arising in such modeling and simulation scenarios. Numerical experiments were performed based on the incorporation of our newly developed conformational kinetic model for the rapid delayed rectifier potassium channel into the dynamic models of human ventricular myocytes. Our results show that the new algorithm significantly outperforms commonly adopted adaptive Runge-Kutta methods. Furthermore, our parallel simulations with coupled algorithms for multicellular cardiac tissue demonstrate a high linearity in the speedup of large-scale cardiac simulations.EGC Cluster-Oriented Ensemble Classifier: Impact of Multicluster Characterization on8222 Ensemble Classifier Learning IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 11. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com All clustering methods have to assume some cluster relationship among the data objects that they are applied on. Similarity between a pair of objects can be defined either explicitly or implicitly. In this paper, we introduce a novel multiviewpoint-based similarity measure and two related clustering methods. The major difference between a traditional dissimilarity/similarity measure and ours is that the former uses only a single viewpoint, which is the origin, while the latter utilizes many different viewpoints, which are objects assumed to not be in the same cluster with the two objects being measured. Using multiple viewpoints, more informative assessment of similarity could be achieved. Theoretical analysis and empirical study are conducted to support this claim. Two criterion functions for document clustering are proposed based on this new measure. We compare them with several well-known clustering algorithms that use other popular similarity measures on various document collections to verify the advantages of our proposal.EGC An Information Theoretic Approach to Constructing Robust Boolean Gene Regulatory8223 Networks We introduce a class of finite systems models of gene regulatory networks exhibiting behavior of the cell cycle. The network is an extension of a Boolean network model. The system spontaneously cycles through a finite set of internal states, tracking the increase of an external factor such as cell mass, and also exhibits checkpoints in which errors in gene expression levels due to cellular noise are automatically corrected. We present a 7-gene network based on Projective Geometry codes, which can correct, at every given time, one gene expression error. The topology of a network is highly symmetric and requires using only simple Boolean functions that can be synthesized using genes of various organisms. The attractor structure of the Boolean network contains a single cycle attractor. It is the smallest nontrivial network with such high robustness. The methodology allows construction of artificial gene regulatory networks with the number of phases larger than in natural cell cycle. EGC 8224 Antilope—A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem Peptide sequencing from mass spectrometry data is a key step in proteome research. Especially de novo sequencing, the identification of a peptide from its spectrum alone, is still a challenge even for state-of-the-art algorithmic approaches. In this paper, we present antilope, a new fast and flexible approach based on mathematical programming. It builds on the spectrum graph model and works with a variety of scoring schemes. ANTILOPE combines Lagrangian relaxation for solving an integer linear programming formulation with an adaptation of Yens k shortest paths algorithm. It shows a significant improvement in running time compared to mixed integer optimization and performs at the same speed like other state-of-the-art tools. We also implemented a generic probabilistic scoring scheme that can be trained automatically for a data set of annotated spectra and is independent of the mass spectrometer type. Evaluations on benchmark data show that antilope is competitive to the popular state-of-the-art programs PepNovo and NovoHMM both in terms of runtime and accuracy. Furthermore, it offers increased flexibility in the number of considered ion types. ANTILOPE will be freely available as part of the open source proteomics library OpenMS. EGC 8225 Assortative Mixing in Directed Biological Networks IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 12. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com We analyze assortative mixing patterns of biological networks which are typically directed. We develop a theoretical background for analyzing mixing patterns in directed networks before applying them to specific biological networks. Two new quantities are introduced, namely the in-assortativity and the out-assortativity, which are shown to be useful in quantifying assortative mixing in directed networks. We also introduce the local (node level) assortativity quantities for in- and out-assortativity. Local assortativity profiles are the distributions of these local quantities over node degrees and can be used to analyze both canonical and real-world directed biological networks. Many biological networks, which have been previously classified as disassortative, are shown to be assortative with respect to these new measures. Finally, we demonstrate the use of local assortativity profiles in analyzing the functionalities of particular nodes and groups of nodes in real-world biological networks.EGC BpMatch: An Efficient Algorithm for a Segmental Analysis of Genomic Sequences8226 Here, we propose BpMatch: an algorithm that, working on a suitably modified suffix-tree data structure, is able to compute, in a fast and efficient way, the coverage of a source sequence S on a target sequence T, by taking into account direct and reverse segments, eventually overlapped. Using BpMatch, the operator should define a priori, the minimum length l of a segment and the minimum number of occurrences minRep, so that only segments longer than l and having a number of occurrences greater than minRep are considered to be significant. BpMatch outputs the significant segments found and the computed segment-based distance. On the worst case, assuming the alphabet dimension d is a constant, the time required by BpMatch to calculate the coverage is {rm O}(l^2n). On the average, by setting lge 2log_d(n), the time required to calculate the coverage is only {rm O}(n). BpMatch, thanks to the minRep parameter, can also be used to perform a self-covering: to cover a sequence using segments coming from itself, by avoiding the trivial solution of having a single segment coincident with the whole sequence.EGC Clustering 100,000 Protein Structure Decoysin Minutes8227 Ab initio protein structure prediction methods first generate large sets of structural conformations as candidates (called decoys), and then select the most representative decoys through clustering techniques. Classical clustering methods are inefficient due to the pairwise distance calculation, and thus become infeasible when the number of decoys is large. In addition, the existing clustering approaches suffer from the arbitrariness in determining a distance threshold for proteins within a cluster: a small distance threshold leads to many small clusters, while a large distance threshold results in the merging of several independent clusters into one cluster. In this paper, we propose an efficient clustering method through fast estimating cluster centroids and efficient pruning rotation spaces. The number of clusters is automatically detected by information distance criteria. A package named ONION, which can be downloaded freely, is implemented accordingly. Experimental results on benchmark data sets suggest that ONION is 14 times faster than IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 13. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com existing tools, and ONION obtains better selections for 31 targets, and worse selection for 19 targets compared to SPICKERs selections. On an average PC, ONION can cluster 100,000 decoys in around 12 minutes. EGC Composition Vector Method Based on Maximum Entropy Principle for Sequence 8228 Comparison The composition vector (CV) method is an alignment-free method for sequence comparison. Because of its simplicity when compared with multiple sequence alignment methods, the method has been widely discussed lately; and some formulas based on probabilistic models, like Haos and Yus formulas, have been proposed. In this paper, we improve these formulas by using the entropy principle which can quantify the nonrandomness occurrence of patterns in the sequences. More precisely, existing formulas are used to generate a set of possible formulas from which we choose the one that maximizes the entropy. We give the closed-form solution to the resulting optimization problem. Hence, from any given CV formula, we can find the corresponding one that maximizes the entropy. In particular, we show that Haos formula is itself maximizing the entropy and we derive a new entropy-maximizing formula from Yus formula. We illustrate the accuracy of our new formula by using both simulated and experimental data sets. For the simulated data sets, our new formula gives the best consensus and significant values for three different kinds of evolution models. For the data set of tetrapod 18S rRNA sequences, our new formula groups the clades of bird and reptile together correctly, where Haos and Yus formulas failed. Using real data sets with different sizes, we show that our formula is more accurate than Haos and Yus formulas even for small data sets. EGC Constructing and Drawing Regular Planar Split Networks 8229 Split networks are commonly used to visualize collections of bipartitions, also called splits, of a finite set. Such collections arise, for example, in evolutionary studies. Split networks can be viewed as a generalization of phylogenetic trees and may be generated using the SplitsTree package. Recently, the NeighborNet method for generating split networks has become rather popular, in part because it is guaranteed to always generate a circular split system, which can always be displayed by a planar split network. Even so, labels must be placed on the "outside” of the network, which might be problematic in some applications. To help circumvent this problem, it can be helpful to consider so- called flat split systems, which can be displayed by planar split networks where labels are allowed on the inside of the network too. Here, we present a new algorithm that is guaranteed to compute a minimal planar split network displaying a flat split system in polynomial time, provided the split system is given in a certain format. We will also briefly discuss two heuristics that could be useful for analyzing phylogeographic data and that allow the computation of flat split systems in this format in polynomial time.EGC Constructing Complex 3D Biological Environments from Medical Imaging Using High8230 Performance Computing IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 14. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com Extracting information about the structure of biological tissue from static image data is a complex task requiring computationally intensive operations. Here, we present how multicore CPUs and GPUs have been utilized to extract information about the shape, size, and path followed by the mammalian oviduct, called the fallopian tube in humans, from histology images, to create a unique but realistic 3D virtual organ. Histology images were processed to identify the individual cross sections and determine the 3D path that the tube follows through the tissue. This information was then related back to the histology images, linking the 2D cross sections with their corresponding 3D position along the oviduct. A series of linear 2D spline cross sections, which were computationally generated for the length of the oviduct, were bound to the 3D path of the tube using a novel particle system technique that provides smooth resolution of self- intersections. This results in a unique 3D model of the oviduct, which is grounded in reality. The GPU is used for the processor intensive operations of image processing and particle physics based simulations, significantly reducing the time required to generate a complete model.EGC CSD Homomorphisms between Phylogenetic Networks8231 Since Darwin, species trees have been used as a simplified description of the relationships which summarize the complicated network N of reality. Recent evidence of hybridization and lateral gene transfer, however, suggest that there are situations where trees are inadequate. Consequently it is important to determine properties that characterize networks closely related to N and possibly more complicated than trees but lacking the full complexity of N. A connected surjective digraph map (CSD) is a map f from one network N to another network M such that every arc is either collapsed to a single vertex or is taken to an arc, such that f is surjective, and such that the inverse image of a vertex is always connected. CSD maps are shown to behave well under composition. It is proved that if there is a CSD map from N to M, then there is a way to lift an undirected version of M into N, often with added resolution. A CSD map from N to M puts strong constraints on N. In general, it may be useful to study classes of networks such that, for any N, there exists a CSD map from N to some standard member of that class.EGC Designing Filters for Fast-Known NcRNA Identification8232 Detecting members of known noncoding RNA (ncRNA) families in genomic DNA is an important part of sequence annotation. However, the most widely used tool for modeling ncRNA families, the covariance model (CM), incurs a high- computational cost when used for genome-wide search. This cost can be reduced by using a filter to exclude sequences that are unlikely to contain the ncRNA of interest, applying the CM only where it is likely to match strongly. Despite recent advances, designing an efficient filter that can detect ncRNA instances lacking strong conservation while excluding most irrelevant sequences remains challenging. In this work, we design three types of filters based on multiple secondary structure profiles (SSPs). An SSP augments a regular profile (i.e., a position weight matrix) with secondary structure information but can still be efficiently scanned against long sequences. Multi-SSP-based filters combine evidence from multiple SSP matches and can achieve high sensitivity and specificity. Our SSP-based filters are extensively tested in BRAliBase III data set, Rfam 9.0, and a published soil metagenomic data set. In addition, we IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 15. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com compare the SSP-based filters with several other ncRNA search tools including Infernal (with profile HMMs as filters), ERPIN, and tRNAscan-SE. Our experiments demonstrate that carefully designed SSP filters can achieve significant speedup over unfiltered CM search while maintaining high sensitivity for various ncRNA families.EGC Detection of Outlier Residues for Improving Interface Prediction in Protein8233 Heterocomplexes Unlike Sequence-based understanding and identification of protein binding interfaces is a challenging research topic due to the complexity in protein systems and the imbalanced distribution between interface and noninterface residues. This paper presents an outlier detection idea to address the redundancy problem in protein interaction data. The cleaned training data are then used for improving the prediction performance. We use three novel measures to describe the extent a residue is considered as an outlier in comparison to the other residues: the distance of a residue instance from the center instance of all residue instances of the same class label (Dist), the probability of the class label of the residue instance (PCL), and the importance of within-class and between-class (IWB) residue instances. Outlier scores are computed by integrating the three factors; instances with a sufficiently large score are treated as outliers and removed. The data sets without outliers are taken as input for a support vector machine (SVM) ensemble. The proposed SVM ensemble trained on input data without outliers performs better than that with outliers. Our method is also more accurate than many literature methods on benchmark data sets. From our empirical studies, we found that some outlier interface residues are truly near to noninterface regions, and some outlier noninterface residues are close to interface regions.EGC8234 DICLENS: Divisive Clustering Ensemble with Automatic Cluster Number Clustering has a long and rich history in a variety of scientific fields. Finding natural groupings of a data set is a hard task as attested by hundreds of clustering algorithms in the literature. Each clustering technique makes some assumptions about the underlying data set. If the assumptions hold, good clusterings can be expected. It is hard, in some cases impossible, to satisfy all the assumptions. Therefore, it is beneficial to apply different clustering methods on the same data set, or the same method with varying input parameters or both. We propose a novel method, DICLENS, which combines a set of clusterings into a final clustering having better overall quality. Our method produces the final clustering automatically and does not take any input parameters, a feature missing in many existing algorithms. Extensive experimental studies on real, artificial, and gene expression data sets demonstrate that DICLENS produces very good quality clusterings in a short amount of time. DICLENS implementation runs on standard personal computers by being scalable, and by consuming very little memory and CPU.EGC Disease Liability Prediction from Large Scale Genotyping Data Using Classifiers with a8235 Reject Option IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 16. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com Many Genome-wide association studies (GWA) try to identify the genetic polymorphisms associated with variation in phenotypes. However, the most significant genetic variants may have a small predictive power to forecast the future development of common diseases. We study the prediction of the risk of developing a disease given genome-wide genotypic data using classifiers with a reject option, which only make a prediction when they are sufficiently certain, but in doubtful situations may reject making a classification. To test the reliability of our proposal, we used the Wellcome Trust Case Control Consortium (WTCCC) data set, comprising 14,000 cases of seven common human diseases and 3,000 shared controls. EGC Drosophila Gene Expression Pattern Annotation through Multi-Instance Multi-Label 8236 Learning In the studies of Drosophila embryogenesis, a large number of two-dimensional digital images of gene expression patterns have been produced to build an atlas of spatio-temporal gene expression dynamics across developmental time. Gene expressions captured in these images have been manually annotated with anatomical and developmental ontology terms using a controlled vocabulary (CV), which are useful in research aimed at understanding gene functions, interactions, and networks. With the rapid accumulation of images, the process of manual annotation has become increasingly cumbersome, and computational methods to automate this task are urgently needed. However, the automated annotation of embryo images is challenging. This is because the annotation terms spatially correspond to local expression patterns of images, yet they are assigned collectively to groups of images and it is unknown which term corresponds to which region of which image in the group. In this paper, we address this problem using a new machine learning framework, Multi-Instance Multi-Label (MIML) learning. We first show that the underlying nature of the annotation task is a typical MIML learning problem. Then, we propose two support vector machine algorithms under the MIML framework for the task. Experimental results on the FlyExpress database (a digital library of standardized Drosophila gene expression pattern images) reveal that the exploitation of MIML framework leads to significant performance improvement over state-of-the-art approaches.EGC Efficient Approaches for Retrieving Protein Tertiary Structures8237 The 3D conformation of a protein in the space is the main factor which determines its function in living organisms. Due to the huge amount of newly discovered proteins, there is a need for fast and accurate computational methods for retrieving protein structures. Their purpose is to speed up the process of understanding the structure-to-function relationship which is crucial in the development of new drugs. There are many algorithms addressing the problem of protein structure retrieval. In this paper, we present several novel approaches for retrieving protein tertiary structures. We present our voxel-based descriptor. Then we present our protein ray-based descriptors which are applied on the interpolated protein backbone. We introduce five novel wavelet descriptors which perform wavelet transforms on the protein distance matrix. We also propose an efficient algorithm for distance matrix alignment named Matrix Alignment by Sequence Alignment within Sliding Window (MASASW), which has shown as much faster than DALI, CE, and IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 17. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com MatAlign. We compared our approaches between themselves and with several existing algorithms, and they generally prove to be fast and accurate. MASASW achieves the highest accuracy. The ray and wavelet-based descriptors as well as MASASW are more accurate than CE.EGC Efficient Genotype Eliminationvia Adaptive Allele Consolidation8238 In We propose the technique of Adaptive Allele Consolidation, that greatly improves the performance of the Lange- Goradia algorithm for genotype elimination in pedigrees, while still producing equivalent output. Genotype elimination consists in removing from a pedigree those genotypes that are impossible according to the Mendelian law of inheritance. This is used to find errors in genetic data and is useful as a preprocessing step in other analyses (such as linkage analysis or haplotype imputation). The problem of genotype elimination is intrinsically combinatorial, and Allele Consolidation is an existing technique where several alleles are replaced by a single "lumped” allele in order to reduce the number of combinations of genotypes that have to be considered, possibly at the expense of precision. In existing Allele Consolidation techniques, alleles are lumped once and for all before performing genotype elimination. The idea of Adaptive Allele Consolidation is to dynamically change the set of alleles that are lumped together during the execution of the Lange-Goradia algorithm, so that both high performance and precision are achieved. We have implemented the technique in a tool called Celer and evaluated it on a large set of scenarios, with good results.EGC8239 Efficient Maximal Repeat Finding Using the Burrows-Wheeler Transform and Wavelet Tree Finding repetitive structures in genomes and proteins is important to understand their biological functions. Many data compressors for modern genomic sequences rely heavily on finding repeats in the sequences. Small-scale and local repetitive structures are better understood than large and complex interspersed ones. The notion of maximal repeats captures all the repeats in the data in a space-efficient way. Prior work on maximal repeat finding used either a suffix tree or a suffix array along with other auxiliary data structures. Their space usage is 19-50 times the text size with the best engineering efforts, prohibiting their usability on massive data such as the whole human genome. We focus on finding all the maximal repeats from massive texts in a time- and space-efficient manner. Our technique uses the Burrows-Wheeler Transform and wavelet trees. For data sets consisting of natural language texts and protein data, the space usage of our method is no more than three times the text size. For genomic sequences stored using one byte per base, the space usage of our method is less than double the sequence size. Our space-efficient method keeps the timing performance fast. In fact, our method is orders of magnitude faster than the prior methods for processing massive texts such as the whole human genome, since the prior methods must use external memory. For the first time, our method enables a desktop computer with 8 GB internal memory (actual internal memory usage is less than 6 GB) to find all the maximal repeats in the whole human genome in less than 17 hours. We have implemented our method as general-purpose open-source software for public use. IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 18. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com EGC Eigen-Genomic System Dynamic-Pattern Analysis (ESDA): Modeling mRNA Degradation 8240 and Self-Regulation The High-throughput methods systematically measure the internal state of the entire cell, but powerful computational tools are needed to infer dynamics from their raw data. Therefore, we have developed a new computational method, Eigen-genomic System Dynamic-pattern Analysis (ESDA), which uses systems theory to infer dynamic parameters from a time series of gene expression measurements. As many genes are measured at a modest number of time points, estimation of the system matrix is underdetermined and traditional approaches for estimating dynamic parameters are ineffective; thus, ESDA uses the principle of dimensionality reduction to overcome the data imbalance. Since degradation rates are naturally confounded by self-regulation, our model estimates an effective degradation rate that is the difference between self-regulation and degradation. We demonstrate that ESDA is able to recover effective degradation rates with reasonable accuracy in simulation. We also apply ESDA to a budding yeast data set, and find that effective degradation rates are normally slower than experimentally measured degradation rates. Our results suggest that either self-regulation is widespread in budding yeast and that self-promotion dominates self-inhibition, or that self- regulation may be rare and that experimental methods for measuring degradation rates based on transcription arrest may severely overestimate true degradation rates in healthy cells. .EGC8241 Empirical Evidence of the Applicability of Functional Clustering through Gene Expression Classification a great range of prior biological knowledge about the roles and functions of genes and gene-gene The availability of interactions allows us to simplify the analysis of gene expression data to make it more robust, compact, and interpretable. Here, we objectively analyze the applicability of functional clustering for the identification of groups of functionally related genes. The analysis is performed in terms of gene expression classification and uses predictive accuracy as an unbiased performance measure. Features of biological samples that originally corresponded to genes are replaced by features that correspond to the centroids of the gene clusters and are then used for classifier learning. Using 10 benchmark data sets, we demonstrate that functional clustering significantly outperforms random clustering without biological relevance. We also show that functional clustering performs comparably to gene expression clustering, which groups genes according to the similarity of their expression profiles. Finally, the suitability of functional clustering as a feature extraction technique is evaluated and discussed. EGC Evaluating Path Queries over Frequently Updated Route Collections 8242 This The recent advances in the infrastructure of Geographic Information Systems (GIS), and the proliferation of GPS technology, have resulted in the abundance of geodata in the form of sequences of points of interest (POIs), waypoints, etc. We refer to sets of such sequences as route collections. In this work, we consider path queries on frequently updated route collections: given a route collection and two points n_s and n_t, a path query returns a path, i.e., a sequence of points, that connects n_s to n_t. We introduce two path query evaluation paradigms that enjoy the benefits of search algorithms (i.e., fast index maintenance) while utilizing transitivity information to terminate the search sooner. IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 19. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com Efficient indexing schemes and appropriate updating procedures are introduced. An extensive experimental evaluation verifies the advantages of our methods compared to conventional graph-based search. .EGC Exploiting Intrastructure Information for Secondary Structure Prediction with Multifaceted8243 Pipelines Predicting the secondary structure of proteins is still a typical step in several bioinformatic tasks, in particular, for tertiary structure prediction. Notwithstanding the impressive results obtained so far, mostly due to the advent of sequence encoding schemes based on multiple alignment, in our view the problem should be studied from a novel perspective, in which understanding how available information sources are dealt with plays a central role. After revisiting a well-known secondary structure predictor viewed from this perspective (with the goal of identifying which sources of information have been considered and which have not), we propose a generic software architecture designed to account for all relevant information sources. To demonstrate the validity of the approach, a predictor compliant with the proposed generic architecture has been implemented and compared with several state-of-the-art secondary structure predictors. Experiments have been carried out on standard data sets, and the corresponding results confirm the validity of the approach. The predictor is available at http://iasc.diee.unica.it/ssp2/ through the corresponding web application or as downloadable stand-alone portable unpack-and-run bundle. EGC Exploiting the Functional and Taxonomic Structure of Genomic Data by Probabilistic 8244 Topic Modeling This Predicting the secondary structure of proteins is still a typical step in several bioinformatic tasks, in particular, for tertiary structure prediction. Notwithstanding the impressive results obtained so far, mostly due to the advent of sequence encoding schemes based on multiple alignment, in our view the problem should be studied from a novel perspective, in which understanding how available information sources are dealt with plays a central role. After revisiting a well-known secondary structure predictor viewed from this perspective (with the goal of identifying which sources of information have been considered and which have not), we propose a generic software architecture designed to account for all relevant information sources. To demonstrate the validity of the approach, a predictor compliant with the proposed generic architecture has been implemented and compared with several state-of-the-art secondary structure predictors. Experiments have been carried out on standard data sets, and the corresponding results confirm the validity of the approach. EGC Fast Local Search for Unrooted Robinson-Foulds Supertrees 8245 A Robinson-Foulds (RF) supertree for a collection of input trees is a tree containing all the species in the input trees that is at minimum total RF distance to the input trees. Thus, an RF supertree is consistent with the maximum number of splits in the input trees. Constructing RF supertrees for rooted and unrooted data is NP-hard. Nevertheless, effective local search heuristics have been developed for the restricted case where the input trees and the supertree are rooted. We describe new heuristics, based on the Edge Contract and Refine (ECR) operation, that remove this restriction, IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 20. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com thereby expanding the utility of RF supertrees. Our experimental results on simulated and empirical data sets show that our unrooted local search algorithms yield better supertrees than those obtained from MRP and rooted RF heuristics in terms of total RF distance to the input trees and, for simulated data, in terms of RF distance to the true tree.EGC Fast Parallel Markov Clustering in Bioinformatics Using Massively Parallel Computing on8246 GPU with CUDA and ELLPACK-R Sparse Format Markov clustering (MCL) is becoming a key algorithm within bioinformatics for determining clusters in networks. However, with increasing vast amount of data on biological networks, performance and scalability issues are becoming a critical limiting factor in applications. Meanwhile, GPU computing, which uses CUDA tool for implementing a massively parallel computing environment in the GPU card, is becoming a very powerful, efficient, and low-cost option to achieve substantial performance gains over CPU approaches. The use of on-chip memory on the GPU is efficiently lowering the latency time, thus, circumventing a major issue in other parallel computing environments, such as MPI. We introduce a very fast Markov clustering algorithm using CUDA (CUDA-MCL) to perform parallel sparse matrix-matrix computations and parallel sparse Markov matrix normalizations, which are at the heart of MCL. We utilized ELLPACK-R sparse format to allow the effective and fine-grain massively parallel processing to cope with the sparse nature of interaction networks data sets in bioinformatics applications. As the results show, CUDA-MCL is significantly faster than the original MCL running on CPU. Thus, large-scale parallel computation on off-the-shelf desktop-machines, that were previously only possible on supercomputing architectures, can significantly change the way bioinformaticians and biologists deal with their data.EGC Faster Mass Spectrometry-Based Protein Inference: Junction Trees Are More Efficient5247 than Sampling and Marginalization by Enumeration The problem of identifying the proteins in a complex mixture using tandem mass spectrometry can be framed as an inference problem on a graph that connects peptides to proteins. Several existing protein identification methods make use of statistical inference methods for graphical models, including expectation maximization, Markov chain Monte Carlo, and full marginalization coupled with approximation heuristics. We show that, for this problem, the majority of the cost of inference usually comes from a few highly connected subgraphs. Furthermore, we evaluate three different statistical inference methods using a common graphical model, and we demonstrate that junction tree inference substantially improves rates of convergence compared to existing methods.EGC Gene Classification Using Parameter-Free Semi-Supervised Manifold Learning8248 The problem of identifying the proteins in a complex mixture using tandem mass spectrometry can be framed as an inference problem on a graph that connects peptides to proteins. Several existing protein identification methods make use of statistical inference methods for graphical models, including expectation maximization, Markov chain Monte IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 21. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com Carlo, and full marginalization coupled with approximation heuristics. We show that, for this problem, the majority of the cost of inference usually comes from a few highly connected subgraphs. Furthermore, we evaluate three different statistical inference methods using a common graphical model, and we demonstrate that junction tree inference substantially improves rates of convergence compared to existing methods.EGC8249 GSGS: A Computational Approach to Reconstruct Signaling Pathway Structures from Gene Sets Reconstruction of signaling pathway structures is essential to decipher complex regulatory relationships in living cells. The existing computational approaches often rely on unrealistic biological assumptions and do not explicitly consider signal transduction mechanisms. Signal transduction events refer to linear cascades of reactions from the cell surface to the nucleus and characterize a signaling pathway. In this paper, we propose a novel approach, Gene Set Gibbs Sampling (GSGS), to reverse engineer signaling pathway structures from gene sets related to the pathways. We hypothesize that signaling pathways are structurally an ensemble of overlapping linear signal transduction events which we encode as Information Flows (IFs). We infer signaling pathway structures from gene sets, referred to as Information Flow Gene Sets (IFGSs), corresponding to these events. Thus, an IFGS only reflects which genes appear in the underlying IF but not their ordering. GSGS offers a Gibbs sampling like procedure to reconstruct the underlying signaling pathway structure by sequentially inferring IFs from the overlapping IFGSs related to the pathway. In the proof- of-concept studies, our approach is shown to outperform the existing state-of-the-art network inference approaches using both continuous and discrete data generated from benchmark networks in the DREAM initiative. We perform a comprehensive sensitivity analysis to assess the robustness of our approach. Finally, we implement GSGS to reconstruct signaling mechanisms in breast cancer cells. EGC Hash Subgraph Pairwise Kernel for Protein-Protein Interaction Extraction 8250 Extracting protein-protein interaction (PPI) from biomedical literature is an important task in biomedical text mining (BioTM). In this paper, we propose a hash subgraph pairwise (HSP) kernel-based approach for this task. The key to the novel kernel is to use the hierarchical hash labels to express the structural information of subgraphs in a linear time. We apply the graph kernel to compute dependency graphs representing the sentence structure for protein-protein interaction extraction task, which can efficiently make use of full graph structural information, and particularly capture the contiguous topological and label information ignored before. We evaluate the proposed approach on five publicly available PPI corpora. The experimental results show that our approach significantly outperforms all-path kernel approach on all five corpora and achieves state-of-the-art performance.EGC8251 Identification of Essential Proteins Based on Edge Clustering Coefficient IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 22. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com Identification of essential proteins is key to understanding the minimal requirements for cellular life and important for drug design. The rapid increase of available protein-protein interaction (PPI) data has made it possible to detect protein essentiality on network level. A series of centrality measures have been proposed to discover essential proteins based on network topology. However, most of them tended to focus only on the location of single protein, but ignored the relevance between interactions and protein essentiality. In this paper, a new centrality measure for identifying essential proteins based on edge clustering coefficient, named as NC, is proposed. Different from previous centrality measures, NC considers both the centrality of a node and the relationship between it and its neighbors. For each interaction in the network, we calculate its edge clustering coefficient. A nodes essentiality is determined by the sum of the edge clustering coefficients of interactions connecting it and its neighbors. The new centrality measure NC takes into account the modular nature of protein essentiality. NC is applied to three different types of yeast protein-protein interaction networks, which are obtained from the DIP database, the MIPS database and the BioGRID database, respectively. The experimental results on the three different networks show that the number of essential proteins discovered by NC universally exceeds that discovered by the six other centrality measures: DC, BC, CC, SC, EC, and IC. Moreover, the essential proteins discovered by NC show significant cluster effect.EGC Identifying Gene Pathways Associated with Cancer Characteristics via Sparse Statistical8252 Methods Information We propose a statistical method for uncovering gene pathways that characterize cancer heterogeneity. To incorporate knowledge of the pathways into the model, we define a set of activities of pathways from microarray gene expression data based on the Sparse Probabilistic Principal Component Analysis (SPPCA). A pathway activity logistic regression model is then formulated for cancer phenotype. To select pathway activities related to binary cancer phenotypes, we use the elastic net for the parameter estimation and derive a model selection criterion for selecting tuning parameters included in the model estimation. Our proposed method can also reverse-engineer gene networks based on the identified multiple pathways that enables us to discover novel gene-gene associations relating with the cancer phenotypes. We illustrate the whole process of the proposed method through the analysis of breast cancer gene expression data.EGC Inferring Gene Regulatory Networks via Nonlinear State-Space Models and Exploiting8253 Sparsity This paper considers the problem of learning the structure of gene regulatory networks from gene expression time series data. A more realistic scenario when the state space model representing a gene network evolves nonlinearly is considered while a linear model is assumed for the microarray data. To capture the nonlinearity, a particle filter-based state estimation algorithm is considered instead of the contemporary linear approximation-based approaches. The parameters characterizing the regulatory relations among various genes are estimated online using a Kalman filter. Since a particular gene interacts with a few other genes only, the parameter vector is expected to be sparse. The state estimates delivered by the particle filter and the observed microarray data are then subjected to a LASSO-based least IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 23. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com squares regression operation which yields a parsimonious and efficient description of the regulatory network by setting the irrelevant coefficients to zero. The performance of the aforementioned algorithm is compared with the extended Kalman filter (EKF) and Unscented Kalman Filter (UKF) employing the Mean Square Error (MSE) as the fidelity criterion in recovering the parameters of gene regulatory networks from synthetic data and real biological data. Extensive computer simulations illustrate that the proposed particle filter-based network inference algorithm outperforms EKF and UKF, and therefore, it can serve as a natural framework for modeling gene regulatory networks with nonlinear and sparse structure.EGC8254 Inferring the Number of Contributors to Mixed DNA Profiles Forensic samples containing DNA from two or more individuals can be difficult to interpret. Even ascertaining the number of contributors to the sample can be challenging. These uncertainties can dramatically reduce the statistical weight attached to evidentiary samples. A probabilistic mixture algorithm that takes into account not just the number and magnitude of the alleles at a locus, but also their frequency of occurrence allows the determination of likelihood ratios of different hypotheses concerning the number of contributors to a specific mixture. This probabilistic mixture algorithm can compute the probability of the alleles in a sample being present in a 2-person mixture, 3-person mixture, etc. The ratio of any two of these probabilities then constitutes a likelihood ratio pertaining to the number of contributors to such a mixture.EGC Intervention in Gene Regulatory Networks viaPhenotypically Constrained Control8255 PoliciesBased on Long-Run Behavior A salient purpose for studying gene regulatory networks is to derive intervention strategies to identify potential drug targets and design gene-based therapeutic intervention. Optimal and approximate intervention strategies based on the transition probability matrix of the underlying Markov chain have been studied extensively for probabilistic Boolean networks. While the key goal of control is to reduce the steady-state probability mass of undesirable network states, in practice it is important to limit collateral damage and this constraint should be taken into account when designing intervention strategies with network models. In this paper, we propose two new phenotypically constrained stationary control policies by directly investigating the effects on the network long-run behavior. They are derived to reduce the risk of visiting undesirable states in conjunction with constraints on the shift of undesirable steady-state mass so that only limited collateral damage can be introduced. We have studied the performance of the new constrained control policies together with the previous greedy control policies to randomly generated probabilistic Boolean networks. A preliminary example for intervening in a metastatic melanoma network is also given to show their potential application in designing genetic therapeutics to reduce the risk of entering both aberrant phenotypes and other ambiguous states IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 24. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com corresponding to complications or collateral damage. Experiments on both random network ensembles and the melanoma network demonstrate that, in general, the new proposed control policies exhibit the desired performance. As shown by intervening in the melanoma network, these control policies can potentially serve as future practical gene therapeutic intervention strategies.EGC8256 Iterative Dictionary Construction for Compression of Large DNA Data Sets Genomic repositories increasingly include individual as well as reference sequences, which tend to share long identical and near-identical strings of nucleotides. However, the sequential processing used by most compression algorithms, and the volumes of data involved, mean that these long-range repetitions are not detected. An order-insensitive, disk- based dictionary construction method can detect this repeated content and use it to compress collections of sequences. We explore a dictionary construction method that improves repeat identification in large DNA data sets. Our adaptation, Comrad, of an existing disk-based method identifies exact repeated content in collections of sequences with similarities within and across the set of input sequences. Comrad compresses the data over multiple passes, which is an expensive process, but allows Comrad to compress large data sets within reasonable time and space. Comrad allows for random access to individual sequences and subsequences without decompressing the whole data set. Comrad has no competitor in terms of the size of data sets that it can compress (extending to many hundreds of gigabytes) and, even for smaller data sets, the results are competitive compared to alternatives; as an example, 39 S. cerevisiae genomes compressed to 0.25 bits per base.EGC k-Information Gain Scaled Nearest Neighbors:A Novel Approach to Classifying Protein-8257 Protein Interaction-Related Documents Although publicly accessible databases containing protein-protein interaction (PPI)-related information are important resources to bench and in silico research scientists alike, the amount of time and effort required to keep them up to date is often burdonsome. In an effort to help identify relevant PPI publications, text-mining tools, from the machine learning discipline, can be applied to help in this process. Here, we describe and evaluate two document classification algorithms that we submitted to the BioCreative II.5 PPI Classification Challenge Task. This task asked participants to design classifiers for identifying documents containing PPI-related information in the primary literature, and evaluated them against one another. One of our systems was the overall best-performing system submitted to the challenge task. It utilizes a novel approach to k-nearest neighbor classification, which we describe here, and compare its performance to those of two support vector machine-based classification systems, one of which was also evaluated in the challenge task.EGC8258 Manifold Adaptive Experimental Design for Text Categorization IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects
- 25. Elysium Technologies Private Limited Approved by ISO 9001:2008 and AICTE for SKP Training Singapore | Madurai | Trichy | Coimbatore | Cochin | Kollam | Chennai http://www.elysiumtechnologies.com, info@elysiumtechnologies.com In many information processing tasks, labels are usually expensive and the unlabeled data points are abundant. To reduce the cost on collecting labels, it is crucial to predict which unlabeled examples are the most informative, i.e., improve the classifier the most if they were labeled. Many active learning techniques have been proposed for text categorization, such as SVMActive and Transductive Experimental Design. However, most of previous approaches try to discover the discriminant structure of the data space, whereas the geometrical structure is not well respected. In this paper, we propose a novel active learning algorithm which is performed in the data manifold adaptive kernel space. The manifold structure is incorporated into the kernel space by using graph Laplacian. This way, the manifold adaptive kernel space reflects the underlying geometry of the data. By minimizing the expected error with respect to the optimal classifier, we can select the most representative and discriminative data points for labeling. Experimental results on text categorization have demonstrated the effectiveness of our proposed approach.EGC8259 Markov Invariants for Phylogenetic Rate Matrices Derived from Embedded Submodels We consider novel phylogenetic models with rate matrices that arise via the embedding of a progenitor model on a small number of character states, into a target model on a larger number of character states. Adapting representation- theoretic results from recent investigations of Markov invariants for the general rate matrix model, we give a prescription for identifying and counting Markov invariants for such "symmetric embedded” models, and we provide enumerations of these for the first few cases with a small number of character states. The simplest example is a target model on three states, constructed from a general 2 state model; the "2 hookrightarrow 3” embedding. We show that for 2 taxa, there exist two invariants of quadratic degree that can be used to directly infer pairwise distances from observed sequences under this model. A simple simulation study verifies their theoretical expected values, and suggests that, given the appropriateness of the model class, they have superior statistical properties than the standard (log) Det invariant (which is of cubic degree for this case).EGC8260 Matching Split Distance for Unrooted Binary Phylogenetic Trees The reconstruction of evolutionary trees is one of the primary objectives in phylogenetics. Such a tree represents the historical evolutionary relationship between different species or organisms. Tree comparisons are used for multiple purposes, from unveiling the history of species to deciphering evolutionary associations among organisms and geographical areas. In this paper, we propose a new method of defining distances between unrooted binary phylogenetic trees that is especially useful for relatively large phylogenetic trees. Next, we investigate in detail the properties of one example of these metrics, called the Matching Split distance, and describe how the general method can be extended to nonbinary trees.EGC8261 Memory Efficient Algorithms for Structural Alignment of RNAs with Pseudoknots IEEE Final Year Projects 2012 |Student Projects | Bio-informatics Projects

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