NDLI: A next generation sequence processing and analysis platform with integrated cloud-storage and high performance computing resources

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Serum antibody repertoire profiling using virtual antigen screen

Genome scale inference of transcriptional regulatory networks using mutual information on complex interactions

An iterative MapReduce approach to frequent subgraph mining in biological datasets

Feature extraction in protein sequences classification: a new stability measure

STEROID: in silico heuristic target combination identification for disease-related signaling networks

miHA-match: computational detection of tissue-specific minor histocompatibility antigens

Unraveling multiple miRNA-mRNA associations through a graph-based approach

High performance phosphorylation site assignment algorithm for mass spectrometry data using multicore systems

Robustness measure for an adeno-associated viral shell self-assembly is accurately predicted by configuration space atlasing using EASAL

ERNE-BS5: aligning BS-treated sequences by multiple hits on a 5-letters alphabet

Decoding dendritic cell function through module and network analysis

A collective NMF method for detecting protein functional module from multiple data sources

Parallelization of the spectral deconvolution stage of the proteomic discovery process

A Monte Carlo approach to measure the robustness of Boolean networks

NetPipe: a network-based pipeline for discovery of genes and protein complexes regulating meiotic recombination hotspots

Using quantitative dose-response data to benchmark B-cell epitope prediction for antipeptide antibodies

A system for acquiring and management of ECG signals by using mobile devices: a support for first intervention in heart attacks

Improved multiple sequence alignments using coupled pattern mining

Immunoinformatic analysis of Chinese hamster ovary (CHO) protein contaminants in therapeutic protein formulations

ArtSurf: a method for deformable partial matching of protein small-molecule binding sites

A multi-directional rapidly exploring random graph (mRRG) for protein folding

Supervised logistic principal component analysis for pathway based genome-wide association studies

Multi-target protein-chemical interaction prediction using task-regularized and boosted multi-task learning

Reverse engineering molecular hypergraphs

Functional site prediction by exploiting correlations between labels of interacting residues

Non-overlapping clone pooling for high-throughput sequencing

Coalescent-based method for learning parameters of admixture events from large-scale genetic variation data

OCR-based image features for biomedical image and article classification: identifying documents relevant to cis-regulatory elements

Inferring ancestry in admixed populations using microarray probe intensities

Anaphora resolution in biomedical literature: a hybrid approach

Functional module identification by block modeling using simulated annealing with path relinking

Biased decoy sampling to aid the selection of near-native protein conformations

Protein blocks versus hydrogen bonds based alphabets for protein structure classification

Discovering geometric patterns in genomic data

Exploring objective functions and cross-terms in the optimization of an energy function for protein design

Efficient SNP-sensitive alignment and database-assisted SNP calling for low coverage samples

Automatic segmentation and quantification of filamentous structures in electron tomography

PseudoDomain: identification of processed pseudogenes based on protein domain classification

Complexity reduction of stochastic master equation simulation based on Kronecker product analysis

Algorithms for detecting complementary SNPs within a region of interest that are associated with diseases

Protein function prediction using weak-label learning

Detecting ECG abnormalities via transductive transfer learning

Biological interpretation of morphological patterns in histopathological whole-slide images

Predicting expression-related features of chromosomal domain organization with network-structured analysis of gene expression and chromosomal location

Multivariate hypergeometric similarity measure

A volumetric method for representing and comparing regions of electrostatic focusing in molecular structure

Evolutionary analysis of functional modules in dynamic PPI networks

Alignment of real-time live-cell growth data for quantitative analysis of growth at the shoot apex of Arabidopsis thaliana: deducing the relationship between primordia growth, gene expression and cell behaviors

Parallel syntenic alignment on GPUs

Finding informative genes for prostate cancer: a general framework of integrating heterogeneous sources

A new algorithm for finding enriched regions in ChIP-Seq data

Hybrid pattern matching for complex ontology term recognition

Integration of genomic and epigenomic features to predict meiotic recombination hotspots in human and mouse

Efficient implementation of the hybrid method for stochastic simulation of biochemical systems

A collective ranking method for genome-wide association studies

Parallel verlet neighbor list algorithm for GPU-optimized MD simulations

DACIDR: deterministic annealed clustering with interpolative dimension reduction using a large collection of 16S rRNA sequences

Signed network propagation for detecting differential gene expressions and DNA copy number variations

Memory-based local search for simplified protein structure prediction

Remote homology detection on alpha-structural proteins using simulated evolution

3D bone microarchitecture modeling and fracture risk prediction

An integer programming approach to novel transcript reconstruction from paired-end RNA-Seq reads

Scalable genome scaffolding using integer linear programming

Alignment seeding strategies using contiguous pyrimidine purine matches

An integrated optimization framework for inferring two generation kinships and parental genotypes from microsatellite samples

Semantic querying over knowledge in biomedical text corpora annotated with multiple ontologies

Towards biophysical validation of constraint modeling for rigidity analysis of proteins

A fast computation of pairwise sequence alignment scores between a protein and a set of single-locus variants of another protein

Network-based classification of recurrent endometrial cancers using high-throughput DNA methylation data

Predicting protective bacterial antigens using random forest classifiers

ADANET: inferring gene regulatory networks using ensemble classifiers

On enumerating the DNA sequences

Microarray vs. RNA-Seq: a comparison for active subnetwork discovery

Simulation and analysis of antibody aggregation on cell surfaces using motion planning and graph analysis

Inferring novel associations between SNP sets and gene sets in eQTL study using sparse graphical model

QSEA for fuzzy subgraph querying of KEGG pathways

Rational design of orthogonal libraries of protein coding genes

Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutions

A pattern mining based integrative framework for biomarker discovery

A novel approach for mining representative spatial motifs of proteins

Systems biology approach to identify markers of differentiation in bladder cancer

454 and SOLiD™ complementary used to filter and build the draft genome of highly abundant cyanobacteria in biological desert crust

An in-depth analysis of the molecular dynamics and structural aspects of IKB proteins

mHMM (multivariate hidden Markov model) application in studying BRD4 and JMJD6 function cooperatively on promoter-proximal polymerase-II (Pol II) pausing release

Phylogenetic and functional divergence analysis of vertebrate IRAK family members

Multi-level structural domain-domain interactions for prediction of obligate and non-obligate protein-protein interactions

Identification of protein stability patches that pinpoint key structural or functional sites

Searching for the relics of primitive codons

Efficient SDH computation in molecular simulations data

A computational metabolic model of the NG108-15 cell for high content drug screening with electrophysiological readout

A novel mathematical basis for predicting somatic single nucleotide variants from next-generation sequencing

Nuclear localization signal prediction based on sequential pattern mining

Pattern analysis: a web-based tool for analyzing response patterns in low-replication, many-treatment gene expression data

ngALL database: a flexible framework for the management and integration of childhood leukemia next generation sequencing data

Secondary structure predictions for long RNA sequences based on inversion excursions: preliminary results

Rapid efficient macromolecular substructure searching in a cloud

Classification of multicolor fluorescence in-situ hybridization (M-FISH) image using regularized multinomial logistic regression

Copy number variation estimation from multiple next-generation sequencing samples

Entropy-based evaluation function for the investigation of genetic code adaptability

Shortest paths ranking methodology to identify alterations in PPI networks of complex diseases

Prediction of candidate genes for neuropsychiatric disorders using feature-based enrichment

A graph-based cluster ensemble method to detect protein functional modules from multiple information sources

Macromolecular modeling of protein structure - SCI1 of Nicotiana tabacum L

A continuum hard-sphere model of protein adsorption

Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data

Predicting possible directed-graph patterns of gene expressions in studies involving multiple treatments

A brief comparison of DSP and HMM methods for gene finding

Computational tool for large-scale GPIomic analysis

A machine-learning approach to retrieving diabetic retinopathy images

An evolutionary search framework to efficiently sample local minima in the protein conformational space

Empirical metabolite identification via GA feature selection and Bayes classification

A next generation sequence processing and analysis platform with integrated cloud-storage and high performance computing resources

gLIMS: Google cloud-based laboratory information management system for NMR metabolomics

A comparative study of codon adaptation in ssDNA and dsDNA phages

RNA-DV: an interactive tool for editing and visualizing RNA secondary structures

Robust differential co-expression discovery: an insight into pharmacodynamics of tyrosine kinase inhibitor

Towards sequence-based DNA flexibility analysis

Simulation and study of large-scale bacteria-materials interactions via BioScape enabled by GPUs

How to select microscopy image similarity metrics?

Approximate subspace pattern mining for mapping copy-number variations

Microbial source tracking by molecular fingerprinting

Random-walk: a stagnation recovery technique for simplified protein structure prediction

A next generation sequence processing and analysis platform with integrated cloud-storage and high performance computing resources

Content Provider	ACM Digital Library
Author	Chapman, Robert W. Morgan, Jeremy C. Anderson, Paul E.
Abstract	The development of Next-Generation Sequencing, or NGS, has heightened the throughput of traditional sequencing by using RNA reads to work backward, assembling a transcriptome from expressed fragments. These methods are designed to lower the cost of DNA sequencing by analyzing vast quantities of RNA fragments but have led to computational and storage obstacles. RNA sequencing produces large files that can be in excess of 20GB, making them unwieldy to the general researcher. Vast data resources have been created to extract the information contained in these massively parallel data. These resources and their associated tools are heterogeneous and highly distributed. This requires the scientist to create and execute highly complex customized analyses that involve gathering and organizing data from heterogeneous sources while interfacing with a variety of software tools. This is often infeasible without the support of computer specialists and significant hardware upgrades. The objective of this work is to combine the strengths of the scientific workflow project, Galaxy, with traditional high performance computing resources and affordable cloud-based data storage that encourages collaboration. The specific goals are to create a Galaxy tool that executes Trinity on a remote cluster and to develop software to download, upload, and manage NGS results to and from the cloud. Trinity is a computationally expensive de novo assembler that processes large RNA files to produce a FASTA transcriptome. Our system facilitates broad-based collaboration and distribution by building around the Google Drive cloud storage solution, where the processing of RNA sequences can be both shared and analyzed with a single upload and be reused for multiple purposes. The system is also able to remotely execute Trinity and other NGS tools on traditional high performance computing infrastructure that is often available as a shared resource at universities. Specifically, we develop a Trinity-based workflow executed in a heterogeneous environment with batch HPC resources that produce the abundances' of RNA fragments to discover patterns of expression. To demonstrate our workflow system with cloud-based storage and sharing, we will analyze duplicate samples of ovarian biopsies that have been generated by 72 base, paired-end sequencing (RNAseq) performed on an Illumina Genome Analyzer IIX. Sequencing was performed utilizing a balanced block design with pooled barcoded samples from 8 fish run in each lane and duplicate lanes employed as sequencing technical replicates. As the Illumina-based RNAseq approach exhibits much higher sensitivity for low abundance transcripts and far deeper sequencing coverage than the Roche 454 pyro-sequencing originally utilized, we expect that thousands of new ovarian gene transcripts will be revealed by this approach after RNAseq reads are quality filtered, assembled de novo into contigs and compared to the existing striped bass ovarian transcriptome, and especially to the tens of thousands of singleton sequences that we obtained but have not previously verified or published. This process will yield a far more comprehensive ovarian transciptome that will represent the overwhelming majority of genes expressed in the ovary of striped bass during oocyte growth and maturation.
Starting Page	594
Ending Page	594
Page Count	1
ISBN	9781450316705
DOI	10.1145/2382936.2383033
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2012-10-07
Publisher Place	New York
Access Restriction	Subscribed
Content Type	Text
Resource Type	Article

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2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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