NDLI: Pancancer analysis of DNA methylation-driven genes using MethylMix

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Year: 2016, Volume: 17

Year: 2015, Volume: 16

Year: 2015, Volume: 16, Issue: Unspecified

Year: 2015, Volume: 16, Issue: 1

De novo assembly of bacterial transcriptomes from RNA-seq data

NF-κB-direct activation of microRNAs with repressive effects on monocyte-specific genes is critical for osteoclast differentiation

ALLMAPS: robust scaffold ordering based on multiple maps

CIRI: an efficient and unbiased algorithm for de novo circular RNA identification

Modulation of microRNA editing, expression and processing by ADAR2 deaminase in glioblastoma

Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics

Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data

An analysis of DNA methylation in human adipose tissue reveals differential modification of obesity genes before and after gastric bypass and weight loss

Quantification of cell identity from single-cell gene expression profiles

Global mRNA selection mechanisms for translation initiation

The draft genome of Primula veris yields insights into the molecular basis of heterostyly

Extending reference assembly models

Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements

Causes and consequences of crossing-over evidenced via a high-resolution recombinational landscape of the honey bee

Chromosome 7 gain and DNA hypermethylation at the HOXA10 locus are associated with expression of a stem cell related HOX-signature in glioblastoma

Pancancer analysis of DNA methylation-driven genes using MethylMix

Comprehensive miRNA sequence analysis reveals survival differences in diffuse large B-cell lymphoma patients

Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

Avianbase: a community resource for bird genomics

Gateways to the FANTOM5 promoter level mammalian expression atlas

Field pathogenomics reveals the emergence of a diverse wheat yellow rust population

Analysis of long non-coding RNAs highlights tissue-specific expression patterns and epigenetic profiles in normal and psoriatic skin

DNA methylation age of blood predicts all-cause mortality in later life

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

Assembling allopolyploid genomes: no longer formidable

Copy number variation in Y chromosome multicopy genes is linked to a paternal parent-of-origin effect on CNS autoimmune disease in female offspring

Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome

Bridger: a new framework for de novo transcriptome assembly using RNA-seq data

Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis

High-depth sequencing of over 750 genes supports linear progression of primary tumors and metastases in most patients with liver-limited metastatic colorectal cancer

Spectacle: fast chromatin state annotation using spectral learning

Erratum to: The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes

PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors

BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies

FRESCo: finding regions of excess synonymous constraint in diverse viruses

DGEclust: differential expression analysis of clustered count data

Unraveling heterogeneous susceptibility and the evolution of breast cancer using a systems biology approach

Transcript and protein expression decoupling reveals RNA binding proteins and miRNAs as potential modulators of human aging

Methylation-dependent SOX9 expression mediates invasion in human melanoma cells and is a negative prognostic factor in advanced melanoma

Fate by RNA methylation: m6A steers stem cell pluripotency

Wheat rusts never sleep but neither do sequencers: will pathogenomics transform the way plant diseases are managed?

Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations

A genomic data viewer for iPad

A functional extracellular transcriptome in animals? implications for biology, disease and medicine

A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes

CopywriteR: DNA copy number detection from off-target sequence data

Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation

MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome

Evaluating intra- and inter-individual variation in the human placental transcriptome

SNES: single nucleus exome sequencing

The Ensembl Regulatory Build

Defective structural RNA processing in relapsing-remitting multiple sclerosis

Deleterious effects of endocrine disruptors are corrected in the mammalian germline by epigenome reprogramming

Disputing Lamarckian epigenetic inheritance in mammals

Denoising perturbation signatures reveal an actionable AKT-signaling gene module underlying a poor clinical outcome in endocrine-treated ER+ breast cancer

Site-specific programming of the host epithelial transcriptome by the gut microbiota

An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome

Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy

High-resolution genomic analysis: the tumor-immune interface comes into focus

Single-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatment

Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease

Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks

5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer

Integrating host gene expression and the microbiome to explore disease pathogenesis

The Fasciola hepatica genome: gene duplication and polymorphism reveals adaptation to the host environment and the capacity for rapid evolution

Detecting non-allelic homologous recombination from high-throughput sequencing data

Expansion of a novel endogenous retrovirus throughout the pericentromeres of modern humans

The making of eusociality: insights from two bumblebee genomes

The genomes of two key bumblebee species with primitive eusocial organization

Comparison of the three-dimensional organization of sperm and fibroblast genomes using the Hi-C approach

Whole genome bisulfite sequencing of cell-free DNA and its cellular contributors uncovers placenta hypomethylated domains

The histone methyltransferase SDG8 mediates the epigenetic modification of light and carbon responsive genes in plants

Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin

Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system

Inter-individual differences in the gene content of human gut bacterial species

Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas

Time for a standardized system of reporting sites of genomic methylation

SNES makes sense? Single-cell exome sequencing evolves

Cloning-free CRISPR/Cas system facilitates functional cassette knock-in in mice

Domain atrophy creates rare cases of functional partial protein domains

The goose genome sequence leads to insights into the evolution of waterfowl and susceptibility to fatty liver

Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes

Fast and scalable inference of multi-sample cancer lineages

HaploShare: identification of extended haplotypes shared by cases and evaluation against controls

Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidates for a major dormancy QTL

Brain tumor is a sequence-specific RNA-binding protein that directs maternal mRNA clearance during the Drosophila maternal-to-zygotic transition

Erratum to: Modeling precision treatment of breast cancer

Erratum to: DNA methylation age of human tissues and cell types

Our unique microbial identity

Most partial domains in proteins are alignment and annotation artifacts

Partial protein domains: evolutionary insights and bioinformatics challenges

When will ‘open science’ become simply ‘science’?

An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum

DNA methylation and epigenomics: new technologies and emerging concepts

Sex chromosome-to-autosome transposition events counter Y-chromosome gene loss in mammals

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes

Intra-tumor genetic heterogeneity and alternative driver genetic alterations in breast cancers with heterogeneous HER2 gene amplification

Sequence-based ultra-dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes

Is mouse embryonic stem cell technology obsolete?

Integrative modeling reveals the principles of multi-scale chromatin boundary formation in human nuclear organization

A versatile reporter system for CRISPR-mediated chromosomal rearrangements

Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression

The ADAMTS (A Disintegrin and Metalloproteinase with Thrombospondin motifs) family

Distinct roles of DNMT1-dependent and DNMT1-independent methylation patterns in the genome of mouse embryonic stem cells

Identification of embryonic lethal genes in humans by autozygosity mapping and exome sequencing in consanguineous families

quantro: a data-driven approach to guide the choice of an appropriate normalization method

Independent genomewide screens identify the tumor suppressor VTRNA2-1 as a human epiallele responsive to periconceptional environment

Differential connectivity of splicing activators and repressors to the human spliceosome

Scalable microfluidics for single-cell RNA printing and sequencing

Widespread rescue of Y-linked genes by gene movement to autosomes

Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation

Ultra-large alignments using phylogeny-aware profiles

Rewriting the blueprint of life by synthetic genomics and genome engineering

Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development

Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells

Extensive rewiring of epithelial-stromal co-expression networks in breast cancer

Marrying microfluidics and microwells for parallel, high-throughput single-cell genomics

FOXM1 binds directly to non-consensus sequences in the human genome

From trainee to tenure-track: ten tips

Comparison of RNA-seq and microarray-based models for clinical endpoint prediction

Comprehensive gene panels provide advantages over clinical exome sequencing for Mendelian diseases

Interactome analysis brings splicing into focus

The nature of evidence for and against epigenetic inheritance

Long non-coding RNA ROR decoys gene-specific histone methylation to promote tumorigenesis

An integrative pan-cancer-wide analysis of epigenetic enzymes reveals universal patterns of epigenomic deregulation in cancer

Better reporting for better research: a checklist for reproducibility

Epigenome data release: a participant-centered approach to privacy protection

A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii

Egg cell-specific promoter-controlled CRISPR/Cas9 efficiently generates homozygous mutants for multiple target genes in Arabidopsis in a single generation

Kiwi genome provides insights into evolution of a nocturnal lifestyle

Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos

Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data

Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome

Year: 2014, Volume: 15

Year: 2013, Volume: 14

Year: 2012, Volume: 13

Year: 2011, Volume: 12

Year: 2010, Volume: 11

Year: 2009, Volume: 10

Year: 2008, Volume: 9

Year: 2007, Volume: 8

Year: 2006, Volume: 7

Year: 2005, Volume: 6

Year: 2004, Volume: 6

Year: 2004, Volume: 5

Year: 2003, Volume: 5

Year: 2003, Volume: 4

Year: 2002, Volume: 4

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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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