ScaleNet, DOMMINO 2.0, FLOR-ID, PhytoPath

Dear all,

These papers were discussed on Friday.

ScaleNet: a literature-based model of scale insect biology and systematics
http://database.oxfordjournals.org/content/2016/bav118.full

DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions.
http://database.oxfordjournals.org/content/2016/bav114.full

FLOR-ID: an interactive database of flowering-time gene networks in Arabidopsis thaliana

https://nar.oxfordjournals.org/content/44/D1/D1167.full

PhytoPath: an integrative resource for plant pathogen genomics

https://nar.oxfordjournals.org/content/44/D1/D688.full

 The next presenters are

Manjunath (10:00 am)

Meenakshi (3:00)

Regards,

Meenakshi

InsectBase, FunTree, dbPTM and KLIFS

Dear all,

The following papers were discussed today

1. InsectBase: a resource for insect genomes and transcriptomes
https://nar.oxfordjournals.org/content/44/D1/D801.full

2. FunTree: advances in a resource for exploring and contextualising protein function evolution
https://nar.oxfordjournals.org/content/44/D1/D317.full

3. dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins
https://nar.oxfordjournals.org/content/44/D1/D435.full

4. KLIFS: a structural kinase-ligand interaction database
https://nar.oxfordjournals.org/content/44/D1/D365.full

Tomorrow's presenters are
Ashwini - 10:00 am
Bhavika - 3:00 pm

Regards,
Meenakshi

NBDB, GPCRdb, dbMAE and DMDD

Dear all,

The papers presented today are

1. Nucleotide binding database NBDB – a collection of sequence motifs with specific protein-ligand interactions
https://nar.oxfordjournals.org/content/44/D1/D301.full

2.  GPCRdb: an information system for G protein-coupled receptors
https://nar.oxfordjournals.org/content/44/D1/D356.full

3.  NAR Breakthrough Article: dbMAE: the database of autosomal monoallelic expression
https://nar.oxfordjournals.org/content/44/D1/D753.full

4.  Deciphering the mechanisms of developmental disorders: phenotype analysis of embryos from mutant mouse lines
https://nar.oxfordjournals.org/content/44/D1/D855.full

Tomorrow's presenters are
Snehal 10:00 am
Rithwik 3:00 pm

Regards,
Meenakshi

DASHR, EBImetagenomics, iPPI-DB, MEROPS

Dear all,

These papers were discussed today

1. DASHR: database of small human noncoding RNAs
https://nar.oxfordjournals.org/content/44/D1/D216.full

2. EBI metagenomics in 2016 - an expanding and evolving resource for the analysis and archiving of metagenomic data
https://nar.oxfordjournals.org/content/44/D1/D595.full

3. iPPI-DB: an online database of modulators of protein–protein interactions
https://nar.oxfordjournals.org/content/44/D1/D542.full

4. Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors
https://nar.oxfordjournals.org/content/44/D1/D343.full

Tomorrow's presenters are 
10:00 am Anshul
3:00 pm Souradeep

Regards,
Meenakshi

JuncDB, Assembly, BioGPS and STITCH5

Dear all,

Today we discussed four papers in the literature meet

1. JuncDB: an exon–exon junction database

A database about the intron-exon boundaries within genes for comparing exonic architectures within sets of orthologous transcripts across 88 eukaryotic species

https://nar.oxfordjournals.org/content/44/D1/D101.full

2. Assembly: a resource for assembled genomes at NCBI

All the genome assemblies of a particular organism available at NCBI Refseq and INSDC databases are classified into four levels according to the degree to which they have been assembled 

1. Contig level assemblies that include only contigs
2. Scaffold level assemblies that include scaffolds and contigs
3. Chromosome level assemblies that include chromosomes or linkage groups, plus scaffolds and contigs
4. Complete genome assemblies in which all molecules are fully sequenced
   
   
   https://nar.oxfordjournals.org/content/44/D1/D73.full

 3. BioGPS: building your own mash-up of gene annotations and expression profiles

A gene annotation portal, which provides gene organisation, gene expression data from 6000 different datasets for nine model organisms (H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, D. rerio, A. thaliana, X. tropicalis and S. scrofa). 

https://nar.oxfordjournals.org/content/44/D1/D313.full

4. STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data

Information on protein-ligand interactions and their affinities derived from experiments or in silico analysis for 430 000 chemical and smore than 9 600 000 proteins.

https://nar.oxfordjournals.org/content/44/D1/D380.full
 

PDBFlex,COMBREX-DB,SIDER and WITHDRAWN

Dear all,

Please find the links for the papers discussed today

1.PDBFlex: exploring flexibility in protein structures https://nar.oxfordjournals.org/content/44/D1/D330.full

2.COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps
https://nar.oxfordjournals.org/content/44/D1/D423.full

3. WITHDRAWN–a resource for withdrawn and discontinued drugs
https://nar.oxfordjournals.org/content/44/D1/D1075.full

4.The SIDER database of drugs and side effect
https://nar.oxfordjournals.org/content/44/D1/D1080.full

Monday's presenters are Atul and Harini.

Regards,
Meenakshi

Gramene 2016 and PlantPAN 2.0

Dear all,

The papers discussed this afternoon can be accessed from the following links

1. PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants
https://nar.oxfordjournals.org/content/44/D1/D1154.full

 2.  Gramene 2016: comparative plant genomics and pathway resources
https://nar.oxfordjournals.org/content/44/D1/D1133.full

Tomorrow's presenters are
Mahita 10:00 am
Oommen 3:00 pm

Regards,
Meenakshi

HGP and CRISPR

Dear all,

Please find links for the papers discussed today morning by Surbhi

1.Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine
https://nar.oxfordjournals.org/content/44/D1/D793.full

2.CRISPRz: a database of zebrafish validated sgRNAs
https://nar.oxfordjournals.org/content/44/D1/D822.full
The afternoon papers will be discussed by Shafi.

Regards,
Meenakshi

Start2Fold and MetaNetX

Dear all,

Here are the links for the afternoon paper alerts

1.Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability
http://nar.oxfordjournals.org/content/44/D1/D429.long

2.MetaNetX/MNXref – reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks
http://nar.oxfordjournals.org/content/44/D1/D523.long

Tomorrow's presenters are:
Surbhi 10:00 am
Shafi 3:00 pm

Regards,
Meenakshi

Tea-time paper alert-II

Dear all,

Please find links for the papers discussed today morning

1.LUCApedia: a database for the study of ancient life                                               http://nar.oxfordjournals.org/content/41/D1/D1079.full

2.KLIFS: a structural kinase-ligand interaction database
http://nar.oxfordjournals.org/content/early/2015/10/22/nar.gkv1082.full

Today afternoon we will have paper alert by Teerna.

Regards,
Meenakshi

Tea-time paper alert

Dear All,

Please find below the links of the papers that were presented today for paper alert

1.CEGA—a catalog of conserved elements from genomic alignments.
https://nar.oxfordjournals.org/content/44/D1/D96.full

 2.The Dfam database of repetitive DNA families.
https://nar.oxfordjournals.org/content/44/D1/D81.full

3.UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures.
https://nar.oxfordjournals.org/content/44/D1/D308.full 

4.An updated version of NPIDB includes new classifications of DNA–protein complexes and their families
https://nar.oxfordjournals.org/content/44/D1/D144.full

Tomorrow's presenters are:
Rithika - 10.00 am
Teerna - 3:00 pm

Regards,
Meenakshi