We are also interested in the large-scale integration of genomic, expression, methylation and proteomic data sets, as well as the application of whole genome sequence analysis in clinical diagnostics.

More at http://millslab.ccmb.med.umich.edu/index.html

Current research interests include next-generation DNA sequencing, structural variation, genome rearrangements in cancer and evolution, and network analysis of somatic mutations in cancer. Earlier research included topics in comparative genomics, multiple sequence alignment, and motif finding.

More athttp://compbio.cs.brown.edu/

• Handle big sequence data, e.g:
  • Compare two vertebrate genomes
  • Align billions of DNA reads to a genome
• Indicate the reliability of each aligned column.
• Use sequence quality data properly.
• Compare DNA to proteins, with frameshifts.
• Compare PSSMs to sequences
• Calculate the likelihood of chance similarities between random sequences.
• Do split and spliced alignment.
• Train alignment parameters for unusual kinds of sequence (e.g. nanopore).

Address of the bookmark: http://last.cbrc.jp/

Address of the bookmark: http://www.bioconductor.org/packages/release/bioc/html/GeneBreak.html

• paired-end (PE) and/or mate-pair libraries (NGS-based mode)
• long reads (NGS-based mode)
• synteny to the genome of some related species (reference-based mode)

Scaffolding 

In reference-based mode, pyScaf uses synteny to the genome of closely related species in order to order contigs and estimate distances between adjacent contigs.

Contigs are aligned globally (end-to-end) onto reference chromosomes, ignoring:

• matches not satisfying cut-offs (--identity and --overlap)
• suboptimal matches (only best match of each query to reference is kept)
• and removing overlapping matches on reference.

In preliminary tests, pyScaf performed superbly on simulated heterozygous genomes based on C. parapsilosis (13 Mb; CANPA) and A. thaliana (119 Mb; ARATH) chromosomes, reconstructing correctly all chromosomes always for CANPA and nearly always for ARATH (Figures in dropbox, CANPA table, ARATH table).
Runs took ~0.5 min for CANPA on 4 CPUs and ~2 min for ARATH on 16 CPUs.

Important remarks:

• Reduce your assembly before (fasta2homozygous.py) as any redundancy will likely break the synteny.
• pyScaf works better with contigs than scaffolds, as scaffolds are often affected by mis-assemblies (no de novo assembler / scaffolder is perfect...), which breaks synteny.
• pyScaf works very well if divergence between reference genome and assembled contigs is below 20% at nucleotide level.
• pyScaf deals with large rearrangements ie. deletions, insertion, inversions, translocations. Note however, this is experimental implementation!
• Consider closing gaps after scaffolding.

Address of the bookmark: https://github.com/lpryszcz/pyScaf

Address of the bookmark: http://www.mgc.ac.cn/GenomeComp/

Main research topics:
- Comparative and Population Genomics of Plant Symbionts
- Parasite Genome Evolution
- Experimental Evolution of Microbial Symbionts and Parasites
- Phylogenomics of Early Branching Fungi

More at http://corradilab.weebly.com/

Staff Scientists

Specialization: Applicant should have a Ph.D. with excellent academic credentials along with the track record of scientific productivity evidenced by publications/patents/products in the frontier areas of Plant Biology such as, Computational Biology, Genome Analysis and Molecular Mapping, Molecular Mechanism of Abiotic Stress Responses, Nutritional Genomics, Plant Development and Architecture, Plant Immunity, Molecular Breeding, Transgenics for crop improvement and other emerging areas based on plant genomics.

Remuneration: The length of experience and scientific accomplishments/quality of scientific productivity record will be major factors in deciding the level of appointment as Staff Scientist as well as starting salary in the Pay Bands of Rs 15,600-39,100 (with grade pay of 5400), and Rs 37,400-67,000 (with grade pay of 8,700 and 8,900) plus usual allowances admissible to the Central Government employees. However, NIPGR reserves the right to select candidates in the lower grade against the foregoing posts depending upon the qualifications and experience of the candidate. Reservation of posts shall be as per Govt. of India norms. Five posts (SC-2, ST-1, OBC-2) in the Pay Band of Rs 15,600-39,100 with Grade Pay of Rs 5400, are reserved.

More at http://www.nipgr.res.in/careers/vacancies_latest.php#

Apply online at http://www.nipgr.res.in/nipgr_recu/nipgr_recu.php

Form http://www.nipgr.res.in/files/careers/Application_Performa_2015.doc

It was first developed to transfer annotations between different genome assembly versions. However, it can also transfer annotations between strains and even different species, like Plasmodium chabaudi onto P. berghei, between different Leishmania species or Salmonella enterica onto other Salmonella serotypes. RATT is able to transfer any entries present on a reference sequence, such as the systematic id or an annotator's notes; such information would be lost in a de novo annotation.

More at http://ratt.sourceforge.net/

Address of the bookmark: http://ratt.sourceforge.net/

• Automatically improve draft assemblies
• Find variation among strains, including large event detection

Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including:

• Single base differences
• Small indels
• Larger indel or block substitution events
• Gap filling
• Identification of local misassemblies, including optional opening of new gaps

More at https://github.com/broadinstitute/pilon/wiki

Address of the bookmark: https://github.com/broadinstitute/pilon/wiki