https://bioinformatics.kmutt.ac.th/about.html

Duangrudee Tanramluk (Ajarn Wi) uses computational biology and machine learning to tackle the key to drug design problems via MANORAA webserver.

https://mb.mahidol.ac.th/en/bioinformatics/

https://graduate.mahidol.ac.th/inter/

This international Doctorate programme is designed to further broaden students’ knowledge in Bioinformatics and Molecular Biology to their maximum capability. 

http://www.mbb.psu.ac.th/programmes/phd

Ph.D. program in Bioinformatics and Computational Biology is a joint effort of the Faculty of Science and Faculty of Medicine, Chulalongkorn University. The program has study plans for both applicants who hold a bachelor’s degree and applicants who hold a master’s degree in any related fields of study.

http://www.bioinfo.sc.chula.ac.th/ph-d-program-specialization/

Additional detail 

https://www.biotec.or.th/en/index.php/research/research-units/genome-technology-research-unit

https://tbrcnetwork.org/labtbrc/index.php/bioinformatics-and-chemoinformatics/

https://genomicsthailand.com/Genomic/home

Address of the bookmark: https://bioinformatics.kmutt.ac.th/

Like other indel callers, Scalpel works by performing de novo assembly of regions of interest, so that misalignment to the reference genome cannot obscure the presence of an insertion or deletion. Scalpel's innovation is to repeatedly check its assembly before comparing to the reference genome, to account for simple sequence repeats that are a regular source of error in indel calling. When Scalpel assembles an exon, it collects reads that map to that exon (including partial matches), splits them into k-mers, and creates a de Bruijn graph to span the exon; however, if it detects repeats in the map, it iteratively increases the size of the k-mers by one base until the repeats are eliminated. This ensures that the final assembly of the exon is highly accurate while minimizing compute time.

The Cold Spring Harbor team's validation of Scalpel, published over the weekend in Nature Methods, compares Scalpel's performance on a live whole exome against HaplotypeCaller and SOAPindel. The donor is an individual with serious neurological disorders, which may be linked to a high incidence of indels. One thousand indels from this individual's exome, called by one or more of the informatics pipelines, were selected for focused resequencing. This resequencing revealed a 77% true positive rate for Scalpel calls, dramatically better than the rates for either of the competing tools; Scalpel performed especially well with indels longer than five base pairs, a traditional weak point for indel callers.

Finally, the authors demonstrate Scalpel's use on a large set of genetic data from nearly 600 families who donated samples to the Simons Simplex Collection, a project of the Simons Foundation Autism Research Initiative. Scalpel found a very high enrichment for indels in children affected by autism, compared with their unaffected siblings, a pattern that persisted even after excluding common variants.

Bioinformatics : https://www.linkedin.com/jobs/view/2681785372/

Engineer: https://www.linkedin.com/jobs/view/2681796993/

1. SPAdes: An assembler specifically designed for single-cell and multi-cell bacterial genomes, as well as small eukaryotic genomes.

2. ABySS: A parallelized assembler for large genomes that uses de Bruijn graphs.

3. Velvet: Another de Bruijn graph-based assembler optimized for short-read sequencing data.

4. SOAPdenovo: A de Bruijn graph-based assembler designed for short reads, widely used for assembling large and complex genomes.

5. MaSuRCA: A hybrid assembler that combines data from multiple sequencing technologies, such as Illumina and PacBio.

6. Canu: A long-read assembler optimized for PacBio and Oxford Nanopore sequencing data.

7. Flye: A long-read assembler suitable for bacterial and small eukaryotic genomes.

8. SMARTdenovo: An assembler designed for long reads, particularly suited for PacBio data.

9. SPAdes Long Read (SPAdesLR): An extension of SPAdes for long-read data, such as those from PacBio or Nanopore.

10. Minia: An assembler optimized for low memory consumption, suitable for small and medium-sized genomes.

11. Unicycler: A hybrid assembler that combines short and long reads for circular bacterial genome assembly.

12. wtdbg2: A de Bruijn graph assembler for long reads, efficient for very large genomes.

13. Shasta: A long-read assembler that uses the Overlap-Layout-Consensus approach, suitable for PacBio and Nanopore data.

14. Sparc: An assembler designed to handle noisy long reads from Nanopore sequencing.

15. CANA: An assembler for metagenomic data, particularly for complex and diverse microbial communities.

16. Ra Assembler: A metagenome assembler for long reads, designed for highly complex metagenomic samples.

Please note that the field of bioinformatics is constantly evolving, and new assembly tools may have emerged since my last update. Additionally, the performance of these tools can vary depending on the characteristics of the sequencing data and the genome being assembled. When selecting an assembly tool, consider the specific requirements of your project, the available data types, and the computational resources at your disposal. Always refer to the respective tool's documentation and publications for the most up-to-date information and recommendations.

Address of the bookmark: https://biokit.readthedocs.io/en/latest/index.html

You can find some useful open source bioinformatics codes for your analysis work. You can use the left bar options to filtere out or narrow down your search result. This webpage can be an useful resource for a beginners bioinformatician as it contain several bioinformatics basics script that are commonly used by biological programmers and biologist.

Stand on the slumped, dandruff-covered shoulders of millions of computer nerds. _/\_

Enjoy the code and research work.

http://code.ohloh.net/search?s=bioinformatics

Address of the bookmark: http://code.ohloh.net/search?s=bioinformatics

Reference & More @

http://www.nature.com/nnano/journal/vaop/ncurrent/full/nnano.2013.189.html

http://www.washington.edu/news/2013/09/30/uw-engineers-invent-programming-language-to-build-synthetic-dna/

Image source: washington.edu

Qualifications:
MSc degree in computer science, engineering, genetics or similar field with a strong emphasis on computational methods.

Deadline
01.08.2015

ancestor -- Any organism, population, or species from which some other organism, population, or species is descended by reproduction.

apomorphy -- specialized (=derived) characters of an organism.

basal group -- The earliest diverging group within a clade; for instance, to hypothesize that sponges are basal animals is to suggest that the lineage(s) leading to sponges diverged from the lineage that gave rise to all other animals.

biological classification -- The orderly arrangement of organisms in hierarchical system that ideally reflects evolutionary history.

cDNA -- Complementary DNA; DNA that is synthesized, by reverse transcriptase, from a Messenger RNA template ( Messenger RNA contains the coded information for protein synthesis).

character -- Heritable trait possessed by an organism.

character state -- characters are usually described in terms of their states, for example: "hair present" vs. "hair absent," where "hair" is the character, and "present" and "absent" are its states.

clade -- A monophyletic taxon; a group of organisms which includes the most recent common ancestor of all of its members and all of the descendants of that most recent common ancestor. From the Greek word "klados", meaning branch or twig.

cladogenesis -- The development of a new clade; the splitting of a single lineage into two distinct lineages; speciation.

cladogram -- A diagram, resulting from a cladistic analysis, which depicts a hypothetical branching sequence of lineages leading to the taxa under consideration. The points of branching within a cladogram are called nodes. All taxa occur at the endpoints of the cladogram.

convergence -- Similarities which have arisen independently in two or more organisms that are not closely related. Contrast with homology. 

crown group -- All the taxa descended from a major cladogenesis event, recognized by possessing the clade's synapomorphy. See: stem group.

derived -- Describes a character state that is present in one or more subclades, but not all, of a clade under consideration. A derived character state is inferred to be a modified version of the primitive condition of that character, and to have arisen later in the evolution of the clade. For example, "presence of hair" is a primitive character state for all mammals, whereas the "hairlessness" of whales is a derived state for one subclade within the Mammalia.

diversity -- Term used to describe numbers of taxa, or variation in morphology. 

evolution -- Darwin's definition: descent with modification. The term has been variously used and abused since Darwin to include everything from the origin of man to the origin of life.

evolutionary tree -- A diagram which depicts the hypothetical phylogeny of the taxa under consideration. The points at which lineages split represent ancestor taxa to the descendant taxa appearing at the terminal points of the cladogram.

expressed sequence tag (EST) -- A partial coding sequence isolated at random from a cDNA library, used for identification and mapping of coding sequences, for discovery of new genes and (by reference to sequence data banks) for discovery of identities with other genes.

extinction -- When all the members of a clade or taxon die, the group is said to be extinct.

genetic marker -- A DNA sequence that can be recognized and thus used to characterize the larger DNA sequence and the chromosome in which it occurs. 

homolog -- A feature that appears similar in two or more taxa with a common ancestor that also possessed that feature.

homology -- Two structures are considered homologous when they are inherited from a common ancestor which possessed the structure. This may be difficult to determine when the structure has been modified through descent.

hypothesis -- A concept or idea that can be falsified by various scientific methods.

ingroup -- In a cladistic analysis, the set of taxa which are hypothesized to be more closely related to each other than any are to the outgroup.

lineage -- Any continuous line of descent; any series of organisms connected by reproduction by parent of offspring.

monophyletic -- Term applied to a group of organisms which includes the most recent common ancestor of all of its members and all of the descendants of that most recent common ancestor. A monophyletic group is called a clade.

outgroup -- In a cladistic analysis, any taxon used to help resolve the polarity of characters, and which is hypothesized to be less closely related to each of the taxa under consideration than any are to each other.

paraphyletic -- Term applied to a group of organisms which includes the most recent common ancestor of all of its members, but not all of the descendants of that most recent common ancestor.

parsimony -- Refers to a rule used to choose among possible cladograms, which states that the cladogram implying the least number of changes in character states is the best.

phylogenetics -- Field of biology that deals with the relationships between organisms. It includes the discovery of these relationships, and the study of the causes behind this pattern.

phylogeny -- The evolutionary relationships among organisms; the patterns of lineage branching produced by the true evolutionary history of the organisms being considered.

plesiomorphy -- A primitive character state for the taxa under consideration.

polarity of characters -- The states of characters used in a cladistic analysis, either original or derived. Original characters are those acquired by an ancestor deeper in the phylogeny than the most recent common ancestor of the taxa under consideration. Derived characters are those acquired by the most recent common ancestor of the taxa under consideration.

polyphyletic -- Term applied to a group of organisms which does not include the most recent common ancestor of those organisms; the ancestor does not possess the character shared by members of the group.

primitive -- Describes a character state that is present in the common ancestor of a clade. A primitive character state is inferred to be the original condition of that character within the clade under consideration. For example, "presence of hair" is a primitive character state for all mammals, whereas the "hairlessness" of whales is a derived state for one subclade within the Mammalia.

radiation -- Event of rapid cladogenesis, believed to occur under conditions where a new feature permits a lineage to move into a new niche or new habitat, and is then called an adaptive radiation.

rank -- In traditional taxonomy, taxa are ranked according to their level of inclusiveness. Thus a genus contains one or more species, a family includes one or more genera, and so on.

relatedness -- Two clades are more closely related when they share a more recent common ancestor between them than they do with any other clade.

repetitive DNA -- Sequences of DNA that are found to be repeated, sometimes thousands of times over.  

reticulation -- Joining of separate lineages on a phylogenetic tree, generally through hybridization or through lateral gene transfer. Fairly common in certain land plant clades; reticulation is thought to be rare among metazoans.

selection -- Process which favors one feature of organisms in a population over another feature found in the population. This occurs through differential reproduction -- those with the favored feature produce more offspring than those with the other feature, such that they become a greater percentage of the population in the next generation.

sister group -- The two clades resulting from the splitting of a single lineage.

stem group -- All the taxa in a clade preceding a major cladogenesis event. They are often difficult to recognize because they may not possess synapomorpies found in the crown group.

sympleisiomorphy – A ancestral character shared by the taxa under consideration

synapomorphy -- A character which is derived, and because it is shared by the taxa under consideration, is used to infer common ancestry (shared derived state).

synteny -- Portions of chromosomes in which gene order is conserved. 

systematics -- Field of biology that deals with the diversity of life. Systematics is usually divided into the two areas of phylogenetics and taxonomy.

taxon -- Any named group of organisms, not necessarily a clade

taxonomy -- The science of naming and classifying organisms. 

Address of the bookmark: http://learn.genetics.utah.edu/