<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/29917?offset=1370 https://bioinformaticsonline.com/bookmarks/view/44445/ppanggolin-depicting-microbial-species-diversity-via-a-partitioned-pangenome-graph-of-linked-neighbors Thu, 01 Feb 2024 00:24:32 -0600 https://bioinformaticsonline.com/bookmarks/view/44445/ppanggolin-depicting-microbial-species-diversity-via-a-partitioned-pangenome-graph-of-linked-neighbors <![CDATA[PPanGGOLiN: Depicting microbial species diversity via a Partitioned PanGenome Graph Of Linked Neighbors]]> PPanGGOLiN (Gautreau et al. 2020) is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. It has the specificity to partition the pangenome using a statistical approach rather than using fixed thresholds which gives it the ability to work with low-quality data such as Metagenomic Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) thus taking advantage of large scale environmental studies and letting users study the pangenome of uncultivable species.

A complete documentation is available here.

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Address of the bookmark: https://github.com/labgem/PPanGGOLiN

]]> LEGE https://bioinformaticsonline.com/researchlabs/view/5623/yau-group Tue, 15 Oct 2013 13:05:15 -0500 <![CDATA[Yau Group]]> Yau Group are a new research group based at the Wellcome Trust Centre for Human Genetics and the Department of Statistics at the University of Oxford.

Yau Group develops statistical and computational methods for the analysis of genomic datasets with a particular interest in cancer sequencing applications and the use of Bayesian Statistics.

Yau Group are currently have projects in somatic mutation analysis of heterogeneous cancers, data fusion or integration techniques and single cell genomics.

More @ http://www.well.ox.ac.uk/~cyau/index.html

]]> https://bioinformaticsonline.com/bookmarks/view/38212/megahit-an-ultra-fast-single-node-solution-for-large-and-complex-metagenomics-assembly-via-succinct-de-bruijn-graph Wed, 14 Nov 2018 04:50:27 -0600 https://bioinformaticsonline.com/bookmarks/view/38212/megahit-an-ultra-fast-single-node-solution-for-large-and-complex-metagenomics-assembly-via-succinct-de-bruijn-graph <![CDATA[MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph]]> MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG contstruction. The GPU-accelerated version of MEGAHIT has been tested on NVIDIA GTX680 (4G memory) and Tesla K40c (12G memory) with CUDA 5.5, 6.0 and 6.5. MEGAHIT v1.0 or greater also supports IBM Power PC and has been tested on IBM POWER8.

https://academic.oup.com/bioinformatics/article/31/10/1674/177884

Address of the bookmark: https://github.com/voutcn/megahit

]]> Jit https://bioinformaticsonline.com/opportunity/view/7218/associate-professor-centre-for-bioinformatics-at-maharshi-dayanand-university-rohtak Thu, 12 Dec 2013 20:49:59 -0600 <![CDATA[Associate Professor - Centre for Bioinformatics at Maharshi Dayanand University, Rohtak]]> ADVERTISEMENT No. PR-54/2013

No. of Posts and Specialization: 1(UR)

Educational Qualification:

(i) Good academic record with a Ph.D. Degree in the concerned /allied /relevant disciplines.

(ii) The Ph.D. Degree shall be a mandatory qualification for all candidates to be appointed as Associate Professor through direct recruitment.

(iii) A Master‟s Degree with at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed).

(iv) A minimum of eight years of experience of teaching and /or research in an academic /research position equivalent to that of Assistant Professor in a University, College or Accredited Research Institution/Industry excluding the period of Ph.D research with evidence of published work and a minimum of 5 publications as books and /or research papers in refereed journals only/policy papers.

(v) Contribution to educations innovation, design of new curricula and courses and technology-mediated teaching learning process with evidence of having guided doctoral candidates and research students.

(vi) A minimum score as stipulated in the Academic Performance Indicator (API) based performance Based Appraisal System (PBAS), set out in this notification in as mentioned in the advertisement.

Send your application to the A.R (Estt.Teaching), M.D.University, Rohtak on or before December 23, 2013.

For more details: http://www.mdurohtak.ac.in/pdf/Notices_Pdf/new_notice/Teaching%20Vacancy%20%28ADVT.%20No.%20PR-54%20of%202013%29.pdf

Last Apply Date: 23 Dec 2013

]]> https://bioinformaticsonline.com/bookmarks/view/42806/graphunzip-phases-an-assembly-graph-using-hi-c-data-andor-long-reads Fri, 05 Feb 2021 21:22:24 -0600 https://bioinformaticsonline.com/bookmarks/view/42806/graphunzip-phases-an-assembly-graph-using-hi-c-data-andor-long-reads <![CDATA[GraphUnzip: Phases an assembly graph using Hi-C data and/or long reads.]]> GraphUnzip, a fast, memory-efficient and accurate tool to unzip assembly graphs into their constituent haplotypes using long reads and/or Hi-C data. As GraphUnzip only connects sequences in the assembly graph that already had a potential link based on overlaps, it yields high-quality gap-less supercontigs. To demonstrate the efficiency of GraphUnzip, we tested it on a simulated diploid Escherichia coli genome, and on two real datasets for the genomes of the rotifer Adineta vaga and the potato Solanum tuberosum. In all cases, GraphUnzip yielded highly continuous phased assemblies.

https://www.biorxiv.org/content/biorxiv/early/2021/02/01/2021.01.29.428779.full.pdf

Address of the bookmark: https://github.com/nadegeguiglielmoni/GraphUnzip

]]> Jit https://bioinformaticsonline.com/opportunity/view/5888/nit-calicut-faculty-jobs-2013-in-bioinformatics Thu, 24 Oct 2013 13:00:37 -0500 <![CDATA[NIT Calicut Faculty Jobs 2013 in Bioinformatics]]> NATIONAL INSTITUTE OF TECHNOLOGY CALICUT, KERALA

NOTIFICATION FOR FACULTY RECRUITMENT – 2013

(Faculty openings in Technology, Science, Architecture and Management at NIT Calicut, Kerala)

National Institute of Technology Calicut, Kerala, established under Act XXIX/ 2007of the Parliament is one of the leading technological institutions in the Country with nearly 6000 students enrolled for various UG, PG and Ph.D. programmes in Technology, Science, Architecture and Management. The Institute invites applications from Indian nationals, possessing consistent excellent academic record, commitment to quality teaching and potential for carrying out outstanding research, for the post of Assistant Professors in various departments against the backlog reserved vacancies for Scheduled Caste (SC), Scheduled Tribe (ST), Other Backward Communities (OBC) and Persons with Disabilities (PWDs) and also under open merit quota as detailed below. Candidates belonging to SC, ST and OBC desirous of considering for selection under UR category also shall specifically indicate so in column 4.

Reservation quota for PWDs will be counted against the respective community. Young, meritorious, dynamic and student friendly academicians are welcome to join hands with the existing team in their effort to transform this Institute to a world class educational institution.

Candidates possessing Ph.D. degree will be considered for appointment on contract basis initially.

They will be considered for movement to AGP `7000 after one year of satisfactory performance.

Meritorious candidates possessing M.Tech./M.Phil. (*) with remarkably good potential to carry out outstanding research and already pursuing Ph.D. or aspiring to pursue Ph.D. will also be considered for appointment on contract, initially for a period of 3 years, extendable for a further period of 2 years on a year to year basis or till the candidate acquires Ph.D. degree whichever is earlier. Renewal of contract
will be done on an annual basis, subject to satisfactory progress of Ph.D. work, good conduct and good performance in teaching. Faculty appointed on contract basis will not be treated as regular staff till they are regularized, subject to the conditions stated earlier. The Institute has adopted 4-tier flexible faculty structure recommended by MHRD.

More Info : http://www.nitc.ac.in/index.php/?url=content/submenu/2345/5

]]> https://bioinformaticsonline.com/bookmarks/view/44497/graphpath-a-graph-attention-model-for-molecular-stratification-with-interpretability-based-on-the-pathway-pathway-interaction-network Wed, 27 Mar 2024 20:51:21 -0500 https://bioinformaticsonline.com/bookmarks/view/44497/graphpath-a-graph-attention-model-for-molecular-stratification-with-interpretability-based-on-the-pathway-pathway-interaction-network <![CDATA[GraphPath: A graph attention model for molecular stratification with interpretability based on the pathway-pathway interaction network]]> Achieving accurate and interpretable clinical predictions requires paramount attention to thoroughly characterizing patients at both the molecular and biological pathway levels. In this paper, we present GraphPath, a biological knowledge-driven graph neural network with multi-head self-attention mechanism that implements the pathway-pathway interaction network. We train GraphPath to classify the cancer status of patients with prostate cancer based on their multi-omics profiling.

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Address of the bookmark: https://github.com/amazingma/GraphPath

]]> LEGE https://bioinformaticsonline.com/opportunity/view/5958/srfjrf-national-institute-of-immunology Wed, 30 Oct 2013 06:45:57 -0500 <![CDATA[SRF/JRF @ National Institute of Immunology]]> ADVERTISEMENT OF WALK-IN-INTERVIEW

NAME OF THE POST : SRF/JRF (Four Posts only)

DURATION : Indicated with the respective project mentioned below:

NAME OF THE PROJECT : As Mentioned below:

1. Serological diversity and molecular characterization of Dichelobector nodusus and development of vaccine against virulent footroot funded by NAIP. (Tenable upto 31.03.2014)

2. Development of oral vaccine against Clostridium perfringenes employing translational fusion of immunodominant epitopes of beta toxin with heat labile entertoxin B funded by DBT. (Tenable upto 25.02.2014)

3. Indo-Norwegian project, “Evaluation of major porins, ompC and ompR of Areomonas hydrophila as potential vaccine candidates and identification and characterization of immune genes of Indian major carp, Labeo rohita” (Tenable upto 31.03.2014)

EDUCATIONAL QUALIFICATIONS: For JRF- M.Sc/M.Tech in any subject of Biological Sciences/Life Sciences

For SRF- M.Sc/M.Tech in any subject of Biological Sciences/Life Sciences with 2 years of Research Experience.

JOB DESCRIPTION : The Candidate should have experience in gene Expression, protein purification, molecular biology techniques and bioinformatics
EMOLUMENTS : SRF: Rs. 18,000/- per month consolidated plus 30% HRA if /NET/GATE qualified otherwise Rs. 14,000/- per month consolidated + 30% HRA.

JRF: Rs. 16,000/- per month consolidated + 30% HRA if NET/GATE qualified otherwise Rs. 12,000/- per month consolidated + 30% HRA

SCIENTIST NAME : Dr. Lalit C. Garg, SS-VII (Gene Regulation Lab)

SCIENTIST’S EMAIL : lalit@nii.ac.in

WALK IN INTERVIEW ON : October 31st, 2013

REGISTRATION OF CANDIDATES: 10.30 AM to 11.00 AM

Advertisement: http://www1.nii.res.in/sites/default/files/project-Dr.Lalit-31oct2013.pdf

]]> https://bioinformaticsonline.com/bookmarks/view/38646/visnetwork-an-r-package-for-network-visualization-using-visjs-javascript-library Wed, 09 Jan 2019 11:00:32 -0600 https://bioinformaticsonline.com/bookmarks/view/38646/visnetwork-an-r-package-for-network-visualization-using-visjs-javascript-library <![CDATA[visNetwork: an R package for network visualization, using vis.js javascript library]]>

visNetwork is an R package for network visualization, using vis.js javascript library (http://visjs.org/). All remarks and bugs are welcome on github : https://github.com/datastorm-open/visNetwork.

Features

Based on htmlwidgets, so :

  • compatible with shiny, R Markdown documents, and RStudio viewer

The package proposes all the features available in vis.js API, and even more with special features for R :

  • easy to use
  • custom shapes, styles, colors, sizes, …
  • works smooth on any modern browser for up to a few thousand nodes and edges
  • interactivity controls (highlight, collapsed nodes, selection, zoom, physics, movement of nodes, tooltip, events, …)
  • visualize rpart tree

Address of the bookmark: https://datastorm-open.github.io/visNetwork/

]]> Jit https://bioinformaticsonline.com/opportunity/view/6104/incob-2014 Thu, 07 Nov 2013 17:53:36 -0600 <![CDATA[InCoB 2014]]> The 13th International Conference on Bioinformatics (InCoB 2014) will be held in Novotel Sydney Brighton Beach, Sydney, New South Wales, Australia. This year, the InCoB will be held earlier from 31st July to 2nd August 2014 to run back-to-back with the International Biophysics Congress 2014 at the Brisbane Convention and Exhibition Centre, Queensland (3-7 Aug).

More at http://incob2014.org/

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