Muhammad Sufian- Ph.D. Molecular Medicine
- Professor (Assistant) at Mirpur University of Science and Technology
Muhammad Sufian
- Ph.D. Molecular Medicine
- Professor (Assistant) at Mirpur University of Science and Technology
Academic and research work of BS and MPhil students
About
12
Publications
158,527
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47
Citations
Introduction
A focused personality aiming for excellence in knowledge and research.
Current institution
Additional affiliations
November 2019 - November 2020
Position
- Professor (Assistant)
Description
- - Teaching coursework to B.S., M.S., and Ph.D. students - Supervising B.S. final year project and M.S. research work
October 2018 - October 2019
Position
- Researcher
Description
- Providing assistance in bioinformatics analysis of experimental data in ongoing projects of the department
January 2017 - June 2017
Position
- Visiting Faculty
Description
- Teaching BS (Bioinformatics) 3rd year students
Education
December 2014 - April 2018
Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi
Field of study
- Molecular Medicine
July 2012 - December 2014
Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi
Field of study
- Molecular Medicine
January 2011 - December 2011
Department of Biiotechnology, University of Karachi
Field of study
- Biiotechnology
Publications
Publications (12)
Background
Priestia genus is an industrially important bacteria used in a variety of procedures. With several patents and industrial applications, P. megaterium (or Bacillus megaterium) is a potent cell factory for biotechnology. P. megaterium strain DSM319 has a genome size of 5.1 Mb and 4,955 proteins in NCBI database.
Objectives
The current res...
Background
Pseudomonas genus is a significant industrial bacteria having wide range of applications. Pseudomonas pseudoalcaligenes (or P. oleovorans) has applications as bio-implant, bioplastics materials, pharmaceuticals, etc. P. pseudoalcaligenes strain E1205 has a genome size of 5.57 Mb and 5,081 proteins in NCBI database. Its genome harbors man...
Bacillus megaterium is a gram positive rod shaped bacterium that is greatly responsible for the formation of spores aerobically and found throughout the world. The size of respective bacterium genome is 5.48 Mb and contains about 5,858 exons. It has two strains named as QMB1551 and DSM319 having GC amount 38%. Regardless, a large number of the gene...
The identity and interrelationship of Morus species were confirmed and authenticated in the current research effort using DNA barcode analysis as a molecular technique. Chloroplast DNA of Specimens were evaluated through PCR, Sequence homology and Neighbor-Joining (NJ) clustering. Sequence recoveries of the rbcL and matK were 91.66 & 88.88% respect...
Campylobacter jejuni (CJJ) is a source of bacterial foodborne diarrhea globally. Mostly found prevalent in children in the developing countries that may lead to mortality. The upsurge in antimicrobial resistance is causing hindrance in the treatment, as highlighted by CDC and WHO. The study hypothesized the application of subtractive genomics appro...
Background
Among the resistant isolates of MTB, multidrug resistant tuberculosis (MDR-TB) and extensively drug resistant tuberculosis (XDR-TB) have been the areas of growing concern. The genomic analysis showed that the respective genomic pool of the XDR-MTB proteome contains more than 30% of the hypothetical proteins for which no functions have be...
Introduction Bacterial resistance toward the first line antibiotics is a big challenge in discovering new regiments against deadly diseases. The discovery of novel antibiotics which bypass the routine biochemical metabolism of the disease causing bacteria is a new strategy to combat infections. LptD (87 kDa, beta-barrel) and LptE (20 kDa, lipoprote...
Background:
Infections caused by Salmonella enterica, a Gram-negative facultative anaerobic bacteria belonging to the family of Enterobacteriaceae, are major threats to the health of humans and animals. The recent availability of complete genome data of pathogenic strains of the S. enterica gives new avenues for the identification of drug targets...
Apomorphine, a dopamine D 1 /D 2 agonist, is an important drug of choice for the treatment of Parkinson's and related disorders. The present study was designed to perform the conformational analysis and geometry optimization of apomorphine. Resultant optimized structure corresponds to a substance as it is found in nature. This could be used for a v...
Microbial pangenomics has enthralled the scientific community which is inspired by the accessibility of sequenced genomes. There is a dire need to come up with novel drugs targeting any of the prevalent strain(s) of a pathogen. Salmonella enterica comprised of multiple pathogenic serovars which include but not limited to Typhi, Paratyphi and Typhim...
Typhoid fever or Salmonellosis is a systemic disease caused by the Gram-negative pathogen Salmonella typhi. It is still a serious problem in most of the third world countries. Many antibacterial drugs are being used for its treatment, but emergence of drug-resistant strains has prompted scientists worldwide to opt for an alternative approach. For t...
Questions
Questions (22)
Taxonomic identification of plants can be done by gene barcoding. There are several reported gene markers to be used to barcode unknown species. My question is "Is it possible to identify the taxonomy of hybrid plants using gene barcoding ?"'. Does the same gene markers will be used for hybrid plants as well ? I need research article references answering this question. An example of hybrid plants is given in the following link.
Whatever field of research we are in, we usually employ many commercial softwares for the analysis of our results. Whether it is Biology, Chemistry or Physics; we cite the commercial software with the manufacturer name in our publications. But, why not Microsoft Excel ? I think it is the most used software for making tables and graphs. Some people might say that we used to cite it, that is why I mentioned 'generally' because I have not encountered any such publication yet.
I want to find out the overall protein sequence similarity among 2 strains of same bacterial specie.
Let say, strain 1 has 4500 proteins and strain 2 has 4300. My strategy was; I performed all-against-all BLASTp of both the strains and selected the best-hit from strain 2 against the query from strain 1. Then sorted them according to their percent identity values. But. I am getting a range of NO HITS to 100% similarity. I was expecting to get a range of 80 to 100% since both the strains belong to same specie.
Kindly guide me to improve my current strategy or suggest me some computational tools to perform similar task.
I have some results tabulated in an Excel file, which consists of 42 fields and 73 records, each record comprised of 8 or 9 digit number (PDF attached). I want to represent it in a reader-friendly manner. Kindly guide me to represent the data in a better way.
I have downloaded complete protein sequences of some bacterial genomes in March 2014 from following NCBI FTP site,
I had a list of NCBI GIs which were accessible in the on-line NCBI interface (www.ncbi.nlm.nih.gov/protein) till mid of 2014, but now when I search them on NCBI, an error appears stating "Record removed" with no reasons. The page provides me a link to obsolete version, but not to updated version which I actually needed. Few of those GIs are;
378699640
537435588
550903479
NCBI Help Center provided me the reason that NCBI has updated its FTP site in August 2014. They have also modified FASTA format with NCBI-GI removed from the header (see following NCBI News)
In this scenario, I needed to repeat my analysis with new genomes. So that other people can access my published results.
My question to NCBI users is that how they tackle such situation ? Has anyone else encountered same issue as mine ?
