Moderator: Khader Shameer

gravatar for Khader Shameer
Reputation:
17,080
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Trusted
Location:
Manhattan, NY
Twitter:
kshameer
Scholar ID:
Google Scholar Page
Last seen:
2 weeks, 5 days ago
Joined:
7 years, 6 months ago
Email:
s******@gmail.com

Currently: 
Director of Bioinformatics, Data Science and Precision Medicine at Philips Healthcare. 

Previously:
Biomedical & Healthcare data scientist at The Dudley Laboratory and Harris Center for Precision Wellness at the Mount Sinai Health System, NY. Also affiliated with the Department of Genetics and Genomics Sciences, and Icahn Institute for Genomics and Multiscale Biology and Icahn School of Medicine of Medicine at the Mount Sinai


Staff scientist in Personal genomics and Genomic Medicine at Mayo Clinic; Lead bioinformatics and computational genomics of MI-GENES trial (See ClinicalTrials.gov link:NCT01936675) Post-doc leading bioinformatics and genomic data analytics, big data management and research projects for electronic Medical Records and Genomics (eMERGE) and cardiovascular genomics at Mayo Clinic; PhD in Computational Biology / Biomedical Informatics from National Centre for Biological Sciences - Tata Institute of Fundamental Research & Indian Institute of Science. Graduate student at The Computational Biology Group, NCBS-TIFR.

I developed/co-developed/lead the development of the following tools and databases during my graduate school: 

  • Harmony - Protein structure validation server 
  • PeptideMine - Identification and analyses of peptides from local interactomes
  • FASSM - Function association using sequence-specific motifs 
  • SEQ2GO: Function annotation of hypothetical proteins using sequence based filtering and domain composition of intermediate homologs.
  • PURE: Prediction of Unassigned REgions in proteins 

 

Posts by Khader Shameer

<prev • 1,185 results • page 1 of 119 • next >
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How many human genomes have sequenced, ever?
... I am looking for a total number of human samples with some form of genomic data generation and interpretation (genotyping, gene-panel, exome, genome). I am sure I can get a rough estimate by combining the human subset from the major biological database (ENA, SRA, dbGAP, GEO, Clinical Trials etc.). ...
genomics written 20 days ago by Khader Shameer17k
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Job: Postdoctoral postion in Bioinformatics, Computational Genomics, Population Genetics, Genomic Medicine, and Biomedical and Healthcare Data Science
... **Postdoctoral postion in Bioinformatics, Computational Genomics, Population Genetics, Genomic Medicine, and Biomedical and Healthcare Data Science** **Description.** A postdoctoral position is available for eligible candidates with training in statistical genetics and computational genomics. [Ku ...
bioinformatics genetics job genomics statistics written 9 weeks ago by Khader Shameer17k
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Blog: Neural identity, neuroethics and neurodegeneration of AI systems
... Am sure some of BioStars are thinking of implications of biological aspects including identity, ethics, aging and probable neurological degeneration that may influence real-time AI systems. Here's my post about this topic at [LinkedIn][1] - would love to hear your thoughts. [Neural identity, neuro ...
data-science ai blog ml written 4 months ago by Khader Shameer17k
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Comment: C: Structure-Based Phylogenetic Analysis
... You can compute SDM as explained in the Methods section under: Evolutionary analysis using a structural divergence measure http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0005736 ...
written 4 months ago by Khader Shameer17k
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Answer: A: How to get complete database of matabolic network of Plasmodium falciparum
... [KBase][1] have metabolic models of [p. falciparum][2] [1]: https://kbase.us/ [2]: https://narrative.kbase.us/search/#/search/?q=plasmodium ...
written 6 months ago by Khader Shameer17k
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Comment: C: Detect trees (newick) with specific topology
... Not aware of tool to subset trees based on topology. Yes, a script/regex could help. I am wondering if you have the images of the trees? If you do, may be it's interesting to try deep learning / computer vision-based approach here? ...
written 6 months ago by Khader Shameer17k
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Comment: C: Looking for walkthrough guide on Rare Variant Association Analysis
... What specific aspect of rare variant analyses are you looking for? Burden test? ...
written 6 months ago by Khader Shameer17k
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Forum: BioStar's List of Predatory Journals and Publishers to Avoid - 2017
... I just talked to a senior investigator who fell for a predatory publisher - he lost one of his significant work in a journal with no reliability. No editorial board, no peer reviewing - all that journal had was an OA model where anyone can publish anything with few hundreds of dollars. We live in a ...
publication bioinformatics forum blog written 6 months ago by Khader Shameer17k
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News: RepurposeDB - A New Reference Database of Drug Repositioning
... Cross-posted from [The SciPreneur][1] TL;DR - Link to manuscript [here][2] and Link to RepurposeDB [here][3] A drug discovery project takes 8-12 years and costs 8-15 billion dollars. It relies on various avenues of pre-clinical development, biomedical research, medicinal chemistry, clinical trials ...
precision medicine drug-repositioning news written 6 months ago by Khader Shameer17k
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Comment: C: Efficiently create PSI-BLAST-like PSSMs from very large MSAs
... We had success in leveraging PSI-BLAST for generating PSSMs for a large number of sequences (See database of PSSM profiles [here][1]; publication [here][2]). Can you give the specifics of the issues? [1]: http://caps.ncbs.res.in/3pfdb/index.html [2]: https://biodatamining.biomedcentral.com/a ...
written 7 months ago by Khader Shameer17k

Latest awards to Khader Shameer

Popular Question 4 months ago, created a question with more than 1,000 views. For Analysis Of Low-Complexity Regions
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Mapping Genes To Pathway
Appreciated 6 months ago, created a post with more than 5 votes. For A: Kegg Paywalled, What Do People Use?
Popular Question 7 months ago, created a question with more than 1,000 views. For What Is The Average Length Of Transcription Factor Binding Site(S) In Human ?
Popular Question 7 months ago, created a question with more than 1,000 views. For What Is The Average Length Of Transcription Factor Binding Site(S) In Human ?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Kegg Paywalled, What Do People Use?
Popular Question 8 months ago, created a question with more than 1,000 views. For What Is The Average Length Of Transcription Factor Binding Site(S) In Human ?
Popular Question 8 months ago, created a question with more than 1,000 views. For What Is The Average Length Of Transcription Factor Binding Site(S) In Human ?
Popular Question 8 months ago, created a question with more than 1,000 views. For What Is The Average Length Of Transcription Factor Binding Site(S) In Human ?
Epic Question 9 months ago, created a question with more than 10,000 views. For How To Map A Snp To A Gene Around +/- 60Kb ?
Great Question 10 months ago, created a question with more than 5,000 views. For Content Management Systems For Bioinformatics Websites
Epic Question 10 months ago, created a question with more than 10,000 views. For How To Map A Snp To A Gene Around +/- 60Kb ?
Great Question 11 months ago, created a question with more than 5,000 views. For Content Management Systems For Bioinformatics Websites
Great Question 12 months ago, created a question with more than 5,000 views. For Content Management Systems For Bioinformatics Websites
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Kegg Paywalled, What Do People Use?
Appreciated 13 months ago, created a post with more than 5 votes. For Visualize / Highlight Specific Nodes In A Taxonomy Tree
Scholar 13 months ago, created an answer that has been accepted. For A: Is there any database to find the protein interfaces that already found experime

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