Main Page: Difference between revisions
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==Genomic Data Browsers== | ==Genomic Data Browsers== | ||
===Collaborative works=== | ===Collaborative works=== | ||
<gallery mode=packed heights=200px perrow="4 | <gallery mode=packed heights=200px perrow="4"> | ||
File:Screenshot_2023-03-24_122016.png| link=http://borreliabase.org/~wgqiu/clickme-khalikuz/temp-Points.html | Phosphoproteome MDM2KD data set (with Bargonetti Lab @Hunter) | File:Screenshot_2023-03-24_122016.png| link=http://borreliabase.org/~wgqiu/clickme-khalikuz/temp-Points.html | Phosphoproteome MDM2KD data set (with Bargonetti Lab @Hunter) | ||
File:Screenshot_2023-03-24_122312.png| link=http://borreliabase.org/~wgqiu/mpai-v3/ | Genes & Pathways Associated with mTP53 (with Bargonetti Lab @Hunter) | File:Screenshot_2023-03-24_122312.png| link=http://borreliabase.org/~wgqiu/mpai-v3/ | Genes & Pathways Associated with mTP53 (with Bargonetti Lab @Hunter) | ||
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===Qiu lab browsers=== | ===Qiu lab browsers=== | ||
<gallery mode=packed heights=200px perrow="4 | <gallery mode=packed heights=200px perrow="4"> | ||
File:Screenshot 2023-03-24 122558.png | link=http://borreliabase.org | Lyme genome browser | File:Screenshot 2023-03-24 122558.png | link=http://borreliabase.org | Lyme genome browser | ||
File:Screenshot 2023-03-24 133320.png | link=http://borreliabase.org/~wgqiu/pf-trees/ | Lyme pathogen plasmid partitioning gene trees | File:Screenshot 2023-03-24 133320.png | link=http://borreliabase.org/~wgqiu/pf-trees/ | Lyme pathogen plasmid partitioning gene trees | ||
File:Screenshot 2023-03-24 133636.png | link=http://borreliabase.org/vls-finder/ | vls Finder in Lyme pathogen genomes | File:Screenshot 2023-03-24 133636.png | link=http://borreliabase.org/vls-finder/ | vls Finder in Lyme pathogen genomes | ||
File:Screenshot 2023-03-24 122521.png | link=http://borreliabase.org/~wgqiu/snp-view | SNP view | |||
File:Screenshot 2023-03-24 122359.png | link=http://borreliabase.org/~wgqiu/code-wheel | Codon Wheel | File:Screenshot 2023-03-24 122359.png | link=http://borreliabase.org/~wgqiu/code-wheel | Codon Wheel | ||
File:Screenshot 2023-03-24 122521.png | link=http://borreliabase.org/~wgqiu/ospC-sequencing | OspC amplicon sequencing from ticks | File:Screenshot 2023-03-24 122521.png | link=http://borreliabase.org/~wgqiu/ospC-sequencing | OspC amplicon sequencing from ticks | ||
Revision as of 17:45, 24 March 2023
Weigang Qiu, Ph.D., Professor Department of Biological Sciences Hunter College of City University of New York Belfer Research Building, Room 402 413 East 69th Street, New York, NY 10021 Office: 1-212-896-0445 Email: wqiu-at-(hunter.cuny.edu) Directions by Google Map |
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Lab publications
Lyme Genomics
Li, Di, Zeglis, Qiu (2022). “Evolution of the vls antigenic variability locus of the Lyme Disease pathogen and development of recombinant monoclonal antibodies targeting conserved VlsE epitopes”. Microbial Spectrum 10 (5):1-15. DOI: https://doi.org/10.1128/spectrum.01743-22
![Di*, Akther*, Bezrucenkovas, Ivanova, Sulkow, Wu, Mneimneh, Gomes-Solecki, Qiu (2021). "Maximum antigen diversification in a lyme bacterial population and evolutionary strategies to overcome pathogen diversity". The ISME Journal. 16, 447-464. [PMID 34413477] (*co-first authors)](/images/9/93/Fig7-small.png)
Di*, Akther*, Bezrucenkovas, Ivanova, Sulkow, Wu, Mneimneh, Gomes-Solecki, Qiu (2021). "Maximum antigen diversification in a lyme bacterial population and evolutionary strategies to overcome pathogen diversity". The ISME Journal. 16, 447-464. [PMID 34413477] (*co-first authors)
Schwartz, Margos, Casjens, Qiu, Eggers (2020). "Multipartite Genome of Lyme Disease Borrelia: Structure, Variation and Prophages". Current Issues in Molecular Biology. 42:409-454. DOI: https://doi.org/10.21775/9781913652616
Barbour & Qiu (2019). Borreliella. In Bergey's Manual of Systematics of Archaea and Bacteria (eds W. B. Whitman, F. Rainey, P. Kämpfer, M. Trujillo, J. Chun, P. DeVos, B. Hedlund and S. Dedysh). John Wiley & Sons, Inc., in association with Bergey's Manual Trust. DOI: https://doi.org/10.1002/9781118960608.gbm01525
![Di*, Akther*, Bezrucenkovas, Ivanova, Sulkow, Wu, Mneimneh, Gomes-Solecki, Qiu (2021). "Maximum antigen diversification in a lyme bacterial population and evolutionary strategies to overcome pathogen diversity". The ISME Journal. 16, 447-464. [PMID 34413477] (*co-first authors)](/w/File:Fig7-small.png)
Evolution & Learning Algorithms
Ely, Koh, Ho, Hassan, Pham, Qiu (2023). Novelty Search Promotes Antigenic Diversity in Microbial Pathogens. Pathogens 12:388. DOI: https://doi.org/10.3390/pathogens12030388
Attie, Sulkow, Di, Qiu (2019). Genetic codes optimized as a traveling salesman problem. PLoS ONE 14(10): e0224552. DOI: https://doi.org/10.1371/journal.pone.0224552
Yan, Deforet, Boyle, Rahman, Liang, Okegbe, Dietrich, Qiu, Xavier (2017). Bow-tie signaling in c-di-GMP: Machine learning in a simple biochemical network. PLoS Comput Biol 13(8): e1005677. DOI: https://doi.org/10.1371/journal.pcbi.1005677
Informatics Tool Development
![Hernandez, Bernstein, Pagan, Vargas, McCaig, Ramrattan, Akther, Larracuente, Di, Vieira, Qiu. (2018). BbWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines. BMC Bioinformatics 19(1):76. [PMID 29499649]](/images/a/a5/12859_2018_2074_Fig1_HTML.png)
Hernandez, Bernstein, Pagan, Vargas, McCaig, Ramrattan, Akther, Larracuente, Di, Vieira, Qiu. (2018). BbWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines. BMC Bioinformatics 19(1):76. [PMID 29499649]
![Di, Pagan, Packer, Martin, Akther, Ramrattan, Mongodin, Fraser, Schutzer, Luft, Casjens and Qiu. (2014). BorreliaBase: a phylogeny-centered browser of Borrelia genomes. BMC Bioinformatics 15:233. [PMID 24994456]](/images/8/8d/12859_2014_Article_6488_Fig3_HTML.png)
Di, Pagan, Packer, Martin, Akther, Ramrattan, Mongodin, Fraser, Schutzer, Luft, Casjens and Qiu. (2014). BorreliaBase: a phylogeny-centered browser of Borrelia genomes. BMC Bioinformatics 15:233. [PMID 24994456]
![Hernandez, Bernstein, Pagan, Vargas, McCaig, Ramrattan, Akther, Larracuente, Di, Vieira, Qiu. (2018). BbWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines. BMC Bioinformatics 19(1):76. [PMID 29499649]](/w/File:12859_2018_2074_Fig1_HTML.png)
![Di, Pagan, Packer, Martin, Akther, Ramrattan, Mongodin, Fraser, Schutzer, Luft, Casjens and Qiu. (2014). BorreliaBase: a phylogeny-centered browser of Borrelia genomes. BMC Bioinformatics 15:233. [PMID 24994456]](/w/File:12859_2014_Article_6488_Fig3_HTML.png)
last update: March 20, 2023
Genomic Data Browsers
Collaborative works
Phosphoproteome MDM2KD data set (with Bargonetti Lab @Hunter)
Genes & Pathways Associated with mTP53 (with Bargonetti Lab @Hunter)
Group B Streptococcus (GBS) genome browser (with Wu Lab @Shenzhen)
1K genome (with Ogunwobi Lab @Hunter)
E faecalis genome browser (with Morales Lab @WCMC)
Proteomics GSEA results (with Melendez Lab @Hunter)
pHis Protein Browser (with Skolnik lab @NYU)
Qiu lab browsers
Lyme genome browser
Lyme pathogen plasmid partitioning gene trees
vls Finder in Lyme pathogen genomes
SNP view
Codon Wheel
OspC amplicon sequencing from ticks
Genomic epidemiology of a Salmonella outbreak (ASM Challenge)
Lab Resources
- Github repositories: https://github.com/weigangq/?tab=repositories
- Mini-Protocols (frequently used computer codes and pipelines)
- Monte Carlo Club (summer projects)
- Tick handling protocols
- Hunter HPC Usage
Wiki Help
- Configuration settings list
- MediaWiki FAQ
- MediaWiki release mailing list
- Localise MediaWiki for your language
- Learn how to combat spam on your wiki
- Consult the User's Guide for information on using the wiki software.