Xiaole Shirley Liu (lead instructor)
Joshua Starmer
Martin Hemberg
Ting Wang
Feng Yue

Ming Tang
Yang Liu
Jack Kang
Scarlett Ge
Jiazhen Rong
Phillip Nicol
Maartin De Vries

We thank many colleagues in the community, who helped Dr. Liu in prepare the STAT115/215 BIO/BST282 course over the years. 

Address of the bookmark: https://liulab-dfci.github.io/bioinfo-combio/

Under   a   NEPAD   initiative,   the   Biosciences   Eastern   and   Central   Africa   (BECA)  (www.biosciencesafrica.org) was established at ILRI. BECA consists of a hub, regional nodes, and  other affiliated laboratories and partner institutes. A state of the art joint Bioinformatics Platform  (www.becabioinfo.org), whose overall goal is to provide a coherent and powerful bioinformatics  infrastructure for use by all scientists in East and central Africa. The Platform goal requires both  physical and intellectual developments that together provide researchers with access to diverse  infrastructure in a wide­area network, thereby addressing four important aspects of bioinformatics: 

1) Science: bioinformatics tools for data integration and visualization, standardization of data  formats and data analysis strategies, and distribution of analysis tasks over local­ and widearea networks are in development; 

2)  Bioinformatics Support Facility: provides assistance and custom programming to projects  and those unable to establish a bioinformatics support function intrinsic to their project due  to shortage of qualified personnel or lack of funding; 

3) Hardware Platform: provide a powerful high performance computing platform capable of  handling the largest analysis needs for projects; 

4) Bioinformatics Training for East and central African scientists: While many Web­based  tools are available to the wet­lab researcher, the Web is not well suited for tasks beyond  single­sequence annotation. Researchers need to become productive in a server­based Unix  environment with its wealth of scripting and automation tools. Even at an entry­level, this  can be an intimidating task if proper guidance is not available.

International Centre of Insect Physiology and Ecology (ICIPE): ICIPE’s research focus is on insect biology, in order to improve the wellbeing of the peoples of the  tropics through insect science. There is a commitment to utilise contemporary science in order to  limit the impact of disease vectors, and agricultural pests. The understanding of the mechanisms  associated with behaviour (e.g. attraction and repellency) is crucial. ICIPE seeks to enhance its  bioinformatics capacity in order to support data from various EST projects designed to gain insights  into the insect ecology and plant pathogen interactions though studies of metabolic pathways  associated with production of all elochemicals. 

Long­term training activities:

Kenyatta University: An introductory course in Bioinformatics is offers to MSc Biotechnology  students. This comprises of 35 hours of lectures and practicals.

University of Nairobi: A centre for Biotechnology and Bioinformatics (CEBIB), which will offer  postgraduate training (diplomas, MSc and PhD) in areas of biotechnology and bioinformatics has  recently been launched. Other universities in Kenya, including Egerton, Maseno and the Jomo Kenyatta University of  Agriculture and Technology offer introductory courses to undergraduates in biomedical sciences. In addition, under the BECA platform MSc and PhD fellowships are being made available for  Bioinformatics students. ILRI is forging links with Universities in South Africa and the United  Kingdom to provide access to courses and training material. 

Research Interest and Activities:

The following are the present areas of research interest: 1. EST clustering 2. Genome sequencing and annotation 3. Functional genomics and proteomics (including key tropical pathogens) 4. Structural bioinformatics 5. Development of Bioinformatics Data Management Systems 6. Gene Mining 7. High Throughput Genotyping 8. Microarray data management and analysis 9. Metagenomics 10. Immunoinformatics 11. Host­pathogen interaction 12. High performance computing and grid development 13. Parasite transfection technologies 14. Cell cycle regulation 15. Population genetics 16. Vector genomics 17. Drug, vaccine and diagnostic target discovery

More at Web site and links:

http://www.ilri.cgiar.org/

http://www.icipe.org/    

http://www.uonbi.ac.ke/cebib

Centre de Biotechnology de Sfax (CBS):
Bioinformatics activity started at CBS in 2001 with the setting­up of a research and service unit of  bioinformatics. This unit currently includes one senior researcher, one engineer and four Phd  students. Activities include sequence annotation (service) and three research programs: ab initio  prediction of short eukaryote genes, statistical modelling by Bayesian networks approach of signal  transduction pathways and statistical analysis of human sequence variation data (haplotype  reconstruction and linkage disequilibrium). Activities of the Bioinformatics unit could be found at  the website: http://www.cbs.rnrt.tn/ and the research activity report is available under request to  Bioinformatics@cbs.rnrt.tn. Although the computing facilities are good, there is still a need for  trained human resources to strengthen bioinformatics capacities at CBS, particularly in structural  bioinformatics.

Web site and links: http://www.cbs.rnrt.tn

Address of the bookmark: https://ocw.mit.edu/courses/biology/7-91j-foundations-of-computational-and-systems-biology-spring-2014/lecture-slides/MIT7_91JS14_Lecture6.pdf

https://grupsderecerca.uab.cat/cacereslab/

Address of the bookmark: https://astrobiomike.github.io/

https://www.mbl.edu/research/research-organisms/rotifer
https://gribblebiolab.org/

https://evirusbioinfc.notion.site/18e21bc49827484b8a2f84463cb40b8d?v=92e7eb6703be4720abf17a901bc9a947

Address of the bookmark: https://evirusbioinfc.notion.site/18e21bc49827484b8a2f84463cb40b8d?v=92e7eb6703be4720abf17a901bc9a947

The job description: "This research position focuses on the science
of bacterial evolution. It will consist of researching theoretical
principles, but could include translational applications. Phylogenomic
and bioinformatic analysis of bacterial populations in nature or
in laboratory experiments will be a key component of the work. Prior
experience is an asset though training will be possible at PMI.
Likewise, laboratory microbiological, molecular, and biochemical
skills are an asset though not essential. Communication and critical
thinking skills are essential for performing the work and for
communicating to the local and international scientific communities.
Participating in team or independent grant writing to obtain research
funding will be required. Student mentoring is a part of the NAU
mission and is a partial expectation."

https://hr.peoplesoft.nau.edu/psp/ph92prta/EMPLOYEE/HRMS/c/HRS_HRAM.HRS_APP_SCHJOB.GBL?Page=HRS_APP_JBPST&Action=U&FOCUS=Applicant&SiteId=1&JobOpeningId=608024&PostingSeq=1

Northern Arizona University is located in Flagstaff, Arizona, a
beautiful mountain town with a surprisingly vibrant restaurant
scene. Located a little over an hour from the Grand Canyon and ~45
min from Sedona, Flagstaff is a hiker's paradise. In fact, the city
of Flagstaff operates more than 50 miles of unpaved trails and there
are, on average, 266 sunny days per year with which to enjoy them.
At 7000 ft in elevation, Flagstaff experiences all four seasons,
but thesummers are mild and, in the winter, you can be on the ski
slopes within 30 min! https://www.flagstaffarizona.org/

As mentioned, joint projects with Professor Sheppard at Oxford
University are possible, including travel to his laboratory in the
United Kingdom. https://www.biology.ox.ac.uk/people/samuel-sheppard

Contact Information:
Paul.Keim@nau.edu

Paul S. Keim, Ph.D.
Regents Professor, &
Cowden Endowed Chair of Microbiology
Northern Arizona University
Flagstaff, AZ 86011-4073

Paul S Keim