2015 NRF-Managed Bioinformatics and Functional Genomics ...
Transcript of 2015 NRF-Managed Bioinformatics and Functional Genomics ...
REPORT
THE DEPARTMENT OF SCIENCE AND TECHNOLOGY
NATIONAL RESEARCH FOUNDATION (DST-NRF) REVIEW
OF THE NRF MANAGED BIOINFORMATICS AND
FUNCTIONAL GENOMICS (BFG) PROGRAMME FOR THE
PERIOD 2009 – 2015
31 August - 4 September 2015
Review panel members:
● Prof John Quackenbush, Director of the Center for
Cancer Computational Biology: Dana-Farber Cancer
Institute, Massachusetts, USA (Convener)
● Mr Dries Oelofse, Business Development Manager:
Drug Discovery and Development Centre, University of
Cape Town, RSA
● Dr Richard Scheuermann, Director of Informatics: J.
Craig Venter Institute, California, USA
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Table of Contents
1. Executive Summary ................................................................................................................ 2
2. History and Background to the BFG ....................................................................................... 4
3. Methodology for the Review of the BFG................................................................................. 4
4. Key Findings of the Review .................................................................................................... 6
5. Summary and Conclusions ................................................................................................... 12
6. Recommendations ................................................................................................................ 12
7. Appendices............................................................................................................................ 16
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THE DEPARTMENT OF SCIENCE AND TECHNOLOGY-NATIONAL
RESEARCH FOUNDATION (DST-NRF) REVIEW OF THE NRF MANAGED
BIOINFORMATICS AND FUNCTIONAL GENOMICS (BFG) PROGRAMME
(NRF)
Review panel members:
● Prof John Quackenbush, Director of the Center for Cancer Computational Biology: Dana-
Farber Cancer Institute, Massachusetts, USA (Convener)
● Mr Dries Oelofse, Business Development Manager: Drug Discovery and Development
Centre, University of Cape Town, RSA
● Dr Richard Scheuermann, Director of Informatics: J. Craig Venter Institute, California, USA
1. Executive Summary
Biomedical and biological research is in the process of transformation from what was once largely
an observational and laboratory science into what is increasingly an information science. Today,
discovery is driven by one’s ability to effectively collect, manage, analyze, and interpret large
quantities of data. The clearest example of this is genomics, where the cost and time required
sequencing a genome has dropped by nearly 1,000,000 fold during the past 15 years. We now have
unprecedented quantities of data that, when linked to other sources of information, are opening new
avenues of research. The availability of vast quantities of genomic information have allowed us to
ask and answer new questions about human evolution, study large-scale and microbial ecosystems,
understand the genetic factors necessary to improve crop resistance to drought and disease while
increasing yield, and to develop personalized “precision” medicine. In this context, fostering a robust
bioinformatics research infrastructure to take advantage of these advances is essential to ensure
that South African biological and biomedical research remains world-class. And ultimately,
development of a strong presence in bioinformatics and a trained workforce is vital if the nation is to
be successful in implementing its Bio-economy Strategy.
The Department of Science and Technology (DST) should be commended for recognizing that
establishing a strong bioinformatics research programme, coupled with a robust training
programme, is essential to the future of biological and biomedical research in South Africa. A key
component in meeting that need has been the establishment of the Bioinformatics and Functional
Genomics (BFG) Programme, which provides support both for training and for research into the
development of new methods in bioinformatics. Complementary to this programme is the
Bioinformatics Service Platform (BSP), which is being designed to meet the growing need for data
analysis support for biological researchers who are wrestling with large data sets, but for whom
existing methods of data analysis, applied by skilled bioinformatics professionals, will suffice to
address their experimental questions.
Launched in 2009 and administered by the National Research Foundation (NRF) since 2010, the
BFG has supported a total of 86 trainees through 93 funded research projects. These trainees were
funded through 138 one year bursaries: 4 Undergraduate student years, 22 Honours student years,
55 Masters student years, 36 Doctoral student years, and 21 Postdoctoral fellow years. The overall
quality of the scientific programmes funded through the BFG has been excellent as reflected by the
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peer-reviewed scientific publication records associated with the various projects funded through the
programme, many of which have appeared in top-tiered journals. The BFG trainees have
collaborated on a large number important national and high-profile international scientific projects
including the South African Human Genome Project, the Human Heredity and Health in Africa
(H3Africa) Initiative, the
sequencing of the Eucalyptus genome, the wine grape genome project, and numerous projects
investigating HIV infection and HIV/TB co-infection, among others. The BFG programme has also
made substantial progress in addressing workforce inequalities, with a significant representation of
female and non-white students and postdoctoral fellows.
The unanimous consensus of the review panel, as well as all of the stakeholders interviewed during
the process, is that the BFG has been extremely successful, but that it should be improved and
expanded to better meet both its stated goals and the broader needs of the research and
biotechnology communities in South Africa. Most critical will be an increase in funding and
expansion of the programme to: i) increase bursaries to help recruit and retain a diverse group
trainees — which will be particularly important in addressing workforce inequalities; ii) support
further trainee career advancement by developing an early career award programme in support of
junior faculty members in transition to independent faculty positions; iii) support limited wet-lab
validation studies through supplementary granting mechanisms.
Further, the BFG must be considered within the broader context of the biological and biotechnology
research ecosystem within the country. First and foremost, expanding human capital in
bioinformatics will require that career paths be created for graduates from the BFG. If this is not
addressed, many of the trainees in this programme will be lost to other market sectors (such as
banking and finance) or to overseas institutions. Addressing this problem will require closer
coordination and collaboration between government agencies, including the Medical Research
Council (MRC), the Agricultural Research Council (ARC), the Department of Higher Education and
Training (DHET), and the Department of Science and Technology (DST), as well as coordination
with the biotechnology and pharmaceutical industries in the country. In addition, implementing the
Bioinformatics Service Platform (BSP) will be essential both to provide job opportunities for
graduates of the programme but also to assure that other research projects across the country
receive the bioinformatics support that they increasingly require. Finally, various government
agencies need to engage with the private sector to spur investment into biotechnology. South Africa
has globally unique resources in its diverse human population, its environment and ecosystems,
and its agriculture, that, when coupled with a highly skilled workforce — including the substantial
number of individuals trained in bioinformatics — should make it attractive for developing active
globally-competitive biotechnology sectors.
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2. History and Background to the BFG
In 2001 DST published the Biotechnology Strategy for South Africa. In this strategy document,
bioinformatics was identified as a critical yet scarce skill and a necessary capacity to achieve
greater economic benefit from the biotechnology sector. As part of the implementation of the
strategy, the DST created the National Bioinformatics Network (NBN), appointed a Board of
Trustees, as well as a Chief Executive Officer. The NBN was to be structured in a “hub-and-spoke”
fashion. The Central Node would be responsible for administrative activities and other non-research
functions, including managing funding, providing bioinformatics analysis services, and providing
training opportunities not available within the academic environment in South Africa.
Within the NBN, there would be a number of distributed nodes to be hosted at academic institutions
throughout South Africa. These nodes would be responsible for training students in bioinformatics
and performing bioinformatics research. The NBN operations officially started in 2003, but by 2007,
largely for operational reasons, the NBN ceased its operations with the trust finally closing during
2008.
To continue with the momentum created by the NBN and to keep building bioinformatics capacity in
the country, the DST created two programmes in bioinformatics distinguished by their academic and
non-academic missions (consistent with the model of the NBN). The non-academic funding was
given to the Cape Biotech Trust (CBT) with the mandate to establish a bioinformatics services
platform (BSP) and to provide training workshops outside of the university setting. The funding for
academic research and primary student training was given to the NRF under the Bioinformatics and
Functional Genomics (BFG) Programme. This programme was conceived to fund bioinformatics and
functional genomics research and training at academic institutions. The first BFG grant awards were
made during the 2009/2010 fiscal year.
Subsequent DST strategy documents, the Ten-Year Innovation Plan (published in 2007) and the
Bio-economy Strategy (published in 2013), both identify bioinformatics as a critical capacity that is
required to establish and maintain a robust biotechnology sector and for increased economic activity
from biotechnology-based products and services. And both provide further support for the BFG
programme’s essential role in meeting the nation’s strategic plan.
3. Methodology for the Review of the BFG
The Bioinformatics and Functional Genomics (BFG) programme was launched in 2009 with the
overall aim of supporting bioinformatics applications in biotechnology projects in line with national
priorities as set out in the South African National Biotechnology Strategy and the DST 10 year plan.
The BFG had four strategic objectives:
● To create a pool of postgraduate students equipped to support the South African
biotechnology sector.
● To generate bioinformatics solutions and knowledge relevant to the South African
biotechnology industry.
● To support bioinformatics based projects funded through the various biotechnology initiatives
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(including COEs, Research Chairs, etc.).
● To promote collaboration between academic institutions as well as between academia and
industry.
The overarching intention of the BFG was to support basic and applied research with particular
emphasis on Health, Agricultural, and Industrial Bio-economies.
The purpose of this review was to assess the performance of the BFG in meeting the stated goals of
the programme, and in supporting the larger objectives of supporting the Bio-economy Strategy, and
to make recommendations about the continued support of the BFG programme and it further
improvement. In addition, the panel was asked to address a number of additional items as detailed
below.
The panel met in person with representatives from various stakeholder communities over the period
of August 31 — September 4, 2015. The review agenda, including a list of the various stakeholder
groups and individual representatives can be found in Appendix 1.
The panel was provided with a series of supporting documents well in advance of the face-to-face
meeting, including the BFG Programme Framework, annual reports of the BFG programme, and
policy documents, including A National Biotechnology Strategy for South Africa, The Bio-economy
Strategy, and South Africa’s National Research and Development Strategy. Although a formal self-
assessment is typically provided in advance of these kinds of programmatic reviews, none was
provided to the panel in advance nor was a written summary presented. Instead, a verbal self-
assessment was provided by Mr Ben Durham, Chief Director, Biotechnology of the Department of
Science and Technology (DST). An additional overview of history of the BFG and a partial summary
of its performance based on quantitative and qualitative metrics was provided in a presentation by
Mr Nathan Sassman, Director, Applied Research, Innovation and Collaboration (ARIC).
The absence of a formal written self-assessment significantly hampered the panel’s ability to
capture the detailed information about the BFG programme’s achievements and to quantitatively
assess some performance metrics. While some of these data were gathered during the course of
the review process, it was challenging to place these measures of programme achievement within
the broader context of other grant programs supported through the DST and managed by the NRF
and other granting agencies.
While targets for quantitative metrics of success for the programme have been established,
including the number of trainees supported, the number of degrees awarded, the number of
publications in peer-reviewed journals, the number of patents awarded, etc., the yearly goals for
these programme metrics were provided in the annual reports rather than the actual yearly
achievements. While the NRF staff members were able to provide detailed information on some of
these metrics during the review process, others were not readily available. Indeed, it is not clear
whether these are being accurately tracked. Consequently the review panel had difficulty assessing
whether some of the BFG programme objectives are being achieved. The performance metrics that
were accurately tracked were the trainee bursaries awarded in each year and the number of grants
awarded. This allowed assessment of the programme’s progress in workforce development but did
not allow the review panel to quantitatively assess the quality of the scientific output for the BFG.
A list of the publications supported by the BFG programme was provided after the completion of the
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review and is included in Appendix 2. A review of this list supports our earlier assessment of the
overall scientific productivity of the programme based both on the number of publications that have
been produced and the quality and impact factor of the journals in which these have appeared.
However, the NRF could and should do a better job of tracking and summarizing these and other
performance metrics.
4. Key Findings of the Review
There was unanimous recognition by the members of the review panel that bioinformatics is and will
continue to be an essential component of achieving the nation’s overall goals stated in the Bio-
economy Strategic Plan. Indeed, as biological and biomedical research become increasingly data
driven, it is unlikely that South Africa will develop a robust bio-economy unless it has both an
adequate supply of individuals trained in bioinformatics and an active bioinformatics research
programme developing new analytical methods. Within this context, the BFG is playing a vital role.
As noted previously the BFG Programme had four primary objectives. The achievements of the
BFG with respect to each of these objectives are summarized below.
● “To create a pool of postgraduate students equipped to support the South African Bio-
economy developments”
○ The panel feels that the BFG has been highly successful in achieving this goal of
human capital development. Given the available resources provided through the BFG
programme and the human capital likely to be required to achieve the long-term bio-
economy objectives, the number and quality of trainees completing the programme
was judged to be excellent.
○ Virtually all of the honours, masters, and doctoral trainees who have completed the
programme have found suitable positions, although some have left the country and
others have moved to sectors, such as finance, where there is also a need for good
quantitative data analysis skills.
○ While the postdoctoral training component was also viewed as being successful in
terms of producing well-trained bioinformatics professionals, there was a clear
indication that their prospects for career advancement are constrained by an
insufficient number of advanced positions in academia and industry. (See
recommendations regarding early faculty career development awards below.)
○ With regard to this previous point, it was also observed by the panel that the long
term impact of the BFG programme is dependent on other components of the
research and technology ecosystem. In this case, the availability of suitable junior
faculty research positions would be at least partly dictated by the level of support
provided by the Department of Higher Education and Training to national universities.
It is important to consider such external dependencies in the assessment of the
performance of the BFG programme.
○ For the majority of trainees, formal education in bioinformatics was limited to the 8-
week centrally-funded training course in Cape Town. However, for many of the
students this was not sufficient to provide them with the required training and
education in many of the sub-disciplines required to pursue their research project. In
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some cases, the students had to engage colleagues with appropriate expertise in a
relevant topic area, or identify online resources (such as online course materials in
Coursera) to fill the gaps. This suggests a need for developing some formal
bioinformatics training in universities.
○ As an inherently interdisciplinary field, bioinformatics requires skills in biology,
mathematics, computer science, and statistics. It was noted that few supervisors had
advanced expertise in all of these areas, suggesting that co-mentorship by faculty
members with complementary expertise might be desirable in some circumstances.
○ Perhaps outside of the BFG programme, it was also noted by the panel that some
basic training and education about the tools used in bioinformatics should be part of
the core curriculum for all students in biological sciences, perhaps starting at the
undergraduate level.
○ An additional goal of the BFG was to increase representation of women and
previously disadvantaged individuals among bioinformatics scientists. While the
representation of women in the programme is quite good, at 40% of the total, there is
an overrepresentation of white trainees as well as of non-white trainees from outside
of South Africa. If fact, of the non-white trainees available to meet with the review
panel, none were South African. A number of the stakeholders, including the funders,
grant holders, and trainees, indicated that the scarcity of non-white South Africans in
the programme was tied to inadequate funding through the bursaries (even when
“topped up” from other sources by the grant holders to the maximum level allowed)
combined with the economic pressures many previously disadvantaged individuals
face. One simple solution to this problem would be to adjust the levels of the
bursaries to better attract and support a more diverse group of trainees, particularly
among non-white South Africans. Doing so while increasing the number of university
positions would also have the advantage of increasing diversity among university
faculty in bioinformatics (and eventually among awardees from the BFG).
● “To generate bioinformatics and functional genomics solutions and knowledge relevant to
the South African Biotechnology industry”
○ The industry representatives interviewed unanimously stressed the value of
bioinformatics and functional genomics as critical components necessary to advance
the objectives of the Bio-economy Strategy to support establishment of a robust
biotechnology industry.
○ However, they also stated that they have found it difficult to identify and recruit
adequately trained bioinformatics specialists into open positions within their
companies. This was found by the panel to be somewhat surprising since during the
interviews with trainees, the trainees had perceived it difficult to find appropriate
positions within the biotech industry. This suggested a need for better communication
between the BFG programme and potential employers through formal placement
strategies and programme marketing initiatives.
○ Several relevant biotech companies, including Kappa Biosystems, Thermo Fisher,
and others, were absent from the review and yet were apparently important
beneficiaries of the BFG training programme. To adequately assess the impact of the
BFG programme on the biotech industry and the Bio-economy Strategy, it would
have been helpful to hear more from these and other relevant industry stakeholders
to obtain a more comprehensive picture of the near-term impact of the BFG
programme on the biotechnology sector.
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● “To support projects funded through various biosciences/biotechnology initiatives such as
the Technology Innovation Agency (TIA), Centres of Excellence and Research Chairs”
○ Throughout the review, there was a tension between the view of bioinformatics as a
service and bioinformatics as a science. There is a clear need for well-trained
bioinformatics professionals to enable both of these areas, but that the skills required
and the organizational structures appropriate to conduct original research in
bioinformatics and those required to provide a service to support the research of
other biologists are quite different. Although the focus stated in the BFG programme
objective appears to be to provide support services, the mechanism by which awards
are granted is directed more toward original research in bioinformatics as a science,
supporting the development and application of new methods. The members of the
panel felt that, indeed, the more important objective should be to support
bioinformatics research in and of itself and that mechanisms other than the BFG
should be used to expand bioinformatics support services within South Africa.
○ Consistent with the panel’s assessment of the importance of bioinformatics and
functional genomics research (versus support services), the majority of trainees were
interested in pursuing their own research programmes, rather than providing support
services for the analysis of data from other biosciences/biotechnology initiatives. The
panel felt that this was very appropriate and should be further supported by an
adjustment to the stated objectives of the BFG programme.
○ With regard to providing support services, the training of “terminal” honours and
postgraduate masters’ students by the BFG should and is also producing the human
capital to provide these support services. And indeed, a number of Masters trainees
indicated that they consider this to be an attractive career option. However, the lack
of a home for these individuals was a problem outside of the control of the BFG
programme. Plans for the development of the Bioinformatics Support Platform (BSP)
would appear to provide such a home for the trainees and would begin to meet need
for bioinformatics support that was clearly articulated by various stakeholders. Again,
the dependency on this external initiative is affecting the ability of BFG to
successfully contribute to and attain this stated objective.
○ Although some coordination among various funding agencies and
biosciences/biotechnology initiatives was apparent, the panel felt that there was need
for substantially greater coordination and communication between many of the
relevant stakeholders and the BFG programme. For example, the lack of a close
coordination between the BFG and programs supported through the Technology
Innovation Agency (TIA) and the Medical Research Council (MRC) represents a
missed opportunity by these other programs to leverage the funding and skills
developed through the BFG to support the bioinformatics needs of their initiatives.
Similarly, there was a clear need expressed by the Agricultural Research Council
(ARC) and the South African Sugarcane Research Institute (SASRI) for
bioinformatics professionals, but no apparent coordination with the BFG.
● “To promote collaborations between academic institutions, science councils and industry”
○ Many of the BFG grant holders indicated that they also have grants from other
agencies and industry to support the wet-lab data generation components,
equipment purchases, and other components required for an integrated research
programme. The fact that parallel industry support is common among BFG grant
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holders speaks to the perceived value of bioinformatics-related research
programmes by the biotech industry and the likely long-term impact of these
programmes on the South African Bio-economy.
○ Many of the projects supported in part by BFG awards involve collaborations
between several academic institutions. This metric would be useful to track in a more
systematic fashion.
○ However, the grant holders noted that they do not generally know which other
projects have been funded, resulting in missed opportunities to collaborate on
projects in bioinformatics and functional genomics research. This could easily be
addressed by simply posting the list of projects funded annually with a brief
description of the project objectives on a publicly-accessible website.
○ The grant holders also noted that the inability to establish subcontracts on BFG
awards inhibited the formation of some collaborative projects. Again, this is
something that should be easy to remedy.
In addition to these stated goals of the BFG programme identified in its inception, the NRF
requested that the review panel address the following additional considerations:
● “Make recommendations on thematic changes and/or possible alternative/additional
initiatives to improve or strengthen current initiatives in the field of bioinformatics and
biosciences”
○ Throughout the discussions with the various stakeholders, it was clear that the BFG
programme is currently funding a broad collection of projects that cover the breadth
of bioinformatics and functional genomics disciplines as applied to a variety of
different biological areas. The projects included bioinformatics as applied to
genomics, proteomics, metabolomics, and structural biology in the context of human
and animal health, especially around chronic and infectious diseases, as well as
agriculture and biodiversity.
○ The only concern noted here was the surprising lack of closer coordination with
research initiatives funded through the Medical Research Council and the
Technology Innovation Agency. Strategies developed within the BFG to encourage
closer collaboration between these complementary agencies would strengthen the
BFG programme and enhance its potential impact.
● “Consider any outreach awareness activities in the BFG to date and make recommendations
with regard to inclusion or not for “wet-lab” costs by the BFG programme”
○ With regard to support for the inclusion of wet-lab costs by the BFG programme,
there was considerable discussion about the value of this possibility throughout the
panel’s review process. It was recognized that “dry-lab” bioinformatics research could
not exist in a vacuum without the need for upstream wet-lab research to generate the
biological datasets necessary for analysis. The current design in which the BFG-
supported dry-lab bioinformatics are expected to collaborate and obtain data from
wet-lab projects funded through separate mechanisms seems to be working
reasonably well under most circumstances to provide the necessary data for
analysis.
○ However, it was also recognized that some data mining dry-lab research projects
would also benefit significantly from the ability to validate hypotheses/discoveries
made during bioinformatics analysis through some limited downstream wet-lab
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experimentation.
○ And yet, there was concern that if the programme were to open up broadly to the
possibility of funding wet-lab components, that these valuable but limited resources
for support of bioinformatics and functional genomics dry-lab research from the BFG
would be diverted into data generation projects.
● “Make recommendations with regard to the inclusion of science engagement (outreach and
science awareness) in the BFG programme”
○ In general, the importance of effective science engagement was noted by many of
the stakeholders interviewed. On the one hand, educating the public and government
decision-makers as to the value and impact of biological and biomedical research,
and the role that bioinformatics and functional genomics plays, on society, public
health and the bio-economy was considered to be very important. On the other hand,
many of the stakeholders interviewed noted that they are already participating in
several existing science engagement initiatives (e.g. Science for Society) on a
voluntary basis. Thus, adding science engagement as a required component of the
BFG does not appear to be necessary, and would add undesirable additional burden
on grant holders.
The panel also considered how achievements of the BFG programme are helping address the three
high level goals of the central South African government, namely to increase employment (jobs),
decrease poverty, and redress inequality.
● At the grant holder level
○ It was noted that the fact that the majority of grant holders were white males who
seemed to be repeated recipients was not ideal. However, the demographic
breakdown of grant recipients appears to reflect the demographics of the senior
faculty in the biological and biomedical research departments of the leading
universities and the quality of their research programmes. And thus, this observation
was judged by the panel to reflect deficiency in the academic appointment strategies
of the universities with inadequate emphasis on the recruitment and retention of well-
qualified and diverse junior faculty members, rather than some deficiency in the BFG
granting programme.
● At the trainee level
○ In contrast to the limited demographic distribution of the grant holders, the diversity of
trainees supported by the programme, which includes a significant proportion of
females and non-whites, was very promising and should help to redress the historical
inequalities in South Africa. This observation was judged by the panel to be very
promising.
○ Having said this, it was also noted that the majority of the non-white trainees
appeared to be coming from other sub-Saharan African countries rather than from
South Africa. Upon further discussion about this curious observation, the possibility
that the relatively low bursary levels may be at least partly responsible for this
phenomenon was identified. Since many of the bursaries awarded barely cover the
university fees, let alone provide adequate cost of living support, it could be very
difficult, if not impossible, for a disadvantaged black South African to commit to such
a training programme. This conclusion is a key motivating factor for the
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recommendation to increase student bursaries detailed below.
○ The panel also found that virtually all of the trainees supported by the BFG
programme were either continuing their training or had obtained gainful employment.
Thus the BFG programme was seen as effectively promoting increased employment
(jobs) for their trainees albeit not in bioinformatics.
During the review, several issues related to the administration of the BFG programme by the NRF
were also identified.
● Unreliability in the frequency of calls for proposals made it difficult for long-term planning of
bioinformatics research programmes.
● Awards made too close to the beginning of the academic calendar to allow enough time to
recruit students and other trainees into the newly-available slots resulted in the inability to
use awards in some years.
● Lack of an adequate number of qualified review panel members who were not in conflict as
applicants to the BFG programme made it difficult to assemble review panels. This also led
to the perception that BFG funding decisions were being controlled by a small number of
“gatekeepers.”
● The majority of awards have been made to senior investigators. Junior investigators may be
experiencing an unfair disadvantage in that they have not yet had a chance to establish a
research programme with a long-term track record or extensive national and international
groups of potential collaborators. This phenomenon may warrant defining a set of parallel
review criteria for the evaluation of proposals by relatively new investigators and/or setting
aside a portion of funds to specifically support this group.
● The BFG has not been successful in attracting applications from historically-disadvantaged
universities.. One possible explanation is the lack of qualified faculty at historically-
disadvantaged universities and the inability to attract suitable candidates to those settings.
An example of this was the fact that the University of Limpopo has a vacant faculty position
in Bioinformatics that they are struggling to fill. The development of the faculty at historically-
disadvantaged universities and the impact it has on the overall BFG programme is an
important issue that needs to be explored further.
● While the NRF is doing a good job in tracking who is receiving awards, who is being trained
through the programme and how the funds are being allocated, they are not doing a good
job in tracking many of the stated performance metrics, like the number of new patents, new
technology innovations, and impact of the resulting journal publications and supported
research programmes. Additional metrics reflecting other stated objectives, including
fostering collaborations between academic institutions, science councils and industry, and
providing support for projects funded through other biosciences/biotechnology initiatives, are
also not being tracked.
Other findings of relevance to the success of the BFG programme also emerged during the review
process.
● Several of the trainees noted that the progress of their research project had been impeded
on occasion by the limited availability of and/or accessibility to adequate compute resources.
● There is a general lack of knowledge about the field of bioinformatics at the undergraduate
level, which has the effect of limiting the potential pool of honours and graduate student
candidates.
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5. Summary and Conclusions
Overall, the BFG programme is viewed as being a resounding success by the review panel.
However, there were also a number of areas in which making strategic adjustments to the current
organization and implementation could have significant positive effects in further achieving the
stated objectives of the BFG programme, the National Biotechnology Strategy for South Africa, the
Bio-economy Strategy, and the national goals for South Africa.
6. Recommendations
1. The panel recommends a renewal of the BFG programme but at a higher level of overall
funding and with changes to the scope of activities supported.
a. The total number of bursaries funded each year is adequate, but the overall level of
bursary support is too low.
Trainee Level Current Bursary Recommended Bursary
Honours R 35,000 R 80,000 + fees
Masters R 60,000 R 100,000 + fees + travel
Doctoral R 100,000 R 140,000 + fees + travel
Postdoctoral R 200,000 R 250,000 + travel (no fees required)
The goal is to provide a “living wage” sufficient to attract the best students from a
diverse pool and to allow them to focus on their research and training.
The recommendation to separate the university fees from the bursary is designed to
adjust the total support to reflect differences in fees associated with each trainee’s
home university and to reflect differences for domestic and international students.
The travel stipend should be set on a per-trip level with the number of trips set based
on level. Many Masters students commented that their current travel stipend, half of
that available to Doctoral students, was not sufficient to allow them to attend
meetings where the cost is independent of the level of training.
These bursaries should also be adjusted annually to keep pace with inflation.
b. The BFG programme should allow trainees to apply for an additional year of funding
should their projects and circumstances warrant such an extension.
c. For large projects, the BFG programme should provide for support staff who can help
provide “routine” analysis for collaborators, freeing students to focus on their own
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research; this should be closely coordinated with the BSP or other bioinformatics
service programmes.
d. The BFG programme should allow grants to include subcontracts to other institutions
as a means of facilitating collaboration.
e. The BFG programme should allow for, and perhaps encourage, the establishment of
co-mentorship teams (with a single responsible supervisor) to provide the
complementary expertise required for training in the inherently interdisciplinary field
of bioinformatics.
2. The BFG, in collaboration with the Department of Science and Technology (DST) and
Department of Higher Education and Training (DHET) should work to establish faculty-line
positions at South African universities (either at the Lecturer or Assistant Professor level)
together with five year “career development awards” for these junior investigators, providing
support for graduate students, postdocs and research materials. The goal would be to
provide job opportunities for highly trained BFG postdocs and to recruit highly-qualified
candidates from abroad. In addition to preserving the investment in bioinformatics by
building the discipline at universities, it would have the advantage of increasing the
representation of previously disadvantaged individuals within the pool of potential
bioinformatics grant applicants.
3. The panel recommends expansion of the BFG programme to include new funding
mechanisms.
a. Within the BFG programme, the NRF should create a programme of individual
fellowships in addition to the current project-based funding scheme. This would likely
increase both the diversity of the funded projects and individuals, while allowing for
bioinformatics training to occur more broadly in other South African universities.
b. The BFG programme should allow award recipients to apply for supplements to an
existing BFG award to support wet-lab work. Many awardees and trainees felt that
the failure of the current BFG programme to support laboratory experiments limited
the impact of their work by preventing them from validating their dry lab discoveries.
However, it will be important to avoid the use of this funding mechanism for large-
scale primary data generation. Thus, the supplement programme should be limited to
support validation-type studies only, and the size of individual awards should be
limited. This small investment could have a major positive impact on the scientific
output quality since the wet-lab validation of bioinformatics discoveries is important
for high quality publications in bioinformatics.
c. The BFG programme should provide for some small curriculum development grants
to encourage universities to develop more extensive curriculum in bioinformatics and
related fields to both augment the 8-week BSP-funded training course in Cape Town
and to open the discipline to a broader group of students. This mechanism could
include curriculum development projects designed to expose all undergraduate
students in the biological sciences to the core principles and methods in
bioinformatics.
14 | P a g e
4. The panel also recommends changes in how BFG grants are awarded and administered by
the NRF.
a. The application, review, and granting cycle should be annual, rather than every three
years, to keep open the funding pool for additional new projects.
b. Renewal applications should be accepted one year before the end of the funding
period (possibly at the end of the second year of a three year project) to help provide
greater continuity for successful existing projects.
c. The NRF should establish a well-defined grant application calendar that includes a
reliable annual call in which the call for proposals is made in January, proposals are
received in April, proposal reviews occur by July, and award notifications are made in
September to allow recruitment of trainees before the start of the academic year.
d. The NRF should consider revisiting the reporting requirements associated with the
grants to reduce the redundancy some perceive to exist in the reporting templates.
Related to this is the balance between qualitative and quantitative reporting, and
thinking carefully about what qualitative data is required and at what level of detail.
e. The NRF should be more rigorous in recording performance metrics of the BFG
programme beyond the number of trainees funded, including accurate lists of
publications, patents, technology innovation products developed, and degrees
awarded. The BFG should also attempt to track former trainees for at least five years
after they complete the programme so as to better understand the overall impact of
the programme on important metrics like job creation and impact on the
biotechnology sector and the overall bio-economy.
5. The BFG should maintain a public catalogue of funded projects, including a description of
the institutions, lead investigators and project aims, to foster both transparency and
collaboration among projects.
6. The BFG should facilitate the creation of a “career match program” to help match trainees to
available positions both within the universities and in private industry. This includes a career
portal where jobs and grant holder-linked study opportunities can be advertised and where
students and graduates can place their CV’s.
7. There is a clear and pressing need for better coordination and communication across
government agencies and in support of strategic initiatives, such as the South African
Human Genome Project (SAHGP), to ensure the integration of the BFG programme and
thereby the continuity and quality of the BFG programme. Larger international programmes
like the H3Africa programme can also have a significant effect on leveraging resources like
the BFG programme so there should be better coordination with such programmes as well.
8. Given the small number of bioinformatics faculty members, the limited resources available,
and the importance of bioinformatics for biological and biomedical research, there needs to
be better coordination among government agencies providing funding for building strong
15 | P a g e
bioinformatics capacity, including the NRF, MRC, ARC and TIA. This is particularly important
as bioinformatics is at the heart of many of the applications and innovations in biomedicine
(including research and precision medicine), modern forestry and agriculture, and other
areas of biological investigation.
16 | P a g e
7. Appendices
Appendix 1: Review Programme
Appendix 2. Programme Publication List
1 | P a g e
Appendix 1
Review Programme
THE DEPARTMENT OF SCIENCE AND TECHNOLOGY-NATIONAL
RESEARCH FOUNDATION (DST-NRF) REVIEW OF THE NRF
MANAGED BIOINFORMATICS AND FUNCTIONAL GENOMICS (BFG)
PROGRAMME (NRF)
Review panel members:
Prof John Quackenbush, Director of the Center for Cancer Computational Biology:
Dana-Farber Cancer Institute, Massachusetts, USA (Convener) Mr Dries Oelofse, Business Development Manager: Drug Discovery and
Development Centre, University of Cape Town, RSA Dr Richard Scheuermann, Director of Informatics: J. Craig Venter Institute,
California, USA Monday 31 August 2015
09:30 Reviewers to proceed to NRF [Xpert Shuttle services] Tel: 082 336 9659
Venue: Nadine Gordimer, NRF, Meiring Naude, Road, Pretoria
10:00 Briefing of reviewers
Dr Dorsamy [Gansen] Pillay, Deputy CEO: RISA Also present:
Dr Rocky Skeef, Executive Director: Reviews and Evaluation (RE), NRF
Ms Joyce Olivier, Director: RE, NRF
Mr David Manamela, Professional Officer (PO): RE, NRF
Ms Anke Rädel, PO: RE, NRF
10:45 Discussion of review programme with staff of NRF’s Reviews and Evaluation unit
Ms Joyce Olivier, Director: RE
Mr David Manamela, PO: RE
Ms Anke Rädel, PO: RE, NRF
11:00 Panel members to prepare their strategy and allocation of tasks among themselves
12:00 Department of Science and Technology
Mr Ben Durham, Chief Director: Biotechnology
Dr Maneshree Jugmohan-Naidu, Director: Biotechnology
13:30 Lunch
2 | P a g e
14:00 NRF Management of BFG Programme
Dr Romila Maharaj, Executive Director: Human and Infrastructure Capacity Development (HICD)
Dr Kaluke Mawila, Acting Executive Director: Applied Research, Innovation and Collaboration (ARIC)
Dr Zolani Dyosi, Director: (ARIC)
Mr Nathan Sassman, Director: ARIC (Via Skype)
Dr Rocky Skeef, Executive Director: RE
Mr Lebusa Monyooe, Director: Grants Management and Systems Administration (GMSA)
16:30 Reviewers to return to City Lodge Hotel [Xpert Shuttle service]
Tuesday, 1 September 2015
08:00 Reviewers to proceed to NRF [Xpert Shuttle service]
Venue: Nadine Gordimer
08:30 Stakeholders from Industry Institutions
Dr Shirley Ferris Whitehead Scientific Dr Reinhard Hiller Centre for Proteomic & Genomic Research(Via Skype)
Dr Silke Arndt Ingaba Biotechnical Industries Mr Ryan Vogt Whitehead Scientific
Prof Celia Abolnik South African Poultry Association
10:30 Tea/coffee
10:45 Research Agencies/ Sciences Councils in South Africa
Dr Charles Hefer Agricultural Research Council
Dr Arshad Ismal National Institute of Communicable Diseases Dr Bernard Potier South African Sugarcane Research Institute
Dr Lungile Shoba-Zikhali Technology Innovation Agency
Dr Rizwana Mia Medical Research Council
12:45 Lunch
13:30 Institutional Stakeholders (Heads of Departments hosting BFG)
Prof Fourie Joubert University of Pretoria (UP)
Prof Michele Ramsay University of Witwatersrand (WITS)
Prof Nicky Mulder University of Cape Town (UCT)
Prof Johan Burger Stellenbosch University (SU)
15:30 Sample of Vice-Chancellors Research
Prof Stephanie Burton UP
Prof Mbudzeni Sibara University of Limpopo (UL)
Prof Zeblon Vilakazi WITS
Prof Danie Visser UCT (Video-Conference)
Prof Frikkie van Niekerk North-West University (NWU)
17:30 Reviewers to return to City Lodge Hotel [Xpert Shuttle service
3 | P a g e
Wednesday, 2 August 2015
08:00 Reviewers to proceed to NRF
Venue: Nelson Mandela Board Room
8:30 Grant-holders
Prof Florian Bauer SUN
Prof Zander Myburg UP
Dr Wilbert Sibanda NWU Prof Simon Travers UWC
Prof Oleg Reva UP
10:30 Tea/coffee
10:45 Postdoctoral Fellows
Dr Ananyo Choudhury WITS
12:45 Lunch
13:30 Doctoral students
Mr Werner Smidt UP
Mr Rian Pierneef UP
Mr Stanley Kimbung UCT
Dr Ovokeraye Oduaran WITS Ms Roux-Cil Ferreira UWC
15:30 Masters’ Students
Mr Hilaire Mobele UCT Mr Louis Cronje UP
Ms Desre Pinard UP
Mr Rian Swanepoel UP
Ms Natasha Pretorius SU
Ms Renee Crous SU
16:30 Reviewers to return to City Lodge Hotel [Xpert Shuttle service]
Thursday 3 September 2015
08:30 Reviewers to proceed to NRF [Xpert Shuttle service]
Venue: Nelson Mandela Board Room
09:00 Report Writing
10:30 Tea/coffee
11:00 Report Writing
13:00 Lunch
14:00 Report Writing
16:30 Reviewers to return to City Lodge [Xpert Shuttle service]
4 | P a g e
Friday, 4 September 2015
08:30 Reviewers to proceed to NRF
Venue: Nelson Mandela Board Room
09:00 Report Writing
10:30 Tea/coffee
11:00 Verbal feedback to the NRF Executives, Namely, Dr Gansen Pillay and Dr Rocky Skeef
13:00 Lunch
14:00 Return home [Xpert Shuttle service]
1
Appendix 2
BFG Programme Publication List
2010 -2012
1. Prof Florian FF Bauer
Articles in Refereed/Peer-reviewed Journals
Title Of Article Many cell wall protein encoding genes are regulated by Mss11p, but esion phenotypes solely depend on FLO gene expression
Title Of Journal G3 (Genes, Genomes, Genetics) Other Authors Bester, M. D. Jacobsen & F.F. Bauer
Status Published/produced
Volume 2 Page from 131 Page to 141
Title Of Article
Effect of alternative NAD+ regenerating pathways on the formation of
primary and secondary aroma compounds in a Saccharomyces
cerevisiae glycerol defective mutant
Title Of Journal Applied Microbiology and Biotechnology Other Authors Jain, V.S., B. Divol, B.A. Prior & F.F. Bauer
Status Published/produced
Volume Page from Page to
Title Of Article The effect of scale on gene expression: Commercial vs. laboratory wine fermentations.
Title Of Journal Applied Microbiology and Biotechnology.
Other Authors Rossouw, D., N. Jolly, D. Jacobson & F.F. Bauer.
Status Published/produced
Volume Page from 1207 Page to 1219
Title Of Article The impact of yeast and bacterial co-inoculation on the transcriptome of Saccharomyces cerevisiae and on the flavour-active metabolite profiles of fermenting must.
Title Of Journal Food Microbiology
Other Authors Rossouw, D., M. Du Toit & F.F. Bauer
Status Published/produced Volume
Page from 121 Page to 131
Title Of Article The Vineyard Yeast Microbiome - A Mixed Model Microbial Map.
Title Of Journal PLOS One
Other Authors Setati, M.E., D. Jacobson, U-C. Andong & F.F. Bauer.
Status Published/produced
Volume 7(12): e52609 Page from e52609 Page to
2
Title Of Article Transcriptional regulation and the diversification of metabolism in wine
yeast strains.
Title Of Journal Genetics 190:251-261
Other Authors Rossouw, D., D. Jacobsen & F.F. Bauer.
Status Published/produced
Volume 190 Page from 251 Page to 261
3
2. Prof Nico NC Gey van Pittius
Articles in Refereed/Peer-reviewed Journals
Title Of Article A metabolomics approach exploring the function of the ESX-3 type VII retion system of M.smegmatis
Title Of Journal Metabolomics Other Authors Loots, D-T., Meissner-Roloff, R.J., Newton-Foot, M., Gey van Pittius, C.
Status Published/produced
Volume 9 (3) Page from 631 Page to 641
Title Of Article Comparative analysis of Mycobacterium tuberculosis pe and ppe genes reveals high sequence variation and an apparent absence of selective constraints.
Title Of Journal PLoS One.
Other Authors McEvoy, C.R.E., Cloete, R., Müller, B., Schürch, A.C., van Helden,
P.D.,Gagneux, S., Warren, R.M.,and Gey van Pittius, N.C.
Status Published/produced
Volume 7(4) Page from e30593 Page to
Title Of Article Emergence and treatment of multidrug resistant (MDR) and extensively
drug-resistant (XDR) tuberculosis in South Africa
Title Of Journal Infect Genet Evol.
Other Authors Streicher, E.M., Müller, B., Chihota, V., Mlambo, C., Tait, M., Pillay, M., Trollip, A., Hoek, K.G., Sirgel,F.A., Gey van Pittius, N.C., van Helden, P.D., Victor, T.C., Warren, R.M.
Status Published/produced
Volume 12(4) Page from 686 Page to 694
Title Of Article Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region
Title Of Journal PLoS One
Other Authors
Weiner, B., Gomez, J., Victor, T.C., Warren, R.M., Sloutsky, A., Plikaytis, B.B., Posey, J.E., van Helden, P.D., Gey van Pittius, N.C., Koehrsen, M., Sisk, P., Stolte, C., hite, J., Gagneux, S., Birren, B., Hung, D., Murray, M., Galagan, J.
Status Published/produced Volume 7(2)
Page from e26038 Page to
Title Of Article The complex architecture of mycobacterial promoters.
Title Of Journal Tuberculosis (Edinb).
Other Authors Newton-Foot, M., Gey van Pittius, N.C.
Status Published/produced
Volume 93(1) Page from 60 Page to 74
4
3. Prof Eileen EG Hoal-Van Helden
Patent
This is an Utility patent FIELD OF THE INVENTION The invention relates to a set of ancestry informative markers which can be used to estimate the ancestry for of a group of individuals from the South African Coloured population for the purposes of adjusting for the effects of admixture in genetic studies. SUMMARY OF THE INVENTION According to a first embodiment of the invention, there is provided a set of markers for estimating the ancestry proportions of an admixed population from the South African Coloured population. The set of markers may be used to adjust for ancestry, such as when doing control studies or genetic association studies of admixed populations. The admixed population may be a group of individuals. The markers may be provided as part of a genotyping device, such as in an array or assay kit, on an array plate or on a chip array. According to a second embodiment of the invention, there is provided a method of estimating the ancestry of an admixed population or adjusting for ancestry of a group of individuals from the South African Coloured population; the method comprising the step of utilising the set of markers described above.smegmatis
Application Date 08 November 2012 Application Type Provisional
Grant Date Daya M, Möller M, van der Merwe L, Hoal EG,
Patent Status Filed Registration
Country South Africa
5
4. Prof Fourie F Joubert
Books
Chapters in Books
Title Of Book Malaria Parasites
Title Of Chapter In Silico Resources for Malaria Drug Discovery
First Author
Other Authors Pieter Burger Pieter Burger and Fourie Joubert
Editor
Status Published/produced
Page from 293 Page to 318
6
5. Prof Nicola NJ Mulder
Articles in Refereed/Peer-reviewed Journals
Title Of Article Understanding TB latency using computational and dynamic modelling
procedures.
Smegmatis
Title Of Journal Infection, Genetics and Evolution Other Authors Mulder N
Status Published/produced
Volume 13 Page from 267 Page to 283
Title Of Article Using the underlying biological organization of the Mycobacterium tuberculosis functional network for protein function prediction
Title Of Journal Infection, Genetics and Evolution
Other Authors Mulder NJ
Status Published/produced
Volume 12(5) Page from 922 Page to 932
Title Of Article Function Prediction and Analysis of Mycobacterium tuberculosis Hypothetical Proteins
Title Of Journal International Journal of Molecular Sciences
Other Authors Mulder NJ
Status Published/produced
Volume 13 Page from 7283 Page to 7302
Chapters in Books
Title Of Book A Treatise of Biological Models
Title Of Chapter Mathematical modelling of infection and treatment of Mycobacterium tuberculosis latency, Chapter 2
First Author Magombedze G
Other Authors Dube N Mulder N, Pieter Burger and Fourie Joubert
Editor Nyabadza F, Kgosimore M, Lungu EM Status Published/produced
Page from 1 Page to 19
Books
Title Of Book Tuberculosis: Risk Factors, Drug Resistance and Treatment
Title Of Chapter Enhancing drug target identification in Mycobacterium tuberculosis First Author Mazandu GK
Other Authors Mulder NJ
Editor Walker SE and Martin DF Status Published/produced
Page from 1 Page to 29
7
6. Prof AA Myburg
Articles in Refereed/Peer-reviewed Journals
Title Of Article High synteny and colinearity among Eucalyptus genomes revealed by high-density comparative genetic mapping. Solely depend on FLO gene expression.
Title Of Journal Tree Genetics and Genomes
Other Authors Hudson CJ, Kumar AR, Freeman JS, MYBURG AA, Faria D, Grattapaglia D, Kilian A, Potts BM, Vaillancourt RE
Status Published/produced
Volume Page from 339 Page to 352
Title Of Article SND2, a NAC transcription factor gene, regulates genes involved in cellulose, hemicellulose and cell wall modification in Arabidopsis fibre secondary cell walls
Title Of Journal BMC Plant Biology Other Authors Hussey SG, Mizrachi E, Berger DK, Myburg AA
Status Published/produced
Volume 11
Page from window3 Page to
Title Of Article Progress in Myrtaceae genomics: Eucalyptus as the pivotal genus
Title Of Journal Tree Genetics and Genomes
Other Authors Grattapaglia D, Vaillancourt RE, Shepherd M, Thumma B, Foley W,
Kulheim C, Potts BM, MYBURG AA
Status Published/produced
Volume 8 Page from 463 Page to 508
Title Of Article A reference linkage map for Eucalyptus
Title Of Journal BMC Genomics
Other Authors Hudson CJ, Freeman JS, Kullan ARK, Petroli CD, Sansaloni CP, Kilian A, Detering F, Grattapaglia D, Potts BM, MYBURG AA and Vaillancourt RE
Status Published/produced Volume 13
Page from 121 Page to 131
Title Of Article
Title Of Journal Genetic dissection of growth, wood basic density and gene expression in interspecific backcrosses of Eucalyptus grandis and E. urophylla BMC Genetics
Other Authors Kullan ARK, Van Dyk MM, Hefer CA, Jones N, Kanzler A, MYBURG AA
Status Published/produced
Volume 13 Page from 60 Page to
8
Title Of Article Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome
Title Of Journal PLOS ONE
Other Authors Petroli CD, Sansaloni CP, Carling J, Hudson J, Steane DA, Vaillancourt RE, MYBURG AA, da Silva OB, Pappas GJ, Kilian A, Grattapaglia D.
Status Published/produced
Volume 7(9) Page from e44684 Page to
9
7. Prof Michele M Ramsay
Articles in Refereed/Peer-reviewed Journals
Title Of Article Appetite regulation genes are associated with body mass index in black South African adolescents: agenetic association study smegmatis
Title Of Journal BMJ Open
Other Authors Lombard, Z., Crowther, N. J., van der Merwe, L., Pitamber, P., Norris, S. A., Ramsay, M.
Status Published/produced
Volume 2 Page from Page to
10
8. Prof Oleg O Reva
Articles in Refereed/Peer-reviewed Journals
Title Of Article Distribution of horizontally transferred heavy metal resistance operons in recent outbreak bacteria.Smegmatis
Title Of Journal Mob Genet Elements
Other Authors Reva O, Bezuidt O
Status Published/produced
Volume 2 Page from 96 Page to 100
Title Of Article Functional metagenomics unveils a multifunctional glycosyl hydrolase
from the family 43 catalysing
Title Of Journal PLoS One
Other Authors Ferrer M, Ghazi A, Beloqui A, Vieites JM, López-Cortés N, Marín-Navarro J, Nechitaylo TY, Guazzaroni ME, Polaina J, Waliczek A, Chernikova TN, Reva ON, Golyshina OV, Golyshin PN.
Status Published/produced
Volume 7 Page from e38134 Page to
11
9. Prof Jacky JL Snoep
Articles in Refereed/Peer-reviewed Journals
Title Of Article A mathematical modelling approach to assessing the reliability of biomarkers of glutathione metabolism
Title Of Journal European Journal of Pharmaceutical Sciences
Other Authors Geenen, S. du Preez, F.B., Reed, M., Nijhout, H.F., Kenna, J.G., Wilson, I.D., Westerhoff, H.V. and Snoep, J.L.
Status Published/produced
Volume 46 Page from 233 Page to 243
12
2013 – 2015
1. Prof Dave Berger Articles in Refereed/Peer-reviewed Journals
Title Of Article Mapping QTL conferring resistance in maize to gray leaf spot disease caused by Cercospora zeina
Title Of Journal BMC Genetics
Other Authors Berger, D.K., Carstens, M., Korsman, J.N., Middleton, F., Kloppers, F.J., Tongoona, P., Myburg, A.A.
Status Published/produced
Volume 15, 60. Page from Page to
13
2. Prof F. Brombacher
Articles in Refereed/Peer-reviewed Journals
Title Of Article A promoter-level mammalian expression atlas.
Title Of Journal Nature
Other Authors
Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M,Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U,Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple CA, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D,Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D,Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV,Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furuno M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T,Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Har
Status Published/produced
Volume 507 Page from 462 Page to 470
Title Of Article An atlas of active enhancers across human cell types and tissues.
Title Of Journal Nature
Other Authors
4.Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F; FANTOM Consortium, Forrest AR, Carninci P, Rehli M, Sandelin A, Kawaji H, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmid C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple CA, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Bl
Status Published/produced Volume 507
Page from 455 Page to 461
Title Of Article Statins mediate protection against Mycobacterium tuberculosis infection by enhancing phagosomal maturation and autophagy
Title Of Journal J. Inf. Dis.
Other Authors Suraj P. Parihar, Reto Guler, Dirk M. Lang, Rethabile Khutlang, Musa M. Mhlanga, Harukazu Suzuki, A. David Marais and Frank Brombacher.
Status Published/produced
Volume 209
Page from Page to
14
Title Of Article The IL-13/IL-4R-alpha axis is involved in tuberculosis-associated pathology.
Title Of Journal J Pathol.
Other Authors Heitmann L, Abad Dar M, Schreiber T, Erdmann H, Behrends J, Mckenzie AN, Brombacher F, Ehlers S, Hölscher C.
Status Published/produced
Volume 234
Page from 338-50 Page to 350
15
3. Prof Don Cowan Articles in Refereed/Peer-reviewed Journals
Title Of Article Draft genome sequence of the aromatic hydrocarbon-degrading bacterium Sphingobium sp. strain Ant17 isolated from Antarctic soil.
Title Of Journal Genome Announc.
Other Authors Adriaenssens EM, Guerrero LD, Makhalanyane TP, Aislabie JM, Cowan DA.
Status Published/produced Volume 2
Page from e00212-14 Page to
Title Of Article Draft genome sequence of Williamsia sp. strain D3, isolated from the Darwin Mountains, Antarctica.
Title Of Journal Genome Announc.
Other Authors Guerrero LD, Makhalanyane TP, Aislabie JM, Cowan DA. Status Published/produced
Volume 2
Page from e01230-13 Page to
Title Of Article The draft genome sequence of Antarctic poly-extremophile Nesterenkonia sp. AN1. Title Of Journal Genome Announc.
Other Authors Aliyu H, De Maayer P, Rees DJG, Tuffin IM, Cowan DA. Status Published/produced Volume 2
Page from e00197-14 Page to
Title Of Article The draft genome sequence of Microbacterium sp. CH12i, isolated from shallow groundwater in Cape Hallet, Antarctica.
Title Of Journal Genom. Announc.
Other Authors Ferreras, E, De Maayer, P, Makhalanyane, TP, Guerrero, L, Aislabie, J, Cowan, DA.
Status Published/produced Volume 2
Page from e00789-14 Page to
16
4. Prof Fourie Joubert
Articles in Refereed/Peer-reviewed Journals
Title Of Article Enabling the genomic revolution in Africa.
Title Of Journal Science
Other Authors
H3Africa Consortium, Rotimi C, Abayomi A, Abimiku A, Adabayeri VM, Adebamowo C, Adebiyi E, Ademola AD, Adeyemo A, Adu D, Affolabi D, Agongo G, Ajayi S, Akarolo-Anthony S, Akinyemi R, Akpalu A, Alberts M, Alonso Betancourt O, Alzohairy AM, Ameni G, Amodu O, Anabwani G, Andersen K, Arogundade F, Arulogun O, Asogun D, Bakare R, Balde N, Baniecki ML, Beiswanger C, Benkahla A, Bethke L, Boehnke M, Boima V, Brandful J, Brooks AI, Brosius FC, Brown C, Bucheton B, Burke DT, Burnett BG, Carrington-Lawrence S, Carstens N, Chisi J, Christoffels A, Cooper R, Cordell H, Crowther N, Croxton T, de Vries J, Derr L, Donkor P, Doumbia S, Duncanson A, Ekem I, El Sayed A, Engel ME, Enyaru JC, Everett D, Fadlelmola FM, Fakunle E, Fischbeck KH, Fischer A, Folarin O, Gamieldien J, Garry RF, Gaseitsiwe S, Gbadegesin R, Ghansah A, Giovanni M, Goesbeck P, Gomez-Olive FX, Grant DS, Grewal R, Guyer M, Hanchard NA, Happi CT, Hazelhurst S, Hennig BJ, Hertz- C, Fowler, Hide W, Hilderbrandt F, Hugo-Hamman C, Ibrahim
Status Published/produced
Volume 344
Page from 1346 Page to 1348
Title Of Article Genome sequence of Eucalyptus grandis: A global tree crop for fiber and energy.
Title Of Journal Nature.
Other Authors
Alexander A. Myburg, Dario Grattapaglia, Gerald A. Tuskan, Uffe Hellsten, Richard D. Hayes, Jane Grimwood, Jerry Jenkins, Erika Lindquist, Hope Tice, Diane Bauer, David M. Goodstein, Inna Dubchak, Alexandre Poliakov, Eshchar Mizrachi, Anand R.K. Kullan, Ida van Jaarsveld, Steven G. Hussey, Desre Pinard, Karen van der Merwe, Orzenil B. Silva-Junior, Roberto C. Togawa, Marilia R. Pappas, Danielle A. Faria, Carolina P. Sansaloni, Cesar D. Petroli, Xiaohan Yang, Priya Ranjan, Timothy J. Tschaplinski, Chu-Yu Ye, Ting Li, Lieven Sterck, Kevin Vanneste, Florent Murat, Marcal Soler, Helene San Clemente, Naijib Saidi, Hua Cassan-Wang, Christophe Dunand, Charles A. Hefer, Erich Bornberg-Bauer, Anna R. Kersting, Kelly Vining, Vindhya Amarasinghe, Martin Ranik, Sushma Naithani, Justin Elser, Alexander E. Boyd, Aaron Liston, Joseph W. Spatafora, Palitha Dharmwardhana, Rajani Raja, Christopher Sullivan, Elisson Romanel, Marcio Alves-Ferreira, Carsten Külheim, William Foley, Victor Carocha, Jorge Pai
Status Published/produced
Volume 509
Page from 356 Page to 362
17
5. Dr Martin Articles in Refereed/Peer-reviewed Journals
Title Of Article Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context
Title Of Journal PLoS One
Other Authors Candresse T, Filloux D, Muhire B, Julian C, Galzi S, Fort G, Bernardo P, Daugrois JH, Fernandez E, Martin DP, Varsani A, Roumagnac P
Status Published/produced
Volume 9(7):e102945. doi: 10.1371/journal.pone.0102945. eCollection 2014.
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Title Of Article Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses.
Title Of Journal J Virol.
Other Authors Muhire BM, Golden M, Murrell B, Lefeuvre P, Lett JM, Gray A, Poon AY, Ngandu NK, Semegni Y, Tanov EP, Monjane AL, Harkins GW, Varsani A, Shepherd DN, Martin DP.
Status Published/produced
Volume 88(4):1972-89. doi: 10.1128/JVI.03031-13
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Title Of Article Extensive recombination-induced disruption of genetic interactions is highly deleterious but can be partially reversed by small numbers of secondary recombination events.
Title Of Journal J Virol.
Other Authors Monjane AL, Martin DP, Lakay F, Muhire BM, Pande D, Varsani A, Harkins G, Shepherd DN, Rybicki EP.
Status Published/produced Volume 88(14):7843-51. doi: 10.1128/JVI.00709-14
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Title Of Article Patterns of recombination in HIV-1M are influenced by selection disfavouring the survival of recombinants with disrupted genomic RNA and protein structures.
Title Of Journal PLoS One
Other Authors Golden M, Muhire BM, Semegni Y, Martin DP
Status Published/produced Volume 9(6):e100400. doi
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Title Of Article Patterns of recombination in HIV-1M are influenced by selection disfavouring the survival of recombinants with disrupted genomic RNA and protein structures.
Title Of Journal PLoS One
Other Authors Golden M, Muhire BM, Semegni Y, Martin DP
Status Published/produced Volume 9(6):e100400. doi: 10.1371/journal.pone.0100400. eCollection 2014.
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18
Title Of Article Pigeon circoviruses display patterns of recombination, genomic secondary structure and selection similar to those of beak and feather disease viruses.
Title Of Journal J Gen Virol
Other Authors Stenzel T, Piasecki T, Chrzastek K, Julian L, Muhire BM, Golden M, Martin DP, Varsani A.
Status Published/produced
Volume 95(Pt 6):1338-51. doi: 10.1099/vir.0.063917-0. Epub 2014 Mar 17
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Title Of Article The influence of secondary structure, selection and recombination on rubella virus nucleotide substitution rate estimates
Title Of Journal Virol J.
Other Authors Cloete LJ, Tanov EP, Muhire BM, Martin DP, Harkins GW
Status Published/produced
Volume 11:166. doi: 10.1186/1743-422X-11-166 Page from Page to
19
6. Prof Mulder Articles in Refereed/Peer-reviewed Journals
Title Of Article Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance.
Title Of Journal BMC Genomics
Other Authors Choudhury A, Hazelhurst S, Meintjes A, Achinike-Oduaran O, Aron S, Gamieldien J, Sefid Dashti MJ, Mulder N, Tiffin N and Ramsay M.
Status Published/produced
Volume 15
Page from 437 Page to
Title Of Article Using biological networks to improve our understanding of infectious diseases.
Title Of Journal Computational and Structural Biotechnology Journal Other Authors Mulder, N.J., Akinola, R.O., Mazandu, G.K., Rapanoel, H.
Status Published/produced Volume 11
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20
7. Prof Myburg
Articles in Refereed/Peer-reviewed Journals
Title Of Article Cell Wall-related Proteins of Unknown Function: Missing Links in Plant Cell
Wall Development.
Title Of Journal Plant and Cell Physiology Other Authors Mewalal R, Mizrachi E, Mansfield SD, Myburg AA
Status Published/produced
Volume 55 Page from 1031 Page to 1043
Title Of Article Investigating the molecular underpinnings underlying morphology and changes in carbon partitioning during tension wood formation in Eucalyptus
Title Of Journal New Phytologist Other Authors 52. Mizrachi E, Malonie V, Silberbauer J, Hefer C, Berger DK, Mansfield SD,
MYBURG AA Status Published/produced
Volume Page from Page to
Title Of Article Protein domain evolution is associated with reproductive diversification and adaptive radiation in the genus Eucalyptus
Title Of Journal New Phytologist
Other Authors Kersting AR, Mizrachi E, Bornberg-Bauer E, Myburg AA.
Status Published/produced
Volume Page from Page to
Title Of Article Recombinant hyperthermophilic enzyme expression in plants: a novel approach for lignocellulose digestion
Title Of Journal Trends in Biotechnology
Other Authors Mir BA, Mewalal R, Mizrachi E, Myburg AA, Cowan DA
Status Published/produced Volume 32
Page from 281 Page to 289
Title Of Article Structural, evolutionary and expression analysis of the NAC domain protein
family in Eucalyptus. Title Of Journal New Phytologist
Other Authors Hussey SG, Saïdi MN, Hefer CA, MYBURG AA, Grima-Pettenati J.
Status Published/produced
Volume Page from Page to
21
Title Of Article The Eucalyptus grandis R2R3-MYB transcription factor family: evidence for woody growth related evolution and function
Title Of Journal New Phytologist
Other Authors Soler M, Camargo ELO, Carocha V, Cassan-Wang H, Clemente SH, Savelli B,
Hefer CA, Myburg Aa, Paiva JP, Grima-Pettenati J.
Status Published/produced
Volume Page from Page to
Title Of Article The floral transcriptome of Eucalyptus grandis
Title Of Journal New Phytologist
Other Authors Vining K, Elisson R, Jones R, Klocko A, Alves-Ferreira M, Hefer CA, Amarasinghe V, Dharmawardhana P, Naithani S, Ranik M, Wesley-Smith J, Jaiswal P, MYBURG AA, Solomon L, Strauss S
Status Published/produced
Volume
Page from Page to
Title Of Article The genome of Eucalyptus grandis
Title Of Journal Nature
Other Authors Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, et al.
Status Published/produced
Volume 510 Page from 356 Page to 362
Title Of Article Uncovering the defence responses of Eucalyptus to pests and pathogens in
the genomics age Title Of Journal Tree Physiology
Other Authors Naidoo S, Zwart L, Kulheim C, Mangwanda R, Oates CN, Visser EA, Wilken FE, Mamni TB and MYBURG AA.
Status Published/produced
Volume 34 Page from 931 Page to 943
22
8. Prof Reva
Books
Chapters in Books
Title Of Book Bioinformatics and Data Analysis in Microbiology
Title Of Chapter Genetic Barcoding of Bacteria and its Microbiology and Biotechnology Applications
First Author
Other Authors Reva ON, Chan WY, Bezuidt OKI, Lapa SV, Safronova LA, Avdeeva LV, Borriss R.
Editor Özlem Taştan Bishop Status Published/produced
Page from 1 Page to 1 Refereed/Peer-reviewed Conference Outputs
Title Of Conference Title Of
Proceedings 35th annual Lorne Genome Conference 2014
Title Of
Contribution
Tracking down the distribution of horizontally acquired mobile genetic elements (MGE) in bacteria and estimation of their role in bacterial evolution by using Pre_GI database and incorporated analytical tools
First Author
Other Authors Oleg Reva, Rian Pierneef, Oliver Bezuidt
Page from 235 Page to 235
Title Of Conference
Title Of
Proceedings
The Ninth International Conference on Bioinformatics of Genome Regulation and Structure/Systems Biology, Novosibirsk, Russia, June 23-28, 2014.
Title Of
Contribution Role of the horizontal gene exchange in evolution of pathogenic Mycobacteria
First Author
Other Authors Reva O, Korotetskiy I, Ilin A
Page from 136 Page to 137
23
9. Prof Travers
Refereed/Peer-reviewed Conference Outputs
Title Of Conference
Title Of Proceedings HIV Research For Prevention
Title Of Contribution Using molecular dynamics to investigate the effects of N-linked glycosylation on the gp120 envelope trimer of HIV-1.
First Author
Other Authors Mercuur C, Wood N, Fadda E, Grant O, Woods R &Travers SA
Page from Page to
Title Of Conference
Title Of Proceedings HIV Research For Prevention
Title Of Contribution The Dynamics of HIV-1 gp120 N-linked Glycans in the Context of Broadly Cross-Neutralizing Antibodies
First Author Other Authors Gabier E, Wood N, Fadda E, Grant O, Woods R, Travers SA
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Title Of Conference Title Of Proceedings HIV Research For Prevention
Title Of Contribution Exploring the influence of oligomannose and complex glycans on the molecular dynamics of HIV-1 gp120 in the context of viral coreceptor tropism.
First Author
Other Authors Wood N, Fadda E, Grant O, Woods R, Travers SA
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Title Of Conference
Title Of Proceedings 5th Warren Workshop
Title Of Contribution Exploring the influence of oligomannose and complex glycans on the molecular dynamics of HIV-1 gp120 in the context of viral coreceptor tropism.
First Author
Other Authors Wood N, Fadda E, Grant O, Woods R, Travers SA
Page from Page to
Refereed/Peer-reviewed Conference Outputs
Title Of Conference
Title Of Proceedings 2nd Joint Congress of the South African Society for Bioinformatics (SASBi) and the South African Genetics Society (SAGS)
Title Of Contribution Exploring the influence of oligomannose and complex glycans on the molecular dynamics of HIV-1 gp120 in the context of viral coreceptor tropism.
First Author
Other Authors Wood N, Fadda E, Grant O, Woods R, Travers SA
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24
Title Of Conference
Title Of Proceedings 21st International HIV Dynamics and Evolution Conference
Title Of Contribution EXPLORING THE INFLUENCE OF OLIGOMANNOSE AND COMPLEX GLYCANS ON THE MOLECULAR DYNAMICS OF HIV 1 GP120 IN THE CONTEXT OF VIRAL CORECEPTOR TROPISM
First Author
Other Authors Natasha Wood, Elisa Fadda, Oliver Grant, Robert Woods, Simon Travers
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25
10. Prof Vorster
Articles in Refereed/Peer-reviewed Journals
Title Of Article Cysteine protease and cystatin expression and activity during soybean nodule development and senescence.
Title Of Journal BMC Plant Biology
Other Authors SG Van Wyk, M Du Plessis, CA Cullis, KJ Kunert and BJ Vorster
Status Published/produced Volume
Page from 1 Page to 13
Title Of Article Proteolysis of recombinant proteins in bioengineered plant cells Title Of Journal Bioengineered
Other Authors P Pillay, U Schlüter, S van Wyk, KJ Kunert, and BJ Vorster
Status Published/produced
Volume 5 Page from 1 Page to 6
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