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)


● 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)


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]


09:00 Report Writing

10:30 Tea/coffee


13:00 Lunch


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



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


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.


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.


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.



3

2. Prof Nico NC Gey van Pittius


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.


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.


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.


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.



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



6

5. Prof Nicola NJ Mulder


Title Of Article Understanding TB latency using computational and dynamic modelling

procedures.

Smegmatis

Title Of Journal Infection, Genetics and Evolution Other Authors Mulder N



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



Title Of Article Function Prediction and Analysis of Mycobacterium tuberculosis Hypothetical Proteins

Title Of Journal International Journal of Molecular Sciences




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


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


Editor Walker SE and Martin DF Status Published/produced


7

6. Prof AA Myburg


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


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


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



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


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


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.


Volume 7(9) Page from e44684 Page to

9

7. Prof Michele M Ramsay


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.


Volume 2 Page from Page to

10

8. Prof Oleg O Reva


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



Title Of Article Functional metagenomics unveils a multifunctional glycosyl hydrolase

from the family 43 catalysing


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.


Volume 7 Page from e38134 Page to

11

9. Prof Jacky JL Snoep


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.



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.


Volume 15, 60. Page from Page to

13

2. Prof F. Brombacher


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



Title Of Article An atlas of active enhancers across human cell types and tissues.


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



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.


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.


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.


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


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


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.



16

4. Prof Fourie Joubert


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


Volume 344


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


Volume 509


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


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


Volume 9(7):e102945. doi: 10.1371/journal.pone.0102945. eCollection 2014.

Page from Page to

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.


Volume 88(4):1972-89. doi: 10.1128/JVI.03031-13

Page from Page to

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

Page from Page to

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.


Other Authors Golden M, Muhire BM, Semegni Y, Martin DP

Status Published/produced Volume 9(6):e100400. doi

Page from Page to

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.


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.

Page from Page to

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.


Volume 95(Pt 6):1338-51. doi: 10.1099/vir.0.063917-0. Epub 2014 Mar 17

Page from Page to

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


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.


Volume 15

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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.


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20

7. Prof Myburg


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



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


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.



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



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.



21

Title Of Article The Eucalyptus grandis R2R3-MYB transcription factor family: evidence for woody growth related evolution and function


Other Authors Soler M, Camargo ELO, Carocha V, Cassan-Wang H, Clemente SH, Savelli B,

Hefer CA, Myburg Aa, Paiva JP, Grima-Pettenati J.



Title Of Article The floral transcriptome of Eucalyptus grandis


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


Volume

Page from Page to

Title Of Article The genome of Eucalyptus grandis


Other Authors Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, et al.



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.



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


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


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

Page from Page to

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

Page from Page to

Title Of Conference

Title Of Proceedings 5th Warren Workshop


First Author


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)


First Author


Page from Page to

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

Page from Page to

25

10. Prof Vorster


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


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



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Documents

2015 NRF-Managed Bioinformatics and Functional Genomics