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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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.
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
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
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.
Title Of Journal PLoS One
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.
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.
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.
Status Published/produced
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
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
Page from Page to
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
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
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
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
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
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