Applied Bioinformatics Group - User contributions [en]

Clementine Merce

2020-03-30T05:32:02Z

Clem: /* Publications */

==Academic history==

*Master degree in Bioinformatics
*Licence of Cellular biology and physiology

==Publications==

*Lepesant JMJ, Iampietro C, Galeota E, Augé B, Aguirrenbengoa M, Mercé C, Chaubet C, Rocher V, Haenlin M, Waltzer L, Pelizzola M, Di Stefano L (2020)

Nucleic Acids Res. doi: 10.1093/nar/gkz1142

*Steffen Dietz, Uwe Schirmer, Clémentine Mercé, Nikolas von Bubnoff, Edgar Dahl, Michael Meister, Thomas Muley, Michael Thomas, Holger Sültmann (2017)

Low Input Whole-Exome Sequencing to Determine the Representation of the Tumor Exome in Circulating DNA of Non-Small Cell Lung Cancer Patients

PONE-D-16-16634R1

*Minia I, Merce C, Terrao M, Clayton C. (2016)

Translation Regulation and RNA Granule Formation after Heat Shock of Procyclic Form Trypanosoma brucei: Many Heat-Induced mRNAs Are also Increased during Differentiation to Mammalian-Infective Forms.

PLoS Negl Trop Dis. doi: 10.1371/journal.pntd.0004982

*Antwi EB, Haanstra JR, Ramasamy G, Jensen B, Droll D, Rojas F, Minia I, Terrao M, Mercé C, Matthews K, Myler PJ, Parsons M, Clayton C. (2016)

Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression.

BMC Genomics doi: 10.1186/s12864-016-2624-3

*Lueong S, Merce C, Fischer B, Hoheisel JD, Erben ED (2016)

Gene expression regulatory networks in Trypanosoma brucei: Insights into the role of the mRNA-binding proteome.

Mol Microbiol doi: 10.1111/mmi.13328

*Mulindwa J, Mercé C, Matovu E, Enyaru J, Clayton C. (2015)

Transcriptomes of newly-isolated Trypanosoma brucei rhodesiense reveal hundreds of mRNAs that are co-regulated with stumpy-form markers.

BMC Genomics. 16(1):1118. doi: 10.1186/s12864-015-2338-y

*Fadda A, Ryten M, Droll D, Rojas F, Färber V, Haanstra JR, Merce C, Bakker BM, Matthews K, Clayton C.(2014)

Transcriptome-wide analysis of trypanosome mRNA decay reveals complex degradation kinetics and suggests a role for co-transcriptional degradation in determining mRNA levels.

Mol Microbiol. 307-26. doi: 10.1111/mmi.12764

*Mulindwa J, Fadda A, Merce C, Matovu E, Enyaru J, Clayton C. (2014)

Methods to determine the transcriptomes of trypanosomes in mixtures with mammalian cells: the effects of parasite purification and selective cDNA amplification.

PLoS Negl Trop Dis. 8(4):e2806. doi: 10.1371/journal.pntd.0002806

*Jha BA, Fadda A, Merce C, Mugo E, Droll D, Clayton C. (2014)

Depletion of the Trypanosome Pumilio domain protein PUF2 or of some other essential proteins causes transcriptome changes related to coding region length.

Eukaryot Cell. 13(5):664-74. doi: 10.1128/EC.00018-14

==Contact==

Clementine Merce

School of Plant Biology

University of Western Australia

Perth, 6009

Australia

Clementine Merce

2020-03-30T05:31:19Z

Clem: /* Publications */

==Academic history==

*Master degree in Bioinformatics
*Licence of Cellular biology and physiology

==Publications==

*Lepesant JMJ, Iampietro C, Galeota E, Augé B, Aguirrenbengoa M, Mercé C, Chaubet C, Rocher V, Haenlin M, Waltzer L, Pelizzola M, Di Stefano L (2020)

Nucleic Acids Res. doi: 10.1093/nar/gkz1142

*Steffen Dietz, Uwe Schirmer, Clémentine Mercé, Nikolas von Bubnoff, Edgar Dahl, Michael Meister, Thomas Muley, Michael Thomas, Holger Sültmann (2017)

Low Input Whole-Exome Sequencing to Determine the Representation of the Tumor Exome in Circulating DNA of Non-Small Cell Lung Cancer Patients

PONE-D-16-16634R1

*Minia I, Merce C, Terrao M, Clayton C. (2016)

Translation Regulation and RNA Granule Formation after Heat Shock of Procyclic Form Trypanosoma brucei: Many Heat-Induced mRNAs Are also Increased during Differentiation to Mammalian-Infective Forms.

PLoS Negl Trop Dis. doi: 10.1371

*Antwi EB, Haanstra JR, Ramasamy G, Jensen B, Droll D, Rojas F, Minia I, Terrao M, Mercé C, Matthews K, Myler PJ, Parsons M, Clayton C. (2016)

Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression.

BMC Genomics doi: 10.1186/s12864-016-2624-3

*Lueong S, Merce C, Fischer B, Hoheisel JD, Erben ED (2016)

Gene expression regulatory networks in Trypanosoma brucei: Insights into the role of the mRNA-binding proteome.

Mol Microbiol doi: 10.1111/mmi.13328

*Mulindwa J, Mercé C, Matovu E, Enyaru J, Clayton C. (2015)

Transcriptomes of newly-isolated Trypanosoma brucei rhodesiense reveal hundreds of mRNAs that are co-regulated with stumpy-form markers.

BMC Genomics. 16(1):1118. doi: 10.1186/s12864-015-2338-y

*Fadda A, Ryten M, Droll D, Rojas F, Färber V, Haanstra JR, Merce C, Bakker BM, Matthews K, Clayton C.(2014)

Transcriptome-wide analysis of trypanosome mRNA decay reveals complex degradation kinetics and suggests a role for co-transcriptional degradation in determining mRNA levels.

Mol Microbiol. 307-26. doi: 10.1111/mmi.12764

*Mulindwa J, Fadda A, Merce C, Matovu E, Enyaru J, Clayton C. (2014)

Methods to determine the transcriptomes of trypanosomes in mixtures with mammalian cells: the effects of parasite purification and selective cDNA amplification.

PLoS Negl Trop Dis. 8(4):e2806. doi: 10.1371/journal.pntd.0002806

*Jha BA, Fadda A, Merce C, Mugo E, Droll D, Clayton C. (2014)

Depletion of the Trypanosome Pumilio domain protein PUF2 or of some other essential proteins causes transcriptome changes related to coding region length.

Eukaryot Cell. 13(5):664-74. doi: 10.1128/EC.00018-14

==Contact==

Clementine Merce

School of Plant Biology

University of Western Australia

Perth, 6009

Australia

Main Page

2017-10-09T08:27:41Z

Clem: /* Master students */

==About the group==

The applied bioinformatics group was founded in 2007 at the University of Queensland and moved to the University of Western Australia in January 2015. Since this time, the group has established itself as a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation.

The group receives funding from the [http://www.uwa.edu.au/ University of Western Australia], the [http://www.arc.gov.au/ Australian Research Council], the [http://www.grdc.com.au/ Grains Research and Development Corporation] and several industry partners to undertake applied bioinformatics research in genetics and genomics.

The group is led by Professor [[David Edwards]] and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and [[publications_DE|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:Dave.Edwards@uwa.edu.au David Edwards] for further information.

We are based at the University of Western Australia's Crawley campus in Perth, Australia.

==Publications==

We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&hl=en Google Scholar]

==Public research projects==

The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups.

===[[Genome sequencing]]===

:[http://www.wheatgenome.info Wheat genome sequencing]

:[http://www.brassicagenome.net Brassica genome sequencing]

:[http://www.cicer.info/ Chickpea genome sequencing]

:[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]

:[[Metagenomics]]

:[[TAGdb]]

===Transcriptomics===

:[[A differential kmer analysis pipeline]]

===Molecular marker discovery===

:[[SNP discovery]]

:[[SSR discovery]]

:[[Genetic map visualisation]]

===Genome annotation and visualisation===

:[[Gene and genome annotation]]

===Knowledge networks===

:[[QTLNetMiner collaboration with Rothamstead Research]]

===Species of interest include:===

:[[Brassica]]

:[[Chickpea]]

:[[Wheat]]

:[[Seagrass]]

:[[Other legumes]]

:[[Metagenomics]]

==Group members==

===Group leader===

[[David Edwards]]

===Postdocs===

[[Kenneth Chan]]

[[Philipp Bayer]]

[[Jenny (HueyTyng) Lee]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Habib Rijzaani]]

[[Andy Yuan]]

[[Armin Scheben]]

[[Bhavna Hurgobin]]

[[Juan Montenegro]]

[[Seyedehmahsa Mousaviderazmahalleh (Mahsa Mousavi)]]

[[Ricky Hu]]

[[Clementine Merce]]

Positions available, please contact David Edwards if interested

=== Master students ===

Positions available, please contact David Edwards if interested

=== Honours students ===

Positions available, please contact David Edwards if interested

=== Interns ===

Positions available, please contact David Edwards if interested

===[[Alumni]]===

===Positions available===

There are current positions available at all levels including Postdoc, PhD students and Interns. Candidates should have a good understanding of one or more areas of Computing, Software development, Complex data analysis, Bioinformatics or Genomics. For consideration, please forward your cv and cover letter to Dave.Edwards@uwa.edu.au.

Main Page

2017-10-09T08:27:32Z

Clem: /* Postdocs */

Main Page

2017-10-09T08:24:01Z

Clem: /* PhD students */

Clementine Merce

2017-10-09T08:16:47Z

Clem: /* Contact */

==Academic history==

*Master degree in Bioinformatics
*Licence of Cellular biology and physiology

==Publications==

*Steffen Dietz, Uwe Schirmer, Clémentine Mercé, Nikolas von Bubnoff, Edgar Dahl, Michael Meister, Thomas Muley, Michael Thomas, Holger Sültmann (2017)

Low Input Whole-Exome Sequencing to Determine the Representation of the Tumor Exome in Circulating DNA of Non-Small Cell Lung Cancer Patients

PONE-D-16-16634R1

*Antwi EB, Haanstra JR, Ramasamy G, Jensen B, Droll D, Rojas F, Minia I, Terrao M, Mercé C, Matthews K, Myler PJ, Parsons M, Clayton C. (2016)

Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression.

BMC Genomics doi: 10.1186/s12864-016-2624-3

*Lueong S, Merce C, Fischer B, Hoheisel JD, Erben ED (2016)

Gene expression regulatory networks in Trypanosoma brucei: Insights into the role of the mRNA-binding proteome.

Mol Microbiol doi: 10.1111/mmi.13328

*Mulindwa J, Mercé C, Matovu E, Enyaru J, Clayton C. (2015)

Transcriptomes of newly-isolated Trypanosoma brucei rhodesiense reveal hundreds of mRNAs that are co-regulated with stumpy-form markers.

BMC Genomics. 16(1):1118. doi: 10.1186/s12864-015-2338-y

*Fadda A, Ryten M, Droll D, Rojas F, Färber V, Haanstra JR, Merce C, Bakker BM, Matthews K, Clayton C.(2014)

Transcriptome-wide analysis of trypanosome mRNA decay reveals complex degradation kinetics and suggests a role for co-transcriptional degradation in determining mRNA levels.

Mol Microbiol. 307-26. doi: 10.1111/mmi.12764

*Mulindwa J, Fadda A, Merce C, Matovu E, Enyaru J, Clayton C. (2014)

Methods to determine the transcriptomes of trypanosomes in mixtures with mammalian cells: the effects of parasite purification and selective cDNA amplification.

PLoS Negl Trop Dis. 8(4):e2806. doi: 10.1371/journal.pntd.0002806

*Jha BA, Fadda A, Merce C, Mugo E, Droll D, Clayton C. (2014)

Depletion of the Trypanosome Pumilio domain protein PUF2 or of some other essential proteins causes transcriptome changes related to coding region length.

Eukaryot Cell. 13(5):664-74. doi: 10.1128/EC.00018-14

==Contact==

Clementine Merce

School of Plant Biology

University of Western Australia

Perth, 6009

Australia

Clementine Merce

2017-10-09T08:16:21Z

Clem: /* Publications */

==Academic history==

*Master degree in Bioinformatics
*Licence of Cellular biology and physiology

==Publications==

*Steffen Dietz, Uwe Schirmer, Clémentine Mercé, Nikolas von Bubnoff, Edgar Dahl, Michael Meister, Thomas Muley, Michael Thomas, Holger Sültmann (2017)

Low Input Whole-Exome Sequencing to Determine the Representation of the Tumor Exome in Circulating DNA of Non-Small Cell Lung Cancer Patients

PONE-D-16-16634R1

*Antwi EB, Haanstra JR, Ramasamy G, Jensen B, Droll D, Rojas F, Minia I, Terrao M, Mercé C, Matthews K, Myler PJ, Parsons M, Clayton C. (2016)

Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression.

BMC Genomics doi: 10.1186/s12864-016-2624-3

*Lueong S, Merce C, Fischer B, Hoheisel JD, Erben ED (2016)

Gene expression regulatory networks in Trypanosoma brucei: Insights into the role of the mRNA-binding proteome.

Mol Microbiol doi: 10.1111/mmi.13328

*Mulindwa J, Mercé C, Matovu E, Enyaru J, Clayton C. (2015)

Transcriptomes of newly-isolated Trypanosoma brucei rhodesiense reveal hundreds of mRNAs that are co-regulated with stumpy-form markers.

BMC Genomics. 16(1):1118. doi: 10.1186/s12864-015-2338-y

*Fadda A, Ryten M, Droll D, Rojas F, Färber V, Haanstra JR, Merce C, Bakker BM, Matthews K, Clayton C.(2014)

Transcriptome-wide analysis of trypanosome mRNA decay reveals complex degradation kinetics and suggests a role for co-transcriptional degradation in determining mRNA levels.

Mol Microbiol. 307-26. doi: 10.1111/mmi.12764

*Mulindwa J, Fadda A, Merce C, Matovu E, Enyaru J, Clayton C. (2014)

Methods to determine the transcriptomes of trypanosomes in mixtures with mammalian cells: the effects of parasite purification and selective cDNA amplification.

PLoS Negl Trop Dis. 8(4):e2806. doi: 10.1371/journal.pntd.0002806

*Jha BA, Fadda A, Merce C, Mugo E, Droll D, Clayton C. (2014)

Depletion of the Trypanosome Pumilio domain protein PUF2 or of some other essential proteins causes transcriptome changes related to coding region length.

Eukaryot Cell. 13(5):664-74. doi: 10.1128/EC.00018-14

==Contact==

Clementine Merce

PhD Candidate

School of Plant Biology

University of Western Australia

Perth, 6009

Australia

Clementine Merce

2017-10-09T08:12:24Z

Clem: /* Academic history */

==Academic history==

*Master degree in Bioinformatics
*Licence of Cellular biology and physiology

==Publications==

==Contact==

Clementine Merce

PhD Candidate

School of Plant Biology

University of Western Australia

Perth, 6009

Australia

Clementine Merce

2017-10-09T08:11:51Z

Clem: Created page with "==Academic history== *Master degree in Bioinformatics ==Publications== ==Contact== Clementine Merce PhD Candidate School of Plant Biology University of Western Australi..."

==Academic history==

*Master degree in Bioinformatics

==Publications==

==Contact==

Clementine Merce

PhD Candidate

School of Plant Biology

University of Western Australia

Perth, 6009

Australia

Main Page

2017-10-09T08:05:13Z

Clem: /* PhD students */