Curriculum Vitae


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\ssection{EDUCATION BACKGROUND}
\textbf{09/2015 PhD in Natural Sciences (Biology)}\quad Justus Liebig University Giessen, Germany\\
\indent Dissertation topic: 'Towards an in-depth view of the reproductive biology of \textit{Schistosoma mansoni}: from gonad isolation to sub-transcriptomics and cell culture'\\
	
\ssection{RESEARCH EXPERIENCE}
\textbf{03/2017 - present\quad Computational Biologist}\quad Wellcome Trust Sanger Institute, UK.\\
  \indent - Bioinformatics.\\
  \indent - Genome Annotation of \textit{Schistosoma mansoni}.\\
  \indent - Analysis of NGS data, including RNA-seq, Chip-Seq, and scRNA-seq.\\
\noindent\textbf{10/2015 - 02/2017\quad Postdoctoral research}\quad Justus Liebig University Giessen, Germany.\\
  \indent - Cell culture and cell line establishment in \textit{Schistosoma mansoni}.\\
  \indent - Single-cell transcriptomics of vitellocytes and oocytes.\\
  \indent - Differential gene expression analysis of cells at different stages.\\
  \indent - Functional analyses of target genes (RNAi, culture effect, etc.).\\  
\noindent\textbf{10/2011 - 06/2015\quad Doctoral research}\quad Justus Liebig University Giessen, Germany. Supervisor: Prof. Dr. Christoph G. Grevelding.\\
  \indent - Establishment of a gonad-isolation approach for adult schistosomes (partial contribution).\\
  \indent - Comparative transcriptomics of gonads and worms by RNA-Seq.\\
  \indent - Proteomic analyse of schistosome ovary.\\
  \indent - Isolation and characterisation of vitelline cells.\\

\ssection{PRESENTATIONS}
\noindent \textbf{British Society for Parasitology (BSP) Spring Meeting 2018}. \quad 8-11 April 2018, Aberystwyth, UK.\\
\indent Poster: 'High-quality genome annotation for the V7 assembly of \textit{Schistosoma mansoni}'\\
\noindent \textbf{Molecular and Cellular Biology of Helminths X}. \quad 4-9 September 2016, Hydra, Greece.\\
\indent Poster: 'Gonad-specific and pairing-dependent gene expression in \textit{Schistosoma mansoni}'\\
\noindent\textbf{International Symposium on Waterborne Diseases and Emerging Parasitic Diseases}.\quad 25-27 November 2014, Guangzhou, China. \\
 \indent Talk: 'Towards an in-depth view of the reproductive biology of \textit{Schistosoma mansoni}: from gonad isolation to subtranscriptomics and cell culture'\\
\noindent \textbf{Lectures for graduate students}. \quad25 November 2014, Wuhan, China. \\
 \indent 1. 'Towards the establishment of cell lines in schistosomes - Cell isolation and characterisation as a basis'; 2. 'Tools for RNA-Seq data (and ordinary work)'\\
\noindent \textbf{7th Annual GGL Conference 2014}. \quad 17-18 September 2014, Giessen, Germany.\\
  \indent Talk: 'Organ-specific sub-transcriptome analyses reveal pairing-dependent processed in the gonads of \textit{Schistosoma mansoni}'\\
\noindent \textbf{Molecular and Cellular Biology of Helminths VIII}. \quad 1-6 September 2014, Hydra, Greece.\\
  \indent Poster: 'Isolation and characterization of vitelline cells from \textit{Schistosoma mansoni}'\\
\noindent \textbf{'Current Topics in Infection Biology' Seminar}. \quad 15 July 2014, Giessen, Germany.\\
  \indent Talk: 'Understanding the sexual maturation of schistosome females: lessons from isolated organs and cells'\\
\noindent \textbf{6th Annual GGL Conference 2013}.\quad 11-12 September 2013, Giessen, Germany.\\
  \indent Poster: 'Understanding female development in \textit{Schistosoma mansoni}: ovaries and vitellaria as a basis'\\
\noindent \textbf{5th Annual GGL Conference 2012}.\quad 18-19 September 2012, Giessen, Germany.\\
 \indent Poster: 'Improved method for the isolation of reproductive organs from \textit{Schistosoma mansoni}'

\ssection{PUBLICATIONS}
\textbf{Research Papers}\\
\noindent - Zhao L, \textbf{Lu Z}, He X, Mughal MN, Fang R, Zhou Y, Zhao J, Gasser RB, Grevelding CG, Ye Q, Hu M, 2018. Serine/threonine protein phosphatase 1 (PP1) control growth and reproduction in \textit{Schistosoma japonicum}. FASEB J. 2018 Jun 7:fj201800725R. doi: 10.1096/fj.201800725R.\\
\noindent - \textbf{Lu Z}, Berriman M, 2018. Meta-analysis of RNA-seq studies reveals genes responsible for life stage-dominant functions in \textit{Schistosoma mansoni}. bioRxiv 308189; doi: https://doi.org/10.1101/308189\\
\noindent - \textbf{Lu Z}, Zhang Y, Berriman M, 2018. A web protal for gene expression across all life stages of \textit{Schistosoma mansoni}. bioRxiv 308213; doi: https://doi.org/10.1101/308213\\
\noindent - Hahnel S, Wheeler N, \textbf{Lu Z}, Wangwiwatsin A, McVeigh P, Maule A, Berriman M, Day T, Ribeiro P, Grevelding CG, 2017. Tissue-specific transcriptome analyses provide new insights into GPCR signaling in adult \textit{Schistosoma mansoni}. PLoS Pathogens 14(1): e1006718. https://doi.org/10.1371/journal.ppat.1006718\\
\noindent - \textbf{Lu Z}, Zhang Y, 2017. Facilitated analysis of large data sets by interactive visualisation. bioRxiv 178616; doi: https://doi.org/10.1101/178616\\
\noindent - \textbf{Lu Z}, Sessler F, Holroyd N, Hahnel S, Quack T, Berriman M, Grevelding CG, 2017. A gene expression atlas of adult schistosomes and their gonads. Sci Data 4: 170118. doi:10.1038/sdata.2017.118\\
\noindent - \textbf{Lu Z}, Sessler F, Holroyd N, Hahnel S, Quack T, Berriman M, Grevelding CG, 2016. Schistosome sex matters: a deep view into gonad-specific and pairing-dependent transcriptomes reveals a complex gender interplay. Sci. Rep. 6. no31150. doi:10.1038/srep31150\\
\noindent - Blohm AS, Maeder P, Quack T, \textbf{Lu Z}, Hahnel S, Schlitzer M, Grevelding CG, 2016. Derivatives of biarylalkyl carboxylic acid induce pleiotropic phenotypes on adult \textit{Schistosoma mansoni in vitro}. Parasitol. Res. doi:10.1007/s00436-016-5146-7\\
\noindent - \textbf{Lu Z}, Quack T, Hahnel S, Gelmedin V, Pouokam E, Diener M, Hardt M, Michel G, Baal N, Hackstein H, Grevelding CG, 2015. Isolation, enrichment and primary characterisation of vitelline cells from \textit{Schistosoma mansoni} obtained by the organ isolation method. Int. J. Parasitol. 45(9-10):663-72. doi:10.1016/j.ijpara.2015.04.002\\
\noindent - Hahnel S, Quack T, Parker-Manuel SJ, \textbf{Lu Z}, Vanderstraete M, Morel M, Dissous C, Cailliau K, Grevelding CG, 2014. Gonad RNA-specific qRT-PCR analyses identify genes with potential functions in schistosome reproduction such as SmFz1 and SmFGFRs. Front. Genet. 5. doi:10.3389/fgene.2014. 00170\\
\noindent - Buro C, Oliveira KC, \textbf{Lu Z}, Leutner S, Beckmann S, Dissous C, Cailliau K, Verjovski-Almeida S, Grevelding CG, 2013. Transcriptome analyses of inhibitor-treated schistosome females provide evidence for cooperating Src-kinase and TGF receptor pathways controlling mitosis and eggshell formation. PLoS Pathog. 9, e1003448. doi:10.1371/journal.ppat.1003448\\
\noindent - Hahnel S, \textbf{Lu Z}, Wilson RA, Grevelding CG, Quack T, 2013. Whole-organ isolation approach as a basis for tissue-specific analyses in \textit{Schistosoma mansoni}. PLoS Negl. Trop. Dis. 7, e2336. doi:10.1371/journal.pntd.0002336\\
\noindent - \textbf{Lu Z}, Zhang Y, Chi Y, Xu N, Yao W, Sun B, 2011. Effects of alcohols on bacterial cellulose production by \textit{Acetobacter xylinum} 186. World J. Microbiol. Biotechnol. 27(10):2281-2285. doi: 10.1007/s11274-011-0692-8\\

\noindent \textbf{Reviews and Book Chapters}\\
\noindent - Grevelding, C.G., Hahnel, S., \textbf{Lu, Z}. (2017) Ova and oogenesis in \textit{Schistosoma}. In: \textit{Schistosoma}, Biology, Pathology and Control. Edited by Barrie G. M. Jamieson; Taylor \& Francis Group, CRC Press, Boca Raton; p. 320-332 [Print ISBN: 978-1-4987-4425-6; eBook ISBN: 978-1-4987-4426-3]

\ssection{PRIZES}
\noindent \textbf{2014} Travel Grant by the International Giessen Graduate Centre for the Life Sciences (GGL)

\ssection{TOOL DEVELOPMENT}
\noindent \textbf{MetaSchisto} - Web portal for gene expression in all life stages of \textit{Schistosoma mansoni} (https://meta.schisto.xyz)\\
\textbf{IVIS} - Chart editor for interactive visualisation (https://ivis.xyz) \\
\textbf{IPRES} - HTML wrapper and presentation editor (https://ipres.xyz)

\ssection{SKILLS}
\noindent \textbf{Languages}\\
- Chinese: Native proficiency; \\
- English: Professional working proficiency;\\
- German: Basic living proficiency.\\

\noindent \textbf{Bioinformatics} \\
- Experience in managing and processing large-scale datasets (esp. RNA-Seq pipeline); \\
- Proficiency in using Linux operating system and shell commands; \\
- Familar with eukaryotic genome annotation pipeline;\\
- Scripting in Python and Perl. \\

\noindent \textbf{Statistics and data mining} \\
- Familiar with R for data exploration, statistical analysis and batch processing; \\
- Ability of applied machine learning in Python / R;\\
- Experience with relational databases, e.g., SQLite;\\

\noindent \textbf{Other Computational Skills} \\
- Experience in using version control systems (e.g., git)\\
- Familiar with Latex for documentation;\\
- Familiar with HTML/CSS and JavaScript for web development.\\

\noindent \textbf{Wet Lab Practice}\\
- Cell isolation; worm and cell culture; staining and imaging; gene and protein expression (\textit{e.g.,} ISH; qPCR; Western Blot); cloning; cell sorting; RNAi in worms, etc. 
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