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Team

LifeBytes first began as a small but dynamic interdisciplinary team of researchers and consultants. Their combined experience spans decades of research and publications in renowned journals such as Nature, Nature Genetics, Genome Research, Bioinformatics, Molecular and Cellular Proteomics and Nucleic Acids Research. Our lead consultants are research fellows funded by prestigious funding bodies and are group leaders with experience in all aspects of scientific research.

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Shivashankar Nagaraj

Founder and Managing Consultant

Dr Shiv Nagaraj’s overall focus is on development and application of bioinformatics approaches that utilize large amounts of data to solve problems in cancer biology. “Big Data” has been his research focus for the last ten years. He has made strong contributions to the field of computational biology with a particular focus on integration and analysis of genome scale datasets. He has been part of an exciting phase in computational biology and has worked on research problems involving genomics, proteomics and bioinformatics. In this process, he has developed bioinformatics methods and software (e.g. ESTExplorer, EST2Secretome, PGTools) that are valuable and are of practical utility to the wider scientific community. He is currently the Vice-Chancellor’s Research Fellow in Systems Biology at Queensland University of Technology.

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Jason Mulvenna

Managing Consultant

Assoc. Prof. Jason Mulvenna has made a number of significant contributions to the fields of parasitology, toxicology and cancer biomarker development and has published consistently in internationally renowned journals. Recently he has worked at integrating NGS and proteomics data to better understand parasitic infection. As part of his work on the carcinogenic liver fluke, Opisthorchis viverrini, he established a biomarker program using NGS and SWATH proteomics to identify protein and miRNA biomarkers of cancer. He is NHMRC Career Development Fellow and has attracted more than $9,000,000 in competitive grants and fellowships. He has strong international collaborations with researchers in Thailand, the United States, Brazil and Australia. He has been a member of the council of the Australian Society for Parasitology (2008-2013) is an editorial board member of the International journal of Parasitology (2012-present), an academic editor for PLoS One and a frequent guest editor for PLoS NTDs.

Consultants

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Mohamed Ashick M

Vice President and Genome Informatics Consultant

Dr. Mohamed Ashick has a PhD in Bio-informatics from IGBMC, affiliated to University of Strasbourg, France. Overall he has seven years of experience in bio-informatics, particularly in NGS data analysis and tool development in both academic and industry sectors. His area of expertise is in Epigenomics, Cancer data, single cell transcriptome, allele-specific analyses, and tools development.

Ashick has an in-depth understanding and analysis experience in NGS data such as Whole genome, Exome, Transcriptome, ChIP-seq and Multi-omics data integration. He is efficient in multiple programming languages like Perl, R, C++ and Shell scripting. He has made significant contributions in several tools development for data analysis such as Epimetheus, NGS-QC, SeqQC & GenoTrim, and also in several scientific articles in international journals. He has significant experience in setting up novel pipelines for Epigenome and Single Cell transcriptome data analysis and also in Microarray data analysis, especially in strategic probe designing for targeted re-sequencing.

Mahardhika Pratama

Mahardhika Pratama

Artificial Intelligence and Machine Learning

Dr. Mahardhika Pratama received his PhD degree from the University of New South Wales in 2014. He completed his PhD in 2.5 years with a special approval of the UNSW higher degree committee due to his outstanding PhD research achievement. Dr. Pratama is currently working at the Department of Computer Science and IT, La Trobe University, Melbourne as Lecturer. Prior to joining La Trobe, he was at the Centre of Quantum Computation and Intelligent System, University of Technology, Sydney as a postdoctoral research fellow.

Dr. Pratama received various competitive research awards in the past 5 years, namely the Institution of Engineers, Singapore (IES) Prestigious Engineering Achievement Award in 2011, the UNSW high impact publication award in 2013 and 2014.  His paper has been nominated for IEEE Transactions on Neural Networks and Learning Systems prestigious paper award. He has published over 50 high-quality papers in journals and conferences, and has been invited to deliver keynote speeches in international conferences. Dr. Pratama serves as an Editor In Chief of International Journal of Business Intelligence and Data Mining and is a member of IEEE, IEEE Computational Intelligent Society (CIS) and IEEE System, Man and Cybernetic Society (SMCS), and Indonesian Soft Computing Society (ISC-INA) and severs as a reviewer in some top tier journals such as: IEEE Transactions on Fuzzy Systems, IEEE Transactions on Cybernetics, Neurocomputing, Soft Computing, and Evolving Systems. His research interests involve machine learning, computational intelligent, evolutionary computation, fuzzy logic, neural network and evolving adaptive systems.

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Deepayan Sarkar

Applied Statistics

Deepayan Sarkar is an applied statistician with a particular interest in high-throughput Bioinformatics experiments. Such experiments typically produce a large volume of data, where it is known a priori that the bulk of the data do not contain useful signal, and the statistical problem is to identify  and interpret the small proportion that does contain information. Deepayan has collaborated extensively with biologists working with high throughput technologies such as microarrays, optical mapping, flow cytometry, and next-generation sequencing to develop novel statistical methods in these fields. In addition to Bioinformatics, he has a general interest in computational statistics and data visualization, and won the 2004 John M. Chambers Statistical Software Award for writing the lattice data visualization package for R. He has several years of experience working with R and Bioconductor. He did his PhD from the University of Wisconsin-Madison and is currently an Associate Professor in the Statistics and Mathematics Unit at the Indian Statistical Institute, Delhi.

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Xiaoqing Claire

Consultant

Claire has a PhD in Plant Pathology from The Ohio State University. Subsequently, she was a post-doc at West Virginia University where she was trained in using bioinformatics approaches, such as genomics, transcriptomics and proteomics, to study the mechanisms regulating the responses to drugs and toxins in the model yeast Saccharomyces cerevisiae. Since 2015 she has been an independent Bioinformatics/Biostatistics consultant. She has worked in diverse data analysis projects and is a highly rated Bioinformatician. Her primary expertise is in Algorithm development, Machine learning, Modeling and Statistical analysis. She has extensive experience in Genomics, Transcriptomics, Proteomics, Meta-omics, Clinical statistics, Network analysis, Genetics, Sequence analysis, Human Health, Microbiology and Plant Science.

Guest Consultants

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Diwakar Pattabiraman

Cancer Biology, Epithelial-To-Mesenchymal transition (EMT), Cancer Stem Cells

GRANTS AND FELLOWSHIPS EXPERTISE: C. J. Martin Overseas Biomedical Fellowship (AUS), NIH K99/R00 Pathway to Independence award (USA)

Diwakar Pattabiraman received his B.Sc. in microbiology from the University of Madras in India, and his M.Phil. and Ph.D. degrees in cancer biology from the University of Queensland,Australia. His graduate work focused on studying the role of the MYB oncoprotein in the pathogenesis of acute myeloid leukaemia in the laboratory of Prof. Tom Gonda. He then moved to Boston to pursue postdoctoral research at the Whitehead Institute for Biomedical Research under the tutelage of Dr. Bob Weinberg, receiving a C. J. Martin Overseas Biomedical Fellowship to pursue questions relating to the epithelial-to-mesenchymal transition, the generation of cancer stem cells, resistance to conventional therapy and the mechanisms of tumor progression. He is currently a Senior Research Associate supported by an NIH pathway to independence award exploring mechanisms by which induction of a mesenchymal-to-epithelial transition can induce the differentiation of aggressive carcinomas and sensitize them to chemotherapeutic drugs.

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