The 58th In Silico Megabank Research Seminar(March 6, 2015)

The 58th In Silico Megabank Research Seminar will be held on Friday, March 6. This Time, we will be welcoming Dr. Shingo Tsuji, Research Center for Advanced Science and Technology, The University of Tokyo as our lecturer, and he will be speaking on “Facts and Future of the Data Analysis in the Field of Life Science”.

・Date: Friday, March 6, 2015
・Time: 4:00 pm ‐ 5:30 pm
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title: Facts and Future of the Data Analysis in the Field of Life Science
・Lecturer: Shingo Tsuji  (Research Center for Advanced Science and Technology, The University of Tokyo)

*This lecture is transferable as a class in the medical research-related lecture course.

・Abstract: In this seminar, my own research results and experience are introduced and I would like to discuss with you on the directionality of that Computational biology should take. The seminar will cover a broad range of topics, and the followings are some of them. As the example of forecast using machine learning algorithms, effect prediction of anticancer agents by Random forests method is introduced. As a case of multi-omics data analysis of cancer, such analyses of 11 types of cancer using the analysis of gene expression data and DNA methylation data for colon cancer and Deep Learning are introduced. Network is often used as a channel of expressing biological knowledge, and I would like to discuss how to extract knowledge from such network. Finally, I would like to consider the social responsibility of Computational biology as presently genomic information is often applied into medicine and health care industry.

・Organizer: Naoki Nariai, Masao Nagasaki

The 57th In Silico Megabank Research Seminar(February 27, 2015)

The 57th In Silico Megabank Research Seminar will be held on Friday, February 27. This Time, we will be welcoming Dr. Mahito Sugiyama, The Institute of Scientific and Industrial Research, Osaka University as our lecturer, and he will be speaking on “Finding Statistically Significant Structure from Big Data ”.

・Date: Friday, February 27, 2015
・Time: 5:00 pm‐6:30 pm
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title: Finding Statistically Significant Structure from Big Data
・Lecturer: Mahito (The Institute of Scientific and Industrial Research,  Osaka University)

*This lecture is transferable as a class in the medical research-related lecture course.

・Abstract: Data mining, whose purpose is knowledge discovery from the big data, is utilized in various fields from basic science such as chemistry and biology to the application to management and marketing. Especially, the development of approaches to find combinational structure hiding in data such as gene pairs co-occurred and expressed and the structure shared by compounds with specific activation is the center of the topic concerning data mining. However, although securing the statistical significance on the discovered knowledge, in other words, the calculation of P value is a requirement in major application domain for data mining including biological science, there was no adequate focus for a long time. In this lecture, initiatives for this rapidly advancing research topic in recent year, triggered by the literature of Terada et al. presented at PNAS in 2013 are introduced. Furthermore, a special attention is paid to the recent outcomes that enable resolution to this matter by combining superfast algorithm developed in the field of data mining and multiple testing procedures developed in the field of statistics.

・Organizer: Takahiro Mimori, Masao Nagasaki

The 56th In Silico Megabank Research Seminar(February 13, 2015)

The 56th In Silico Megabank Research Seminar will be held on Friday, February 13.
This Time, we will be welcoming Dr. Kosuke Teshima, Faculty of Sciences, Kyushu University as our lecturer, and he will be speaking on “Population Genetics and Coalescent Theory ”.

・Date/Time: February 13(Friday) 17:00‐18:30
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title: Population Genetics and Coalescent Theory
・Lecturer: Kosuke Teshima (Faculty of Sciences, Kyushu University)

*This lecture is transferable as a class in the medical research-related lecture course.

・Abstract: Various researchers especially having an interest in evolution are giving considerable attention to estimating the evolutionary change of organisms from genomic diversity data. Here, the definition of the evolutionary change is a change of organisms in a very long evolutionary timescale. Population genetics is thought to be effective as a theoretical analysis framework when estimating the evolutional change based on genomic diversity data. In this seminar, the perception of evolutionary process and basic analysis method in population genetics are first introduced. Then, the overview of coalescent theory, a frequently used theory in recent population genetic analysis, is provided. Coalescent theory is mainly used in the estimation of evolution parameters in association of the recent development of Bayesian method using calculators. In addition, as examples of studies using coalescent theory, two cases are introduced: a study examining the coincidence probabilities of Y-chromosome haplotype in forensic medicine and another study examining the evolutionary process of overlapping gene using coalescent theory.

・Organizer: Yosuke Kawai, Masao Nagasaki

The 55th In Silico Megabank Research Seminar(February 6, 2015)

The 55th In Silico Megabank Research Seminar will be held on Friday, February 6.  This Time, we will be welcoming Dr. Yukinori Okada, Tokyo Medical and Dental University as our lecturer, and he will be speaking on “Elucidation of Disease Pathology, New Drug design, and Challenges to Epidemiology with Genetic Statistical Analysis ”.

・Date/Time : February 6 (Friday) 17:00‐18:30
・Venue : Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title : Elucidation of Disease Pathology, New Drug design, and Challenges to Epidemiology with Genetic Statistical Analysis
・Lecturer : Yukinori Okada (Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University)

*This lecture is transferable as a class in the medical research-related lecture course.

・Abstract: Genetic Statistics is a research area that reveals the connection between the genetic information and trait information in living organisms through statistical analysis. It has been more than 10 years since the human genome sequences was mapped, and now we are in the era when genomic information of several thousands and hundreds of thousands of samples is available. Through massive human genome analysis based on such a large quantities of genomic information, various genes associated with the onset of human diseases have been identified.  In addition, genomic statistical analysis which reconciles acquired disease-related genes with various biological and medical databases and drug target gene groups in a cross-sectional manner have slowly revealed its contribution to the additional elucidation of disease pathology and new drug design though drug repositioning. Various approaches from the aspect of genetic statistical analysis has been implemented in order to resolve issues pointed out by epidemiologic studies such as changes in disease complications based on the combination of certain diseases. In this seminar, the results of genetic statistical analysis which we have conducted targeting at various human diseases are introduced and future prospect of human genomic analysis is discussed.

・Organizer : Yumi Yamguchi, Masao Nagasaki

 

The 54th In Silico Megabank Research Seminar(January 30, 2015)

The 54th In Silico Megabank Research Seminar will be held on Friday, January 30. This Time, we will be welcoming Dr. Masaki Nishioka, Graduate School of Medicine, The University of Tokyo as our lecturer, and he will be speaking on “Searching Genome Architecture that Brings Variability to Brain Functions: Focusing on LINE 1”.

・Date/Time: January 30 (Friday) 16:00‐17:30
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title: Searching Genome Architecture that Brings Variability to Brain Functions: Focusing on LINE 1
・Lecturer: Masaki Nishioka (Department of Molecular Psychiatry, Graduate School of Medicine, The University of Tokyo)

*This lecture is transferable as a class in the medical research-related lecture course.

・Abstract: Genetic studies such as on psychiatric disorders have been actively conducted in order to understand various brain functions from the aspect of genes. The relationship between specific gene polymorphisms/ genetic variants and psychic functions has been reported in many studies; however, most of them have low odds ratio and penetration rate. Thus, it is thought that various genes are complexly associated. We hypothesized that, in addition to gene polymorphisms and genetic variants at individual level, somatic mutations occurred in the process of brain development were accountable of the variability in brain functions such as the development of psychiatric disorders, and we have proceeded with the analysis of somatic mutations in human brain. Special attention is paid to retrotransposon LINE-1.

A s the study methods, we utilize 1) an in silico method in which we extract the LINE-1 array from full genome sequence analysis data and identify novel insertion mutation and organ- (cell type-) specific somatic mutations and 2 ) a method (L1Hs-seq) that determines the location of insertion with the next generation sequencer and TAIL-PCR which uses specific primers for L1Hs that has an autonomic activity. In this lecture, we report the results of the ongoing preliminary examinations and discuss the future of the analysis of somatic mutations in brain and relationship with psychiatric disorders based on the interpretation of the data.

・Organizer: Yukuto Sato, Masao Nagasaki

First year Phd student Yuji Yoshida receives Tohoku University’s Research Encouragement Award at The 8th Annual Retreat Student Conference

First year Phd student Yuji Yoshida received Tohoku University’s Research Encouragement Award for his study about the development and evaluation of mitochondrial mutation detection at the 8thAnnual Retreat Student Conference on 17th January.
He greatly anticipates the progress of his doctoral research based on his results since last April and its future direction.
Yuji Yoshida
First year Phd student Yuji Yoshida

The 53rd In Silico Megabank Research Seminar(January 9, 2015)

The 53rd In Silico Megabank Research Seminar will be held on Friday, January 9.

This Time, we will be welcoming Dr. Tomoko Shibata, The National Institute for Basic Biology as our lecturer, and she will be speaking on “Development of a New Genomic Analysis Method Using Single Module Sequencing from Small Quantities of DNA”.

・Date/Time: January 9 (Friday) 9:00‐10:15
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title: Development of a New Genomic Analysis Method Using Single Module Sequencing from Small Quantities of DNA
・Lecturer: Tomoko Shibata (The National Institute for Basic Biology )

・Abstract: Single Module Sequencer, PacBio RSII, has a long average length of readable sequence of 7−8 kb with maximum of 30 kb, and it is possible to determine the base sequence without the amplification through PCR during the process of sequencing. Thus, domains with difficulty in amplification and long repetitive sequences became readable, which enabled more exhaustive genomic analysis. However, on the contrary to the unnecessity of amplification, large quantities of DNA are required for analyses. Moreover, in many cases sufficient amount of DNA cannot be secured depending on living organisms. Hence, we aimed to develop a method which enables genomic analyses with small quantities of DNA by using PacBio sequencer on DNA amplified with Phi29 DNA polymerase which is known to amplify DNA without causing a bias. In this seminar, we will introduce the results of the data analysis of bacterial genome and eukaryotic genome and discuss the future prospects.

・Organizer: Masao Nagasaki

The 52nd In Silico Megabank Research Seminar(January 7, 2015)

The 52nd In Silico Megabank Research Seminar will be held on Wednesday, January 7.

This Time, we will be welcoming Dr. Andre Fujita, University of Sao Paulo as our lecturer, and he will be speaking on “Computational Statistics in Biological Big Data: Methods and Applications”.

・Date/Time: January 7(Wednesday) 17:00‐18:30
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building 
・Title: Computational Statistics in Biological Big Data: Methods and Applications
・Lecturer: Andre Fujita (University of Sao Paulo)

*This lecture is transferable as a class in the medical research-related lecture course.

・Abstract: The understanding of the biological mechanisms underlying human diseases is one of the main challenges in biological sciences. Although several efforts, the large number of heterogeneous factors that influence the genesis of a disease makes it a very hard task. One of the challenges consists in understanding diseases by developing methods to statistically analyze and computationally manipulate big data. This difficulty is generated by ultra large data size, heterogeneity, multidimensionality, and presence of intrinsic noise. In this context, computationally intensive statistical methods developed by our group are presented with applications in neuroscience and molecular biology. In neuroscience, the focus is on the analysis of resting-state fMRI data of ~600 individuals diagnosed with ADHD and ~900 subjects with ASD. In the context of molecular biology, partial results obtained from the study of miRNA expression of a cohort of ~2,000 breast cancer subjects are presented.

・Organizer : Kaname Kojima, Masao Nagasaki

The 51st In Silico Megabank Research Seminar(December 12, 2014)

The 51st In Silico Megabank Research Seminar will be held on Friday, December 12 . This Time, we will be welcoming Dr. Ryosuke Kimura, University of the Ryukyus as our lecturer, and he will be speaking on “Encouragement of Learning Genome Anthropology”.

・Date/Time: December 12 (Friday) 17:00‐18:30
・Venue : Small Conference Room 2(3rd Floor), Tohoku Medical Megabank
・Title: Encouragement of Learning Genome Anthropology
・Lecturer : Ryosuke Kimura (Faculty of Medicine, University of the Ryukyus)

*This lecture is transferable as a class in the medical research-related lecture course.

・Abstract : Each human being has different combinations of genomes, which creates genomic variations. Thus, there are variations in phenotypes such as people’s appearances and constitutions. In order to understand how human biological variability was shaped and maintained, it is important to know 1) how humans spread all over the world and how they have adapted to their environment, 2) how large the variability generated as a result of chance. At present, in our laboratory, we put special focus on the people in the Ryukyu Chain to deepen our research on the features of genome and phenotypes in Asians and the background on how such features were formed. Furthermore, we are tackling to identify the genomic factors on visible traits such as complexion. The advancement of the recent genome analysis technology and dense catalog of genomic variations have dramatically transformed the strategy of biomedical studies, and it was required for researchers to face a large volume of data. In this seminar, we would like to introduce our study as well as to show the overview of the fast-evolving research methods of population genomics.

・Organizer : Yosuke Kawai, Masao Nagasaki