The 24th In Silico Megabank Research Seminar will be held on Friday, February 22.

・Date/Time: February 22 (Fri.) 17:00‐19:00
・Venue: Seminar Room 303 (3F), Research Building No.3, Electrical Engineering and Applied Physics, Aobayama Campus, Tohoku University
http://www.eng.tohoku.ac.jp/english/map/?menu=campus&area=g&build=02
・Title: MPI/CUDA programming using Allinea DDT/MAP
・Lecturer: Ian Lumb  (System Engineer, Allinea Software Ltd)

・Abstract:
With the development of sequencing technology, genome information is being computerized incredibly faster than Moore’s Law. These data analyses will definitely need super parallel analysis in the near future. Debugging the software by parallelization can be puzzlingly difficult in these super parallel software analyses. In this seminar, the person in charge of the development is going to introduce Allinea DDT/MAP which has track record of being introduced to well-known computing centers in Europe and the U.S. as well as to the University of Tsukuba, Research Organization for Information Science & Technology (RIST) and Japan Aerospace Exploration Agency (JAXA) in Japan, and which is also one the parallel debuggers that can be used easily for parallel analysis. In the seminar, he is going to introduce what can be done at this stage and what needs to be solved in the future through demonstration.

・Organizer: Masao Nagasaki, Naoki Nariai

The 23rd In Silico Megabank Research Seminar will be held on Friday, February 8.
This Time, we will be welcoming Dr. Mamoru Kato, National Cancer Center as our lecturer and he will be speaking on “Comparison of the Next-generation Sequencer Platform and Development of the Computer System for Clinical Sequencing.”

・Date/Time: February 8 (Fri.) 17:00‐18:30
・Venue: Conference Room 1 (2F), Tohoku Medical Megabank Organization
http://www.megabank.tohoku.ac.jp/english/info/access.html
・Title: Comparison of the Next-generation Sequencer Platform and Development of the Computer System for Clinical Sequencing
・Lecturer: Mamoru Kato （National Cancer Center）

・Abstract: While cancer-specific DNA mutations are cataloged by the large projects such as ICGC (International Cancer Genome Consortium) and TCGA (The Cancer Genome Atlas), clinical sequencing is now being implemented to serve as a bridge between the results of the study and the clinical practice. Clinical sequencing is a framework for the realization of the personalized medicine to make a proper selection of anticancer drugs, in which samples obtained at hospitals are sequenced by using the next-generation sequencer technology and decoded by referring to the catalog. National Cancer Center is now developing the system of clinical sequencing with an aim to start the operation from the next year, and our unit is working on the computer system development to deal with the sequence data and the comparative analysis of the sequence data such as Ion Torrent and HiSeq/MiSeq. In this seminar, I would like to discuss the characteristics of each platform data based on our experience as well as the selection of an appropriate algorism with regard to these ongoing topics.

・Organizer: Masao Nagasaki

The 22nd In Silico Megabank Research Seminar will be held on Thursday, January 17.

・Date/Time: January 17(Thu.) 16:30‐18:00
・Venue: Conference Room 1 (2F), Tohoku Medical Megabank Organization
http://www.megabank.tohoku.ac.jp/english/info/access.html
・Title: A small set of transcription factors governs global chromatin structure
・Lecturer: Tatsunori Hashimoto（MIT）

・Organizer: Masao Nagasaki

The 21st In Silico Megabank Research Seminar will be held on Friday, January 11.
This Time, we will be welcoming Ms. Yoko Kuroki, Institute of Physical and Chemical Research as our lecturer, and she will be speaking on “Comparative Genomic Analysis of Mammal Sex-Chromosome.”

・Date/Time: January 11(Fri.) 17:00‐18:30
・Venue: Conference Room 1 (2F), Tohoku Medical Megabank Organization
http://www.megabank.tohoku.ac.jp/english/info/access.html
・Title: Comparative Genomic Analysis of Mammal Sex-Chromosome
－Availability and Issues of the Next-Generation Sequencer－
・Lecturer: Yoko Kuroki （RIKEN; Institute of Physical and Chemical Research）

・Abstract: We got interested in the genomic structure of the mammal sex-chromosome and its evolution, and have done the genomic sequencing and the comparative analysis of Y-chromosome. So far, we have performed a genomic analysis of Y-chromosome of the primate chimpanzee and the marsupial tammar wallaby, and have found a species-specific or chromosome-specific structural change. The hierarchical shotgun approach to genomic clone, a conventional method, used to be used for these comparative analyses. Over the past few years, however, the next-generation sequencer has become used for these analyses. In this seminar, we would like to discuss the availability, issues, and future prospects of the next-generation sequencer as well as to introduce the current status of it.

・Organizer: Jun Yasuda

The 20th In Silico Megabank Research Seminar will be held on Tuesday, December 18. This Time, we will be welcoming Dr. Edgar Wingender, University Medical Center Göttingen as our lecturer, and he will be speaking on “Construction and analysis of gene regulatory networks.”

・Date/Time: December 18(Tues.) 17:00‐18:30
・Venue: Conference Room 1 (2F), Tohoku Medical Megabank Organization    http://www.megabank.tohoku.ac.jp/english/info/access.html
・Title: Construction and analysis of gene regulatory networks: The continuation of the TRANSFAC concept
・Lecturer: Edgar Wingender（Dept. of Bioinformatics, University Medical Center Göttingen, Göttingen, Germany）
・Language:　English

・Abstract:
The database TRANSFAC, which represents sequence-specific regulatory DNA-protein interactions in their different aspects, became a gold-standard in the field of gene expression analysis during the last twenty years. It has provided the basis for approaches to detect potential transcription factor binding sites in genomic sequences, which have been systematically exploited to generate transcriptional networks. It could be shown that combining this approach of pattern-based TFBS prediction with a multi-genome conservativity analysis enables to identify a set of highly relevant TF-target interactions.

The systematic collection of transcription factors (TFs) also helped establish a comprehensive classification of TFs according to their DNA-binding domains. This classification (TFClass) has been recently updated and profoundly revised (http://tfclass.bioinf.med.uni-goettingen.de/). It proved useful in identifying groups of paralogous TFs among which information about DNA-binding specificities and predicted target genes can be passed on to the paralogs. The networks obtained by such “paralogous expansion” provided a suitable basis for reconstructing tissue-specific transcription networks with interesting features.

The transcriptional networks thus constructed have been extended to gene regulatory networks by including micro-RNAs as another important player, both with regard to their targets (TF- and non-TF genes), as well as their own transcriptional regulation by TFs. Comparing the tissue-specific gene regulatory networks of a number of different tissues exhibited typical properties for individual and groups of tissues.

・Organizer: Takako Takai

The 19th In Silico Megabank Research Seminar will be held on Friday, December 14.

・Date/Time: December 14(Fri.) 17:00‐
・Venue: Seminar Room 303 (3F), Research Building No.3, Electrical Engineering and plied Physics
http://www.megabank.tohoku.ac.jp/english/info/access.html
・Title: Robust Sparse Regression Modeling
・Lecturer: Heewon Park (Chuo University)
・Abstract:
The L1 type of the regularization technique, which has been attracting attention recently, has the advantage in that presumption and the variable selection can be performed simultaneously by adding a L1 type of penalty to the likelihood function, and it is especially effective to analyze high-dimensional data including the genomic data. In this study, I introduce an effective algorithm for the analysis of the genomic data and propose a variety of robust sparse regression modeling techniques based on the L1 type of the regularization technique that is more effective than any existing research. As a result of verifying the proposal technique utilizing a numerical experiment, the effectiveness of it has become clear compared with existing techniques.

・Organizer: Masao Nagasaki

Prof. Masao Nagasaki will give an invited talk at 2012 Bilateral Workshop between Tohoku University and National Tsing Hua University.

・Date/Time:  December 12, 2012
・Place: Akiu Resort Hotel Sakan　http://www.sakan-net.co.jp/en/access/index.html
・Language: English
・Title: Data Management and Bioinformatics of High Throughput Sequencing Data on the Massive Parallel Supercomputer Environment and Future
http://www.smapip.is.tohoku.ac.jp/~dex-smi/2012/BW-Tohoku-TsingHua-201212/

The 18th In Silico Megabank Research Seminar will be held on Friday, November 30.

・Date/Time: November 30(Fri.) 17:00‐18:30
・Venue: Conference Room 1 (2F), Tohoku Medical Megabank Organization

・Lecturer: Yukuto Sato (National Institute of Genetics)
・Title: Evolutionary Conserved Feature of Mitochondrial Genome : a New Insight into  Functional Impairment and Disorder

・Abstract:
Although mitochondrial gene arrangement has been highly conserved among vertebrates from jawless fishes to mammals for more than 500 million years, the functional nature of such long-term persistence has yet to be defined over the past 20 years. We analyzed mitochondrial genome by sequence comparison, focusing on translation and replication. The result showed that the tRNA genes used more frequently for translation are more likely to be located in high expression regions (r = -0.1260, p = 0.0104, n = 336), and the regions spend in the single-stranded state during replication for a longer time are richer in G and T bases in the anti-codon regions. (r = 0.4281 p = 0.0234, n = 22).
This result indicates that arrangement of genes in mitochondrial genome is rational for both efficiency of translation and prevention of loss of function of tRNA during replication, and also provides a new insight into impairment of genome function caused by de novo mutations.

The 17th In Silico Megabank Research Seminar will be held on Friday, November 16.

・Date/Time: November 16(Fri.) 17:00‐18:30
・Venue: Conference Room 1 (2F), Tohoku Medical Megabank Organization

・Title: Type 2 diabetic patients’ intestinal bacterial flora that is uncovered by the meta-genome-wide related analysis
・Lecturer: Shujiro Okuda (Ritsumeikan University)

・Abstract:
Type 2 diabetes is a kind of endocrine disease which has been rapidly increasing in the number of patients all over the world now.
In this study, I conducted a comparative study of the intestinal bacterial flora of the type 2 diabetic patients and that of the healthy persons using a new technique of meta-genome-wide related analysis. As a result, a number of markers related to type 2 diabetes were successfully identified. In addition, a possibility was suggested that type 2 diabetes could be diagnosed using these markers. From now on, a possibility of diagnosis and medical treatment with an application of the meta-genome-wide related markers to the other diseases is highly expected.
In general, meta-genome analysis generally requires high-speed sequence determination capability such as a next-generation sequencer, but it is still expensive and the process is also complicated.
I will also introduce a virtual meta-genome constructive method which does not need such a meta-genome sequence determination.

Tohoku University Graduate School of Medicine is going to hold an explanatory session of Graduate School as follows. This session will also include a talking session with graduate students, presentation of the past tests, and distribution of the application guidebook. We are really looking forward to your active participation.

Date/Time: December 1(Sat.) 13:30‐15:30
Venue: Lecture Room 1, Building #1, Tohoku University School of Medicine

・The past tests will be presented from 13:00 to 13:30 and after the end of the session until 16:00.
・The time for visiting a laboratory is allocated after the end of the session.
・Please be advised that you should make a direct contact with the field you hope to visit in advance.

・Neither prior application nor participation fee is necessary.
・Since parking lot is not available, visitors are encouraged to use public transportation.

・You can see a video clip of a part of the last session on the website.http://www.med.tohoku.ac.jp/mov/intro/index.html