Архив метки: Philipp Khaitovich

The biggest mystery of our body can be solved with big data science

The most important and complex part of our body is our brain. Everything that happens in our body, goes through it. Humanity has learned quite a lot about the brain and how it functions, yet there is much much more to learn and discover. MRI and other technologies that were developed through the last decades, give us a lot of raw and coded data about the brain. The biggest challenge facing scientists is to decipher this data. On December 13th Skoltech and ENIGMA held the international workshop “Big Data and the Human Brain”, which presented how big data science can help us better understand our brain. As part of the workshop, the two sides discussed the concept of the joint Skoltech-ENIGMA Center to be inaugurated at Skotlech.

Skoltech President Alexander Kuleshov opens the workshop.

Skoltech President Alexander Kuleshov opens the workshop.

The ENIGMA Consortium is an international effort by leaders worldwide, to bring together researchers in imaging genomics, neurology and psychiatry, to understand brain structure and function, based on MRI, DTI, fMRI, genetic data and many patient populations.

The consortium was initiated at the University of Southern California (USC), and it now consists of over 280 institutions in 35 countries of the world. It combines the data, talents and infrastructure of over 700 scientists working on genome-wide, neuroimaging and clinical data from over 53,000 subjects. Skoltech scientists take part in this international effort.

Director of the ENIGMA Consortium, Paul Thompson, Ph.D.

Director of the ENIGMA Consortium, Paul Thompson, Ph.D.

Skoltech President Alexander Kuleshov opened the workshop with greetings to the participants, but didn’t waste time and invited the first speaker, Director of the ENIGMA Consortium, Paul Thompson, Ph.D., to deliver his presentation.

Dr. Thompson described the complexity of brain research and the efforts made by ENIGMA to understand how the brain works through combination of different mapping methods. He told the audience how this scientific network is connecting research centers around the world. The meta-analysis of information from different data centers, he said, will improve their efficiency.

Prof. Leyla Namazova, Chairman of the Russian Public Academy of Pediatrics.

Prof. Leyla Namazova, Chairman of the Russian Public Academy of Pediatrics.

After Dr. Thompson, it was Prof. Leyla Namazova – Chairman of the Russian Public Academy of Pediatrics, Vice-chairman of the Executive Committee Union of Pediatricians of Russia, and an Academician of the Russian Academy of Sciences – who described brain initiatives in Russia, and spoke on her experience of working in pediatrics with ENIGMA-produced data. Prof Namazova was among the organizers of the ENIGMA workshop “Neuroscience in Pediatrics” that was held in the Scientific Center of Children’s Health on December 11-12.

Skoltech Prof. Philipp Khaitovich presents project CoBrain.

Skoltech Prof. Philipp Khaitovich presents project CoBrain.

Next it was Skoltech’s turn to present its part in the research of the brain. First came Prof. Philipp Khaitovich, Associate Director of Skoltech Center for Data Intensive Biomedicine and Biotechology, and described project CoBrain – a large-scale analysis of the brain lipidome in healthy aging and brain disorders – from the point of view of biology. After him came Mikhail Belyaev, a research scientist at Skoltech Center for Computational and Data-Intensive Science and Engineering, who presented the computational point of view of how to analyze Neuroimaging data using big data and deep learning.

Renowned Russian-American scientist, Skoltech Prof. Vladimir Zelman.

Renowned Russian-American scientist, Skoltech Prof. Vladimir Zelman.

The second part of the workshop was opened by Prof. Vladimir Zelman. Prof. Zelman, a renowned Russian-American scientist, and one of the pioneers of neuroanesthesia, is the bridge that connects USC and Skoltech, since he is a professor in both institutions. He spoke about Innovations in Translational Neuroscience, Neurosurgery and Brain Computer Interfaces.

His presentation was followed by Prof. Henrik Walter, a world renowned expert in psychiatry, Professor for Psychiatry, Psychiatric Neuroscience and Neurophilosophy at the Charité Universitätsmedizin Berlin, Germany. Prof. Walter spoke about functional brain connectivity, imaging, and psychiatry.

Prof. Hilleke Hulshoff Pol, chair of ENIGMA-Plasticity.

Prof. Hilleke Hulshoff Pol, chair of ENIGMA-Plasticity.

The last speaker of the day was Prof. Hilleke Hulshoff Pol, world renowned expert in genetics of the human brain, Professor of Neuroscience at the Brain Center Rudolf Magnus, University Medical Center Utrecht, The Netherlands. Prof. Hulshoff Pol, who is also the chair of ENIGMA-Plasticity, talked about international genetic studies of the human brain.

At the end of the workshop, Prof. Zelman described the ties between ENIGMA and Russia: “the brain is so complicated that not only one lab, institute, or university can solve this mystery. It’s really an international magnum effort to find out about human cerebrum.  This is the reason that when we had this ENIGMA at USC, I immediately proposed to Dr. Thompson “let’s go out, we need mathematicians and Russia is famous about mathematicians for centuries”. We immediately contacted Dr. Kuleshov, and he responded very positively. We also contacted Academic City in Novosibirsk, and in three years we developed more interesting projects than 35 other countries in our network. We found support and understanding. This conference is the result of a three-year cooperation. From now on we will have yearly conferences, and I would like it to be not only in Moscow.

The strategic partnership is between USC and Skoltech. Skoltech is a vibrant new kind of university, and I believe it will play a major role as a bridge between countries, not only the United States and Russia, but all over the world. It’s new but it’s already growing”.

OMICS Intensive Module

DNA analysis. Image courtesy of Berkeley Lab, Flickr

DNA analysis. Image courtesy of Berkeley Lab, Flickr

Genomics, proteomics, transcriptomics and metabolomics. These are some of the rising stars of biology studies, which are informally referred to as OMICS.

This summer Skoltech offers students and researchers a unique opportunity to get acquainted with and gain hands-on experience in cutting edge “OMICS Data Analysis and Medical Applications”.

The university’s Center for Data-Intensive Biomedicine and Biotechnology (CDIB) organizes in collaboration with Rusnano an intensive one-week educational module (July 20-26), jam-packed with presentations by some of the world’s leading scientists in the field. The program was developed in collaboration with top research institutes, including Institut Curie (France), University of Oxford (UK), Harvard Medical School (USA), and the Max Planck Institute for Computational Biology (Shanghai, China).

The program will provide an introduction to OMICS to the 20 competitively selected participants – Skoltech Ph.D. students, researchers from labs across Russia and employees of big companies. Instructors will review novel research methods, present practical applications in clinical diagnostics, therapy, pharmacy, and experimental biomedicine, and help attendees gain critical hands-on skills in computational biomedicine.

Program

Monday, July 20th

09:00               Registration

10:00               Introduction to the course

Tatiana Nikolenko, Andrey Zinovyev, Alexander Kanapin

11:00               Lecture: Omics data in precision oncology: past, present, and future

Emmanuel Barillot

13:00               Lunch

14:00               Lecture: Types of omics data and current omics technology overview

Alexander Kanapin

16:00               Omics data in virology

Manja Marz

18:00               Discussion

19:30               Welcome Party

Tuesday, July 21st

09:00               Lecture: Modern methods for visualization and exploratory analysis of omics data

Andrei Zinovyev

11:00               Lecture: High-throughput sequencing of the genome, epigenome and transcriptome for studying cancer

Valentina Boeva

13:00               Lunch

14:00               Lecture: Single cell omics data analysis and projects

Peter Kharchenko

16:00               Lecture: Modern computational infrastructure for omics data analysis

Lennart C. Karssen

18:00               Break

19:00               Practical session: High-throughput sequencing computational tools

Valentina Boeva + assistants

20:30               Dinner

Wednesday, July 22nd

09:00               Lecture: Machine learning for precision medicine and analysis of omics data (Part 1)

Felix Agakov

11:00               Lecture: Mobile genetic elements: postgenomic view

Alexander Kanapin

13:00               Lunch

14:00               Lecture: Cancer genome and approaches for understanding it

Tatiana Popova

16:00               Lecture: European genomics programs: objectives and challenges

Alexander Kanapin

18:00               Break

19:00               Practical session: Analyzing cancer genome

Tatiana Popova + assistants

20:30               Dinner

Thursday, July 23rd

09:00               Lecture: Machine learning for precision medicine and analysis of omics data (Part 2)

Felix Agakov

11:00               Lecture: Gut metagenomics and its application in medicine

Dmitry Ravcheev

13:00               Lunch

14:00               Lecture: Genomic instability and cancer prognosis, treatment and predisposition

Tatiana Popova

16:00               Lecture: Constructing, maintaining and using databases of molecular networks in medical applications

Maria Kondratova

18:00               Break

19:00               Practical session: Tools for dimension reduction and data visualization

Andrei Zinovyev + assistants

20:30               Dinner

Friday, July 24th

09:00               Lecture: How to decipher the biological and medical impact of somatic events in cancer?

Ekaterina Kotelnikova

11:00               Lecture: Mathematical modeling of biological processes using omics data

Andrei Zinovyev

13:00               Lunch

14:00               Lecture: Perspectives of precision medicine in Russia and worldwide

Evgeny Imyanitov

16:00               Lecture: Omics data for studying brain in health and disease

Philipp Khaitovich

18:00               Break

19:00               Practical session: Use of network-based methods for analysis of omics data

Maria Kondratova+assitants

20:30               Dinner

Saturday, July 25th

09:00               Lecture: The regulatory sequence level of protein-nucleic acids interaction: what we can and can’t do with sequence motif analysis of high-throughput omics data

Ivan Kulakovsky

11:00               Lecture: Discovery and analysis of eukaryotic enhancers using alternative genomic approaches

Dmitri Papatsenko

13:00               Lunch

14:00               Lecture: Algorithms of biological network analysis together with omics data

Mikhail Pyatnitskiy

16:00               Group discussion with lecturers: Q&A

18:00               Break

19:00               Remote lecture: Omics data for studying aging

Vadim Gladyshev

20:30               Dinner

Sunday, July 26th

09:00               Lecture: Evolutionary studies of human brain

Philipp Khaitovich

11:00               Lecture: Sniderome and similar projects and the future of personalized omics medicine

Andrei Zinovyev

13:00               Lunch

14:00               Summary and final discussion

18:00               Departure

 

Colloquium: Molecular features of human evolution

Brain Computer Interface. Image courtesy of Ars Electronica, Flickr

Brain Computer Interface. Image courtesy of Ars Electronica, Flickr

We are pleased to invite you to the Skoltech Colloquium. And this time Skoltech Professor Philipp Khaitovich takes you on a journey down the rabbit hole of the human brain’s evolution.

 

When: November 6, 4 pm

What: Molecular features of human evolution

Where: Hypercube, 4th floorHuman evolution has resulted in a species that possesses an apparently unique set of phenotypic capabilities. In our laboratory, we search for molecular features specific to humans, through integrative analysis of genetic, transcriptomic and metabolomic data measured in modern and archaic humans, as well as closely related mammalian species: chimpanzees, macaques and mice. Here, I will share recent insights into uniquely human features of brain development and brain organization, as well as a hidden link between brain and muscle evolution.

 Speaker: Professor Philipp Khaitovich, born in Moscow, Russia in 1973. Completed undergraduate studies at Moscow State University in 1995 and PhD at the University of Illinois at Chicago in 1999. From 2000 till 2006, worked as a postdoctoral researcher at the Max Planck Institute for Evolutionary Anthropology at the department of Evolutionary Genetics headed by Prof. Svante Pääbo. In September 2006, he took a faculty position at the Institute for Computational Biology jointly established by the Chinese Academy of Sciences and the Max Planck Society in Shanghai, China and in 2012 became an institute director. In 2014, Philipp joined Skoltech as a professor ate the Bio Medicine initiative.

We look forward to seeing you.

* The Skolkovo Institute of Science and Technology (Skoltech) is a private graduate research university in Skolkovo, Russia, a suburb of Moscow. Established in 2011 in collaboration with MIT, Skoltech educates global leaders in innovation, advances scientific knowledge, and fosters new technologies to address critical issues facing Russia and the world. Applying international research and educational models, the university integrates the best Russian scientific traditions with twenty-first century entrepreneurship and innovation.

 

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