Author: besteturanli

ISMB2018- 26th Conference on Intelligent Systems for Molecular Biology


We as RSG-Turkey are so proud to be part of great organization ISCB and ISCBSC. ISMB2018, one of the conferences organized by ISCB, was held in Chicago between 6-11 July. I have nominated for ISCB-SC RSG Leadership Travel Fellowship for the conference and she had the opportunity to attend the conference. Despite this post were overdue, it has a bunch of highlights which should be recorded.

The first thing worth to mention is ISCB Communities of Special Interest (COSIs) which are topically-focused collaborative communities of shared interest wherein scientists communicate with one another on research problems and/or opportunities in specific areas of computational biology. For detailed information about sixteen COSIs of ISCB, click on the link. One of my favorites is  SysMod COSI where I got a chance to present my Ph.D. project and meet the great scientist as well as my future collaborators.

In the first day of the conference, Thomas Lengauer, ISCB president welcomed over 1,600 delegates to Chicago and started the tight schedule of ISMB2018. During the event, ISCB Conferences mobile application helped each participant to create their own program.
The conference hosted very successful and interesting talks including keynotes. The conference-leading keynote was Steven Salzberg from the Center for Computational Biology McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins University. His keynote, titled “25 years of human gene finding: are we there yet?” focused on how The Human Genome Project was launched with the promise of revealing all of our genes, the “code” that would help explain our biology. The publication of the human genome in 2001 provided only a very rough answer to this question. For more than a decade following, the number of protein-coding genes steadily shrank, but the introduction of RNA sequencing revealed a vast new world of splice variants and RNA genes. His talk reviewed where we’ve been and where we are today, described a new effort to use an unprecedentedly large RNA sequencing resource to create a comprehensive new human gene catalog. The ISCB Overton Prize Keynote, Cole Trapnell of the University of Washington gave an engaging and informative talk titled “Reconstructing and deforming developmental landscapes” focused on how developing embryos are comprised of highly plastic individual cells that shift from one functional state to another, often reversibly so. A cell executes a different gene expression program for each of its possible roles, switching between them as needed throughout its life. How does the genome encode the developmentally intended sequence of program switches? Which gene regulatory events are crucial for a given cell fate decision? Quantifying each gene’s contribution in governing even one developmental step is a staggeringly difficult challenge. However, massively scalable single-cell transcriptome and epigenome profiling offer a way to quantitatively dissect developmental regulatory circuits. He discussed new assays and algorithms developed by his laboratory to realize this goal, and offer some lessons from several recent projects. Martha L Bulyk from Brigham & Women’s Hospital and Harvard Medical School in Boston was the next day keynote Her talk titled Transcription factors, and cis-regulatory elements focused on mapping the impact of unique variants on the expression of transcription factors.  Specifically, it highlighted that similar target sequences can have far-reaching impacts when mutated.  The difficulties associated with establishing a proper background were also addressed. The engaging talk culminated in an informative question and answer period. Madan Babu of the MRC Laboratory of Molecular Biology in the United Kingdom was another keynote speaker. His talk focused on understanding how the amino acid sequence of a protein contributes to its function (sequence-function relationship) and foundation for the sequence–structure–function paradigm. He presented IDR-Screen, which is a high-throughput experimental and computational approach for discovering functional disordered regions in a biologically relevant context and identifying features of functional sequences through statistical learning. The final keynote of the conference, the ISCB Accomplishments by a Senior Scientist Award winner, Ruth Nussinov had inspiring talk entitled A woman’s computational biology journey focused on her journey through the field, beginning when revolutionary sequencing methods produced the first long DNA sequences with the development of an efficient algorithm to fold RNA, followed by pioneering bioinformatic DNA sequence analyses.

Throughout the conference days, attendees were able to meet and seek out information on new technologies, platforms, and ideas. Addition to having an opportunity to meet with exhibitors, attendees could view the poster presentations of the day to seek out new ideas and approaches. With nearly 300 attendee participants interacting with 15 recruiting entities the ISCB Career Fair was also a notable event.  The Career Fair allowed for a designated time for engaging discussion among talented candidates seeking positions in the fields of computational biology and bioinformatics.

Attending an ISCB conference is also a good chance for understanding the ISCB organization structure, transparency should be one of their strengths. Bruno Gaeta, ISCB Treasurer, reviewed the Society’s financial statements and current membership numbers.  Scott Markel, the Nominations Co-Chair, reminded members to vote and gave a brief overview of the Nominations process.  The student council delivered their annual report and highlighted this year’s ISMB Student Symposium.

ISCB offers poster or oral presentation and different numbers of travel fellowship opportunity as well as competitions like Art in Science or Wikipedia in every ISMB. In ISMB2018, 2017-2018 Wikipedia Winners were announced, 2018 Art in Science winners were announced, and over 40 students and post-docs were recognized as ISMB travel fellowship recipients. The ISCB aims to improve the communication of scientific knowledge to the public at large, so the ISCB Wikipedia Competition aims to improve the quality of Wikipedia articles relating to computational biology. Entries to the competition are open now; the competition closes on 31 Dec 2018. Prizes of up to $500 will be awarded to the best contributions as chosen by a judging panel of experts; these will be awarded at the ISMB/ECCB conference in Basel, Switzerland in July 2019. Detailed information on this link. Another annual event is Art in ScienceArt in Science competition which offers a way to show the beauty of science in the art form. The winners presented with a USD 200 prize, as well as be the feature cover image for the ISCB Fall Newsletter.

I write just some highlights from the conference, however, more information about the conference is also available in ISCB-newsletter.  If you wonder the selected works from ISMB2018 presenters, you can find the special issue in Bioinformatics

If you feel sorry that you missed this breathtaking event after you read the post, no worries. You can watch the presentations online by clicking the link

Moreover, please save the date for next ISMB in Basel, Switzerland between July 21 – July 25, 2019.


Beyin metabolizmasının genom ölçeğinde modellenmesi ve hastalıklara uygulamaları


Son webinarimiz 11 Haziran’da, Gebze Teknik Universitesi Biyomuhendislik Bolumu’nden Doc. Dr. Tunahan Cakir tarafindan verildi. En yuksek ilginin oldugu webinarlardan biri olan bu oturumda, genel olarak hücre içi moleküler ağların ve moleküler verilerin birlikte genom ölçeğinde modellenmesi ve metabolizma incelemelerinde kullanilmasi hakkinda bilgi verildi. Konusmanin odak noktalari ise 1) beyindeki iki önemli hücre tipi olan nöron ve astrosit hücrelerinin metabolizması ve etkilesimi, 2) nörodejeneratif hastalıklara ait transkriptom verilerinin beyine özgü metabolik ağa çizge tabanlı bir yöntem kullanılarak haritalanması, 3) beyin tümörlerinin hücre metabolizmasına etkisini literatürde kısıt-tabanlı yaklaşım olarak bilinen akı dengesi analizi (İng. Flux Balance Analysis) yontemi ile incelenmesiydi.

Eger canli oturumu kacirdiysaniz veya tekrar dinlemek isterseniz, Youtube uzerinden ulasabilirsiniz:

Bu aydinlatici webinar icin tum takipcilerimiz adina Tunahan Cakir hocamiza cok tesekkur ediyoruz!Sunum_screenshot

Genome-scale brain metabolic networks as scaffolds for mapping disease-related alterations


Our recent webinar on June 11st was given by Assoc. Prof. Tunahan Cakir from Gebze Technical University. In this session with high attendance, systems-wide analysis of cell metabolism and modeling networks at genome-scale were major topics. Focuses through the presentation were on 1) metabolism and interactions between neuron-astrocyte, two essential cell types in the brain, 2) mapping transcriptome data for neurodegenerative diseases using a graph-based approach termed reporter pathways, 3) constraint-based modelling of brain metabolic networks and flux balance analysis (FBA) for the metabolic evaluation of brain tumors.

If you missed the live session or you may want to watch it again, it is on the Youtube:

We appreciate this enlightening webinar and thank Dr.Cakir on behalf of our community!!


An easy way to understand a study: Student Presentations

Turkce icin tiklayin!


First student webinar of this year, which held on March 12th has presented by Melike Donertas. Ageing as one of the inevitable biological process was focus of the presentation named “Gene Expression-Based Drug Repurposing to Target Ageing “. During almost two hours, Melike presented not only the methodology of the study for drug repurposing, but also a general overview of ageing studies, until now. Simultaneously, all applicants contributed the presentation by questions and suggestions.

Brief explanation of the study by herself as follows: “Ageing is the largest risk factor for a variety of non-communicable diseases. Previous studies on model organisms suggest life- and health-span can be modulated through genetic and chemical perturbations. In this study, instead of a target-centric approach, we adopt a systems level drug repurposing methodology to discover drugs that can combat human ageing. Using multiple publicly available gene expression datasets, we first identify the expression changes that can characterize ageing in human brain. We then compare these changes in gene expression with the drug induced expression changes to find drugs that are likely to modulate ageing. The drugs that we identified included significant number of already identified pro-longevity drugs, indicating that the method can discover de novo drugs that meliorate ageing. The approach has the advantages that, by using data from human brain ageing data it focuses on processes relevant in human ageing and that it is unbiased, making it possible to discover new targets for ageing studies.”

If you feel curious about this study, you may find the link here.

2018 yili ogrenci sunumlari basladi!

Follow here for English!

Yilin ilk ogrenci sunumu, 12 Mart 2018 tarihinde, doktora ogrencisi Melike Donertas tarafindan yapildi. Her canlinin tecrube ettigi biyolojik bir surec olan yaslanmanin konusuldugu ”Yaslanmayi hedef alan gen ekspresyon temelli ilac repozisyonu” isimli sunuma, dinleyiciler de sorulariyla eslik etti. Melike, bir bucuk saatlik sunum boyunca, kendi calismasinin metodolojisinin yani sira simdiye kadar yaslanma ile ilgili yapilan calismalarla ilgili de genel bir bilgi verdi. Calismanin sonuclarinda yaslanma karsiti ilac onerileri ise heyecan vericiydi cunku onerilen bazi ilaclar hali hazirda omru uzattigi dusunulen ilaclardi. Sunumun sonunda Melike, yaslilikla iliskisi bilinenler disindaki diger ilac onerilerinin ise deneysel calismalarla irdelenecegini soyleyerek sunumunu bitirdi. Eger calismayi siz de okumak isterseniz, link burada.
Ayrica ogrenci sunumlarinda siz de yer almak istiyorsaniz, buradaki formu doldurmaniz yeterli.
Bir sonraki webinar etkinligini kacirmak istemiyorsaniz da lutfen takipte kalin 🙂