Resources to Learn Computational Biology

We have started to compile a list of resources to learn or improve computational biology skills: Resources for Computational Biology & Bioinformatics

You can add new resources to relevant sheets or just check the list to find your new favourite book/course!

The list includes different type of resources to learn programming languages, a specific type of analysis, or pure theory. We also added a sheet for the databases, which we hope to be full of exciting databases soon – you can add yours as well ­čÖé

Don’t forget to add the resources you found useful and share with your circle!

Please contact turkey.rsg@gmail.com for any suggestion/comment.

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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.
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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┬áJohns Hopkins University.┬áHis keynote, titled “25 years of human gene finding: are we there yet?” focused on┬áhow┬áThe Human Genome Project was launched with the promise of revealing all of our genes, the ÔÇťcodeÔÇŁ 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 weÔÇÖve 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.┬áThe ISCB Overton Prize Keynote, Cole Trapnell of the┬áUniversity of Washington gave an engaging and informative talk titled “Reconstructing and deforming developmental landscapes” focused on┬áhow 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 geneÔÇÖs 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.┬áMartha L Bulyk from Brigham & Women’s Hospital and Harvard Medical School in┬áBoston was the next day keynote Her talk titled┬áTranscription factors, and cis-regulatory elements┬áfocused on┬ámapping the impact of unique variants on the expression of transcription factors.┬á Specifically, it highlighted that similar target sequences can have far-reaching impacts when mutated.┬á The difficulties associated with establishing a proper background were also addressed. The engaging talk┬áculminated in an informative question and answer period.┬áMadan Babu of the MRC Laboratory of Molecular Biology in the United Kingdom was another keynote speaker.┬áHis talk focused on understanding how the amino acid sequence of a protein contributes to its function (sequence-function relationship) and foundation for the sequenceÔÇôstructureÔÇôfunction 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┬áA womanÔÇÖs computational biology journey┬áfocused on┬áher 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.┬áBruno Gaeta, ISCB Treasurer, reviewed the SocietyÔÇÖs financial statements and current membership numbers.┬á Scott Markel, the Nominations Co-Chair, reminded members to vote and gave a brief overview of the Nominations process. ┬áThe student council delivered their annual report and highlighted this yearÔÇÖs┬áISMB┬áStudent 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┬áISMB┬áin┬áBasel, Switzerland┬ábetween July 21 – July 25, 2019.

Yan─▒tlaY├Ânlendir

Short Tandem Repeats in Tumours and Immunotherapy

T├╝rk├že

Our July webinar was given by Tugce Bilgin Sonay, from the Department of Computational Biology in the University of Lausanne. In this session, apart from her work, Tugce also explained other studies in this area.

At the beginning of the talk, she gave a general introduction on the detection of short tandem repeats and their impact on phenotype, gene expression and epigenetics. The primary focus of the talk was (1) Microsatellite Instability (MSI) in tumours, which mostly occurs due to the increase in the number of short tandem repeats as a result of a faulty DNA damage repair system, (2) Identification of the effect of the short tandem repeats in these tumours and (3) how these effects can be utilized for immunotherapy.

If you are interested in how short tandem repeats influence cancer and how they can be used for immunotherapy purposes, we strongly suggest you watch this webinar: https://youtu.be/GmjwyTZinjU (unfortunately, this webinar is only available in Turkish)

As ISCB RSG Turkey, we want to thank Tugce again for accepting our invitation and giving this very informative talk!

T├╝m├Ârlerdeki Ard─▒┼č─▒k K─▒sa Tekrar Dizileri ve ─░mm├╝noterapi

English

Temmuz ay─▒nda ger├žekle┼čtirdi─čimiz webinar; Lozan ├ťniversitesi, Hesaplamal─▒ Biyoloji Departman─▒ndan Tu─č├že Bilgin Sonay taraf─▒ndan verildi. Bu oturumda Tu─č├že, kendi ├žal─▒┼čmalar─▒n─▒n yan─▒ s─▒ra d├╝nyada bu alanda nas─▒l ├žal─▒┼čmalar yap─▒ld─▒─č─▒ hakk─▒nda bilgi verdi.

Konu┼čman─▒n ba┼č─▒nda k─▒sa tekrar dizilerine (KAT) nas─▒l bak─▒ld─▒─č─▒, KATÔÇÖlar─▒n fenotip, gen ifadesi, epigenetik ├╝zerine etkileri hakk─▒nda genel bir giri┼č yapt─▒. Konu┼čman─▒n odak noktalar─▒ ise: (1) T├╝m├Ârlerde, DNA onar─▒m mekanizmalar─▒n─▒n ├žal─▒┼čmamas─▒ndan dolay─▒ KAT mutasyonlar─▒n─▒n daha fazla g├Âr├╝lmesi ile olu┼čan, mikrosatelit instabilitesi (─░ng. Microsatellite Instability, MSI) olarak adland─▒r─▒lan t├╝m├Ârlerde KATÔÇÖlar─▒n nas─▒l belirlendi─či, (2) bu t├╝m├Ârlerde KAT mutasyonlar─▒n─▒n etkilerinin belirlenmesi ve (3) belirlenen etkilerin imm├╝noterapi de nas─▒l kullan─▒ld─▒─č─▒ ├╝zerineydi.

Ard─▒┼č─▒k k─▒sa tekrar dizilerinin kanser ├╝zerinde etkileri ve tedavi y├Ântemlerinde nas─▒l kulland─▒─č─▒yla ilgileniyorsan─▒z, bu webinar─▒ mutlaka izlemenizi ├Âneriyoruz. Webinar─▒ dinlemek i├žin: https://youtu.be/GmjwyTZinjU

Bu g├╝zel webinar i├žin RSG Turkey olarak Tu─č├žeÔÇÖye ├žok te┼čekk├╝r ediyoruz.

Beyin metabolizmas─▒n─▒n genom ├Âl├že─činde modellenmesi ve hastal─▒klara uygulamalar─▒

English

Son webinarimiz 11 HaziranÔÇÖda, Gebze Teknik Universitesi Biyomuhendislik BolumuÔÇÖnden Doc. Dr. Tunahan Cakir tarafindan verildi. En yuksek ilginin oldugu webinarlardan biri olan bu oturumda, genel olarak h├╝cre i├ži molek├╝ler a─člar─▒n ve molek├╝ler verilerin birlikte genom ├Âl├že─činde modellenmesi ve metabolizma incelemelerinde kullanilmasi hakkinda bilgi verildi. Konusmanin odak noktalari ise 1) beyindeki iki ├Ânemli h├╝cre tipi olan n├Âron ve astrosit h├╝crelerinin metabolizmas─▒ ve etkilesimi, 2) n├Ârodejeneratif hastal─▒klara ait transkriptom verilerinin beyine ├Âzg├╝ metabolik a─ča ├žizge tabanl─▒ bir y├Ântem kullan─▒larak haritalanmas─▒, 3) beyin t├╝m├Ârlerinin h├╝cre metabolizmas─▒na etkisini literat├╝rde k─▒s─▒t-tabanl─▒ yakla┼č─▒m olarak bilinen ak─▒ dengesi analizi (─░ng. Flux Balance Analysis) yontemi ile incelenmesiydi.

Eger canli oturumu kacirdiysaniz veya tekrar dinlemek isterseniz, Youtube uzerinden ulasabilirsiniz: https://youtu.be/z8MV-eu65zI

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

Turkce

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:  https://youtu.be/z8MV-eu65zI

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

Sunum_screenshot

Student Symposium 2018

We are ready for our next event: Student Symposium 2018. Our event will be a satellite to┬áHIBIT’18 and will take place in Antalya, a lovely city in Turkey. Check the details and register for free!┬áLooking forward to seeing you all in Antalya!

S─▒radaki etkinli─čimiz i├žin haz─▒r─▒z: 2018 ├ľ─črenci Sempozyumu. HIBIT’18e uydu olarak d├╝zenlenen bu etkinli─čimiz Antalya’da ger├žekle┼čecek. Detaylar ve ├╝cretsiz kay─▒t i├žin t─▒klay─▒n!┬áAntalya’da g├Âr├╝┼čmek ├╝zere!!

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