Barış Salman Ph.D.
Curriculum vitae
E-mail Phone Website
Github Linkedin Biostars Orcid

Education

Doctorate, 2021—2026 Genetics, Institute of Health Sciences, Istanbul University, Turkey GPA 3.5
Thesis Investigating the Genetic Basis of Epilepsies with Genomic Approaches  
Adviser Prof. Dr. Sibel Uğur İşeri  
Notable Courses Advanced Molecular Genetics, Mendelian and non Mendelian Diseases, Chromosomal Diseases, Systems Biology  
     
Master, 2016—2019 Genetics, Institute of Health Sciences, Istanbul University, Turkey GPA 2.14
Thesis Study of Split Hand/Foot Malformation with Genomic Techniques and Bioinformatic Approaches  
Adviser Assoc Prof. Dr. Sibel Uğur İşeri  
Notable Courses Bioinformatics, Genetic Counseling, Medical Genetics, Hospital Rotation for Genetic Counseling  
     
Bachelor, 2011—2016 Molecular Biology and Genetics, Istanbul University, Turkey GPA 2.44
Thesis Metabolic Regulation in Prokaryotes with Small Non-Coding RNAs  
Adviser Asst. Prof. Dr. Semian Karaer Uzuner  
Notable Courses Methods Used in Molecular Biology(lab), Molecular Genetics, Genetic Engineering  

Jobs

Company İzmir Biomedicine and Genome Center (ERDERA Project) Omics approaches to the rare and undiagnosed diseases
Date Feb 2025—Ongoing Diagnostic data availability, Genome re-analysis research pipeline,
Position Researcher Innovation to shorten time to RD diagnosis
     
Company Refgen Biotechnology Development of platform for bioinformatics
Date Mar 2021—Ongoing Pipeline research and development
Position Genetics and Bioinformatics Specialist  
     
Company Gen-Era Diagnostics Development of pipelines for NGS
Date Oct. 2018—Mar 2021 Variant pathogenity classification automatization
Position Genetics and Bioinformatics Specialist  
     
Company Aktif Gen Development of bioinformatic pipelines
Date Jan. 2018—Oct 2018  
Position R&D Personnel  

Internships & Rotations

Genetic Counseling Fall 2018
rotation IU Cerrahpaşa, Department of Pediatric Genetics and Teratology
   
Genetic Counseling Spring 2018
rotation IU Cerrahpaşa, Department of Medical Genetics
   
Cell Culture August 2016
internship IU Cerrahpasa Department of Medical Biology
   
Genomics June-July 2015
internship IU A.S. Institute of Exprmental Medicine Department of Genetics
   
Cytogenetics June-July 2014
internship IU Department of Medical Genetics
   
Molecular Dynamics 2012-2013
internship IU Faculty of Science Quantum Technologies Laboratory

Certificates

Use and care of Mar 21 - Apr 08
laboratory animals IU HADYEK 46. Laboratory Animal Use Training
   
Liquid handling 2-5 November 2021
robot Hamilton Venus Online Advanced Software Training
  9-12 August 2021
  Hamilton Venus Online Basic Software Training
   

Technical skills

Wet lab and Bioinformatics

DNA/RNA/Protein Isolation, quantative/qualitative PCRs, Blotting, Cytogenetics and Karyotyping Sequencing WGS, WES, Panels, RNAseq, scRNAseq, Sanger
       
Functional Studies Cell Culture, in vivo models, Microscopy Micro-arrays Genotyping, Expression
       
Genetic Engineering Recombinant DNA technologies    

Computers and Data Analyses

Sequencing short read DNA/RNA sequencing, long read DNA sequencing Web Development Django, Javascript
       
Development Python, R, Unix Shell, Nextflow, Containers Analysis Python Scientific Toolkit(numpy, pandas, scipy etc.), R language, Gnu Utils (awk, sed, datamash, etc.), Bioinformatic tools, Machine Learning, PCA, Clustering
       
Workflow Linux, Doom Emacs, Git, Jupyter Statistics and Probability Hypothesis testing, Bayesian Theorem, Data distributions
       
Writing Orgmode, Zotero, Bibtex, LaTeX Visualization Matplotlib, Plotly/Dash, LaTeX
       

Publications

Akçakaya, Nihan Hande, Barış Salman, Zeliha Görmez, Yelda Tarkan Argüden, Ayşe Çırakoğlu, Raif Çakmur, Berril Dönmez Çolakoğlu, et al. 2019. “A Novel and Mosaic WDR45 Nonsense Variant Causes Beta-Propeller Protein-Associated Neurodegeneration Identified Through Whole Exome Sequencing and X Chromosome Heterozygosity Analysis.” Neuromolecular Medicine 21 (1): 54–59. https://doi.org/10.1007/s12017-018-08522-6.
Haryanyan, Garen, Ozkan Ozdemir, Kemal Tutkavul, Aysin Dervent, Semih Ayta, Cigdem Ozkara, Baris Salman, et al. 2021. “The Rare Rs769301934 Variant in NHLRC1 Is a Common Cause of Lafora Disease in Turkey.” Journal of Human Genetics 66 (12): 1145–51. https://doi.org/10.1038/s10038-021-00944-8.
Khalilov, Dovlat, Garen Haryanyan, Baris Salman, Emrah Yucesan, Sibel Ugur Iseri, and Nerses Bebek. 2022. “Epilepsy or Neurodevelopmental Disorders Are Associated with Homozygous and Pathogenic ELP2 Variation in Three Siblings.” Neurocase 28 (6): 488–92. https://doi.org/10.1080/13554794.2023.2176779.
Mercan, Sevcan, Nihan Hande Akcakaya, Baris Salman, Zuhal Yapici, Ugur Ozbek, and Sibel Aylin Ugur Iseri. 2022. “Clinical and Genetic Analyses in Syndromic Intellectual Disability with Primary Microcephaly Reveal Biallelic and de Novo Variants in Patients with Parental Consanguinity.” Genes & Genomics, November. https://doi.org/10.1007/s13258-022-01344-8.
Oguz-Akarsu, Emel, Barıs Salman, Sibel Ugur-Iseri, and Betul Baykan. 2022. “An Extraordinary EEG Phenomenon Misdiagnosed as Nonconvulsive Status Epilepticus: Frequent Subclinical Periodic Discharges Terminated by Sudden Auditory Stimuli.” Clinical Eeg and Neuroscience, October, 15500594221129965. https://doi.org/10.1177/15500594221129965.
Salman, Barış. 2019. “Yarık el/ayak yapısal bozukluğunun genomik teknikler ve biyoenformatik yaklaşımlar ile incelenmesi.” Yüksek lisans tezi, Istanbul: İstanbul Üniversitesi.
Salman, Barış, Nerses Bebek, and Sibel Uğur İşeri. 2026. “XhetRel: A Pipeline for X Heterozygosity and Relatedness Analysis of Sequencing Data.” Bioinformatics Advances 6 (1): vbag002. https://doi.org/10.1093/bioadv/vbag002.
Salman, Barış, Yeşim Kesim, Seda Süsgün, Güneş Altıokka Uzun, Nermin Görkem, Nerses Bebek, Betül Baykan, and Sibel Uğur İşeri. 2024. “Novel Genetic Insights into Lateral Temporal Lobe Epilepsy: Findings from Whole Exome Sequencing.” Archives of Neuropsychiatry. https://doi.org/10.29399/npa.28894.
Susgun, Seda, Mert Demirel, Gul Yalcin Cakmakli, Baris Salman, Kader K. Oguz, Bulent Elibol, Sibel Aylin Ugur Iseri, and Zuhal Yapici. 2023. “Targeted Resequencing Reveals High-Level Mosaicism for a Novel Frameshift Variant in WDR45 Associated with Beta-Propeller Protein-Associated Neurodegeneration.” The International Journal of Neuroscience, May, 1–6. https://doi.org/10.1080/00207454.2023.2208279.
Susgun, Seda, Yesim Kesim, Dovlat Khalilov, Nermin Gorkem Sirin, Hasim Gezegen, Baris Salman, Emrah Yucesan, Gulden Gokcay, et al. 2023. “Reanalysis of Exome Sequencing Data Reveals a Treatable Neurometabolic Origin in Two Previously Undiagnosed Siblings with Neurodevelopmental Disorder.” Neurological Sciences 44 (7): 2527–40. https://doi.org/10.1007/s10072-023-06699-8.
Uğur İşeri, Sibel. 2021. “Combined Analysis of Linkage and Whole Exome Sequencing Reveals CIC as a Candidate Gene for Isolated Dystonia.” Journal of Istanbul Faculty of Medicine 84 (4, 4): 457–63. https://doi.org/10.26650/IUITFD.2021.913346.
Uğur İşeri̇ Sibel Aylin, Barış Salman, Kesi̇m Fatma Yeşim, Betül Baykan, Bekdi̇k Şi̇ri̇nocak Pınar, and Nerses Bebek. 2019. “Jüvenil Miyoklonik Epilepside EFHC1 Geni Ile İlişkili Yatkınlık: Türkiye’den İlk Olgu Sunumu.” Türk Nöroloji Dergisi 25 (4, 4): 233–36. https://doi.org/10.4274/tnd.galenos.2019.61214.
Wenson, Leonie, Johan Heldin, Marcel Martin, Yücel Erbilgin, Barış Salman, Anders Sundqvist, Wesley Schaal, et al. 2025. “Precise Mapping of Single-Stranded DNA Breaks by Sequence-Templated Erroneous DNA Polymerase End-Labelling.” Nature Communications 16 (1): 7130. https://doi.org/10.1038/s41467-025-62512-4.

Posters

  1. Susgun S., Kesim Y., Salman B., Yucesan E., Khalilov D., Sirin G., Baykan B, Bebek N., Iseri Ugur S., Two candidates bi-allelic variant to neurodevelopmental disorder in a consanguineous family from Turkey, ESHG 2022
  2. Acar A., Say M., Salman B., Dulger M.V., Comparison of Established Microsatellite Instability Detection Tools in Next Generation Sequencing, ESHG 2021
  3. Ugur Iseri S., Akçakaya N. H., Salman B., et al., Exome Sequencing Identifies a FBXO38 Variant Inherited from a Mosaic Mother to cause Distal Hereditary Neuronopathy Type IID with Distinct Features, ASHG 2017

Congresses

  1. Investigation of Gene Variants Associated with Syndromic Intellectual Disability, 7. International Congress of Cerebral Palsy and Developmental Disorders, February 23-25 2018, Istanbul, Turkey

Projects

  1. 2021-2022 TUBITAK 1501 Project, 3210420, Modeling and Automatic Analysis of Genotype-Phenotype Related Copy Number Variations Researcher
  2. 2021-2022 Research Fund of Istanbul University, ONAP-37862, Transcriptomics Approaches To Biomarker Potential Of B Cell Expression Analyses In Anti-Neuronal Antibody Related Autoimmune Epilepsy Researcher
  3. 2018-2019 Research Fund of Istanbul University, TYL-2018-30315, Study of Split Hand/Foot Malformation with Genomic Techniques and Bioinformatics Approaches Researcher
  4. 2018–2018 TUBITAK 1512 Project, 3210420 Development of Cloud Based Software for Next Generation Amplicon Sequencing Technologies, Jan 2018- Oct 2018 Research Fellow
  5. 2017-2018 Research Fund of Istanbul University, TDP-2017-25510, Genetic Analyses of Progressive Myoclonic Epilepsy Researcher
  6. 2016–2018 TUBITAK 1001 Project, Investigation of Epileptogenesis After Febrile Seizures Research Fellow

Software

VVC Variant Version Control (in development)
  Tool for tracking changes in variant annotation using git.
   
χΣΔ Cross-symbol checker
  This tool checks Ensembl and NCBI annotation files for different genome versions and shows which gene symbol is used. This way a more appropriate gene set can be used to avoid the false negatives in the variant discovery process.
   
Dove Downstream VCF Evaluation
  Tool for annotating VCF files, multi genome analysis and filtering variants.
   
Pigeon Pipelining Genomic Operations
  Tool for pipelining bioinformatics tools written considering NGS applications.
   
Picus Pointed Interpretation of Clinical Variant Significance
  Tool for classifying sequence variants according to ACMG/AMP criteria.

Awards

III. Rare Neurological Diseases Symposium and Neurogenetics Course, Second place project award, Istanbul, Turkey, 2017

Congresses&Courses

  1. 2023 YTÜ Biyogen, II. Bioinformatic Conference, Nov 10, Bioinformatics in uncovering the genetic basis of human diseases (Oral Presentation)
  2. 2023 İSTisNa, Strategies, Genomic Approaches and Data Analysis for Rare and Undiagnosed Diseases Course, Oct 12-13, Quality metrics in sequencing data (Oral Presentation)
  3. 2022 Turkish Society of Medical Genetics, Nov 9-13, Genome-Level Evaluation of Copy Number Changes, One of the Important Risk Factors for Genetic Epilepsy (Oral Presentation)
  4. 2020 ESHG 2020, June 6-9, Virtual Conference, GenerAVI: Variant Interpreter and Genetic Analysis Summary Generator (Poster Presentation)
  5. 2019 7th International Congress of the Molecular Biology Association of Turkey, Sep 27-29, Istanbul, Turkey, PICUS: Pointed Interpretation of Clinical Variant Significance (Poster Presentation)
  6. 2019 Bioinformatics Days III, Gazi University Faculty of Medicine, May 25, Ankara, Turkey, NGS Pipelines with Python (Oral Presentation)
  7. 2019 Erciyes University Faculty of Medicine Genetics Days, February 21-23, Kayseri, Turkey, Making Sense of Human Genome with Databases and Bioinformatic Tools (Oral Presentation)
  8. 2018 IV. Rare Neurological Diseases Symposium and Neurogenetics Course, May 31-July 1, Istanbul, Turkey, Analysis of Neurogenetics Data Interactive Training and Practice (Instructor)
  9. 2018 11. National Epilepsy Congress, May 3–6, 2018, Dalaman, Turkey, Meta Analysis of SCN1A Gene Variants of 114 Patients from Epi25 Exome Data (Oral Presentation)
  10. 2018 7. International Congress of Cerebral Palsy and Developmental Disorders, February 23-25, Istanbul, Turkey, Investigation of Gene Variants Associated with Syndromic Intellectual Disability
  11. 2017 53. National Neurology Congress, November 24–30, Antalya, Turkey, Genomic Approaches to Intellectual Disability Case with Epilepsy (Oral Presentation)
  12. 2017 III. Rare Neurological Diseases Symposium and Neurogenetics Course, July 1–2, Istanbul, Turkey, Profiling Anti-Epileptic Drug Resistance an Genetic Diagnosis with Epilepsy Panel (Poster Presentation)

General skills

Languages

Turkish Mother Tongue  
English Advanced Fluent
These are the languages I am still learning  
French Beginner Basic words and phrases
Japanese Beginner Basic words and phrases
Latin Beginner Basic words and phrases

Date: 2024-01-15 Pzt 00:00

Author: Barış Salman

Created: 2026-06-27 Cts 16:43