A5052523221- Genomics and Phylogenetic Studies
- Genomic variations and chromosomal abnormalities
- Diet and metabolism studies
- Gut microbiota and health
- Clostridium difficile and Clostridium perfringens research
- Genomics and Rare Diseases
- Chromosomal and Genetic Variations
- Identification and Quantification in Food
- Forensic and Genetic Research
- Genetic factors in colorectal cancer
- Genetics, Bioinformatics, and Biomedical Research
- Biomedical Text Mining and Ontologies
- CRISPR and Genetic Engineering
- Fractal and DNA sequence analysis
- Algorithms and Data Compression
- Parvovirus B19 Infection Studies
- Gene expression and cancer classification
- Radiation Dose and Imaging
- Genetic diversity and population structure
- Online Learning and Analytics
- Digital Humanities and Scholarship
- Infrastructure Maintenance and Monitoring
- Advanced Graph Neural Networks
- Hand Gesture Recognition Systems
- Human Motion and Animation
Heinrich Heine University Düsseldorf
2022-2024
Konya Food and Agriculture University
2019-2023
Bilkent University
2017-2019
Necmettin Erbakan University
2015-2017
Işık University
2017
KTO Karatay University
2013-2014
Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest the gut microbiome. However, establishing reproducible insights into determinants succession has been formidable challenge.
Structural variants (SVs) contribute significantly to human genetic diversity and disease
Diverse sets of complete human genomes are required to construct a pangenome reference and understand the extent complex structural variation. Here, we sequence 65 diverse build 130 haplotype-resolved assemblies (130 Mbp median continuity), closing 92% all previous assembly gaps reaching telomere-to-telomere (T2T) status for 39% chromosomes. We highlight continuity loci, including major histocompatibility (MHC), SMN1/SMN2, NBPF8, AMY1/AMY2, fully resolve 1,852 variants (SVs). In addition,...
Abstract New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution, comprehensiveness. Translating these routine research clinical practice requires robust benchmark sets. We developed the first set for identification of both false negative positive germline SVs, which complements recent efforts emphasizing increasingly comprehensive characterization SVs. To create this a broadly consented son in Personal...
Abstract Advances in whole-genome sequencing (WGS) promise to enable the accurate and comprehensive structural variant (SV) discovery. Dissecting SVs from WGS data presents a substantial number of challenges plethora SV detection methods have been developed. Currently, evidence that investigators can use select appropriate tools is lacking. In this article, we evaluated performance on mouse human using polymerase chain reaction-confirmed gold standard set genome-in-a-bottle set,...
Abstract Motivation Several algorithms have been developed that use high-throughput sequencing technology to characterize structural variations (SVs). Most of the existing approaches focus on detecting relatively simple types SVs such as insertions, deletions and short inversions. In fact, complex are crucial importance several associated with genomic disorders. To better understand contribution human disease, we need new accurately discover genotype variants. Additionally, due similar...
Abstract Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest the gut microbiome. However, establishing reproducible insights into determinants succession has been formidable challenge. Here we use fecal microbiota transplantation (FMT) an natura experimental model to investigate association between metabolic independence resilience stressed environments. Our genome-resolved metagenomics survey suggests that FMT serves...
The linear human reference genome that we use today does not represent the haplotypic diversity of global population. This raises bias in genomic read alignment and limits our ability to call large structural variations (SV), especially at highly polymorphic loci. Thus, many SV alleles remain unresolved. Recent efforts transition a graph-based resulted generation first draft pangenome reference, but tools SVs relative are presently lacking. In this study, present SVarp algorithm, aiming...
A major challenge in zooarchaeology is to morphologically distinguish closely related species' remains, especially using small bone fragments. Shotgun sequencing aDNA from archeological remains and comparative alignment the candidate reference genomes will only apply when nuclear of comparable quality are available, may still fail coverages low. Here, we propose an alternative method, MTaxi, that uses highly accessible mitochondrial DNA (mtDNA) between pairs species ancient sequences. MTaxi...
The improvements in the Internet technology led an evolution education. Some students’ lives have changed since 2012 when MOOCs gained popularity among academia. students now take courses from top universities all around world without time limitations and they even earn credits for their courses. They are able to discuss lecture topics not only with instructors class but also thousands of other online can get just-in-time help regarding questions teaching assistants. These some practices new...
To date, ancient genome analyses have been largely confined to the study of single nucleotide polymorphisms (SNPs). Copy number variants (CNVs) are a major contributor disease and evolutionary adaptation, but identifying CNVs in shotgun-sequenced genomes is hampered by typical low coverage (<1×) short fragments (<80 bps), precluding standard CNV detection software be effectively applied genomes. Here we present CONGA, tailored for genotyping at coverage. Simulations down-sampling experiments...
Abstract Advances in whole genome sequencing promise to enable the accurate and comprehensive structural variant (SV) discovery. Dissecting SVs from (WGS) data presents a substantial number of challenges plethora SV-detection methods have been developed. Currently, there is paucity evidence which investigators can use select appropriate tools. In this paper, we evaluated performance tools using PCR-confirmed gold standard set SVs. contrast previous benchmarking studies, our dataset included...
In this paper, using motion capture, we study on Turkish Sign Language Animation. A markerless system, Microsoft Kinect sensor and a professional optical system are compared. Besides, use the capture data in two different approaches; driven real time. To animate sign language, merge output with cartoon character. first approach, which is data-driven, recorded, processed converted to character animation off-line. This stored database it can be used mobile devices or any other necessary ways....
Teorik hesaplamalara dayalı olarak geliştirilmiş ses yalıtım modellerinin amacı, deneysel malzemeye ait "Ses Azaltım İndisi (R)" değerlerinin bulunması sırasında harcanan zaman, emek ve maliyeti azaltmaktır.Bu çalışmada, literatürde var olan simülasyon modelleri ile ticari programları kullanılarak, yapı malzemelerinin R değerleri araştırmacılar tarafından daha önce yapılan verilerle 11 farklı malzeme için karşılaştırmalı incelenmiştir.Deneyler Bastian
Linear reference genomes are ubiquitously used in genomics research, despite known biases associated with their use. In recent years, there has a been shift towards using graph-based to address some of these biases, which required new algorithms and file formats be developed. This created the need develop tools capable utilizing performing operations similar those carried out by traditional methods. this paper we present "gaftools", multi-purpose tool that introduces several utilities for...
<ns3:p>In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics Structural Variation, Pan-genomes, and SARS-CoV-2 research. </ns3:p><ns3:p> The overarching focus was to assess current status field identify remaining challenges. Furthermore, how combine strengths interests drive research method development forward. Over four days, eight groups each designed developed new...
Biological networks, mostly abstracted as graphs, are key to many important activities inside the cell. Similarity-based analysis is one of techniques for understanding role a query network. In that context, database consisting biological networks aligned with network and having similarity score higher lower than predefined cutoff value separated. Because NP-complete sub-graph isomorphism problem, nontrivial calculation computationally too expensive. To this end, several methods proposed in...
Abstract Motivation Several algorithms have been developed that use high throughput sequencing technology to characterize structural variations. Most of the existing approaches focus on detecting relatively simple types SVs such as insertions, deletions, and short inversions. In fact, complex are crucial importance several associated with genomic disorders. To better understand contribution human disease, we need new accurately discover genotype variants. Additionally, due similar...
<ns4:p>A major challenge in zooarchaeology is to morphologically distinguish closely related species’ remains, especially using small bone fragments. Shotgun sequencing aDNA from archeological remains and comparative alignment the candidate reference genomes will only apply when nuclear of comparable quality are available, may still fail coverages low. Here, we propose an alternative method, MTaxi, that uses highly accessible mitochondrial DNA (mtDNA) between pairs species ancient sequences....
<ns3:p>In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics Structural Variation, Pan-genomes, and SARS-CoV-2 research. </ns3:p><ns3:p> The overarching focus was to assess current status field identify remaining challenges. Furthermore, how combine strengths interests drive research method development forward. Over four days, eight groups each designed developed new...
A bstract To date, ancient genome analyses have been largely confined to the study of single nucleotide polymorphisms (SNPs). Copy number variants (CNVs) are a major contributor disease and evolutionary adaptation, but identifying CNVs in shotgun-sequenced genomes is hampered by typical low coverage (<1 ×) short fragments (<80 bps), precluding standard CNV detection software be effectively applied genomes. Here we present CONGA, tailored for genotyping at coverage. Simulations...
It is well-known that in wireless sensor networks using minimum-energy paths to transfer data from nodes base station not an energy-balancing option and the optimal solution if lifetime, defined as duration till first node network exhausts all its energy, of concern. However, net effect routing on lifetime has been studied detail before. In this study, we present comparative analysis both simulations linear programming models investigate issue with respect various system parameters such...