Results 71 to 80 of about 296,746 (277)

GateSeeder: Near-memory CPU-FPGA Acceleration of Short and Long Read Mapping

CoRR, 2023
Motivation: Read mapping is a computationally expensive process and a major bottleneck in genomics analyses. The performance of read mapping is mainly limited by the performance of three key computational steps: Index Querying, Seed Chaining, and Sequence Alignment. The first step is dominated by how fast and frequent it accesses the main memory (i.e.,
Eudine, Julien, Alser, Mohammed, Singh, Gagandeep, Alkan, Can, Mutlu, Onur   +4 more
openaire   +2 more sources

Three phosphatase families form a community: The phosphohydrolases that act upon inositol pyrophosphates

FEBS Letters, EarlyView.
Inositol pyrophosphates are energy‐rich signaling molecules that perform critical functions in cells. Three different families of phosphatases hydrolyze the β phosphate of the inositol pyrophosphate molecules: two have narrow specificities and one is promiscuous.
Ronda J. Rolfes
wiley   +1 more source

Evaluation of methods to detect circular RNAs from single-end RNA-sequencing data

BMC Genomics, 2022
Background Circular RNA (circRNA), a class of RNA molecule with a loop structure, has recently attracted researchers due to its diverse biological functions and potential biomarkers of human diseases.
Manh Hung Nguyen, Ha-Nam Nguyen, Trung Nghia Vu   +2 more
doaj   +1 more source

A long read mapping method for highly repetitive reference sequences [PDF]

, 2020
Abstract About 5-10% of the human genome remains inaccessible for functional analysis due to the presence of repetitive sequences such as segmental duplications and tandem repeat arrays. To enable high-quality resequencing of personal genomes, it is crucial to support end-to-end genome variant discovery using repeat ...
Chirag Jain, Arang Rhie, Nancy Hansen, Sergey Koren, Adam M. Phillippy   +4 more
openaire   +1 more source

Design and analysis strategies for robust microbiome ageing research

FEBS Letters, EarlyView.
The gut microbiome changes with age and associates with age‐related morbidity and mortality, establishing it as a potential biomarker and intervention target for ageing. Realising this potential requires methodological rigour, yet distinguishing biological signals from methodological artefacts remains challenging across cohorts. This review provides an
Mark Olenik, İsmail Güderer, Yi Wang, Tayyaba Alvi, Prasoon Pandey, Handan Melike Dönertaş   +5 more
wiley   +1 more source

Density-reducing Jaccard estimators for sketch-based long read applications

BMC Bioinformatics
Sequence sketching—a class of techniques aimed at generating compact representations of longer sequences—has become widely used in numerous long read applications, including assembly and mapping.
Tazin Rahman, Ananth Kalyanaraman
doaj   +1 more source

TRAIL‐PEG‐Apt‐PLGA nanosystem as an aptamer‐targeted drug delivery system potential for triple‐negative breast cancer therapy using in vivo mouse model

Molecular Oncology, EarlyView.
Aptamers are used both therapeutically and as targeting agents in cancer treatment. We developed an aptamer‐targeted PLGA–TRAIL nanosystem that exhibited superior therapeutic efficacy in NOD/SCID breast cancer models. This nanosystem represents a novel biotechnological drug candidate for suppressing resistance development in breast cancer.
Gulen Melike Demirbolat, Aslihan Kucuk, Omer Erdogan, Samed Ozer, Bensu Kozan, Tugba Cuceli, Erkan Gumus, Evrim Cevik, Ozge Cevik   +8 more
wiley   +1 more source

Accelerating read mapping with FastHASH [PDF]

, 2013
With the introduction of next-generation sequencing (NGS) technologies, we are facing an exponential increase in the amount of genomic sequence data. The success of all medical and genetic applications of next-generation sequencing critically depends on ...
Alkan, Can, Lee, Donghyuk, Alkan C., Xin, H., Mutlu, Onur, Yedkar, S., Mutlu, O., Hormozdiari, Farhad, Yedkar, Samihan, Lee, D., Xin, Hongyi, Hormozdiari, F.   +11 more
core   +2 more sources

Tumour–host interactions in Drosophila: mechanisms in the tumour micro‐ and macroenvironment

Molecular Oncology, EarlyView.
This review examines how tumour–host crosstalk takes place at multiple levels of biological organisation, from local cell competition and immune crosstalk to organism‐wide metabolic and physiological collapse. Here, we integrate findings from Drosophila melanogaster studies that reveal conserved mechanisms through which tumours hijack host systems to ...
José Teles‐Reis, Tor Erik Rusten
wiley   +1 more source

Illuminating the dark side of the human transcriptome with long read transcript sequencing

BMC Genomics, 2020
Background The human transcriptome annotation is regarded as one of the most complete of any eukaryotic species. However, limitations in sequencing technologies have biased the annotation toward multi-exonic protein coding genes. Accurate high-throughput
Richard I. Kuo, Yuanyuan Cheng, Runxuan Zhang, John W. S. Brown, Jacqueline Smith, Alan L. Archibald, David W. Burt   +6 more
doaj   +1 more source