Results 91 to 100 of about 22,385,248 (304)

Integration of transcriptomic data in a genome-scale metabolic model to investigate the link between obesity and breast cancer

BMC Bioinformatics, 2019
Background Obesity is a complex disorder associated with an increased risk of developing several comorbid chronic diseases, including postmenopausal breast cancer.
Ilaria Granata, Enrico Troiano, Mara Sangiovanni, Mario Rosario Guarracino   +3 more
doaj   +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

A distributed computing approach to improve the performance of the Parallel Ocean Program (v2.1) [PDF]

, 2014
The Parallel Ocean Program (POP) is used in many strongly eddying ocean circulation simulations. Ideally it would be desirable to be able to do thousand-year-long simulations, but the current performance of POP prohibits these types of simulations.
Bal, H.E., H. E. Bal, F. J. Seinstra, H. A. Dijkstra, van Werkhoven, B.J.C., J. Maassen, B. van Werkhoven, van Meersbergen, M.A.J., Seinstra, F.J., Brunnabend, S.A., Kliphuis, M., M. Kliphuis, Dijkstra, H.A., M. van Meersbergen, Bal, H.E.; id_orcid, S. E. Brunnabend   +15 more
core   +2 more sources

From trash to treasure: detecting unexpected contamination in unmapped NGS data

BMC Bioinformatics, 2019
Background Next Generation Sequencing (NGS) experiments produce millions of short sequences that, mapped to a reference genome, provide biological insights at genomic, transcriptomic and epigenomic level. Typically the amount of reads that correctly maps
Mara Sangiovanni, Ilaria Granata, Amarinder Singh Thind, Mario Rosario Guarracino   +3 more
doaj   +1 more source

Reconstructing enzyme evolution by protein engineering

FEBS Letters, EarlyView.
Natural enzyme evolution can be retraced by protein engineering methods such as directed evolution, rational design, and ancestral sequence reconstruction. These approaches reveal how enzymes emerged from ligand‐binding scaffolds, developed varying substrate preferences, formed oligomeric complexes, adapted to environmental changes, and evolved novel ...
Lukas Drexler, Markus R. Busch, Reinhard Sterner   +2 more
wiley   +1 more source

Automating fault tolerance in high-performance computational biological jobs using multi-agent approaches [PDF]

, 2014
Background: Large-scale biological jobs on high-performance computing systems require manual intervention if one or more computing cores on which they execute fail.
Varghese, Blesson, McKee, Gerard, Alexandrov, Vassil   +2 more
core   +1 more source

Investigating transcription factor dynamics in health and disease using FRAP

FEBS Letters, EarlyView.
FRAP analysis of GFP‐tagged transcription factors reveals how molecular mobility and target engagement change in response to drug treatment. By combining live‐cell imaging, quantitative model fitting, and statistical analysis, this approach uncovers transcription factor dynamics linked to disease mechanisms, providing a powerful framework for ...
Kannan Govindaraj, Carolina Vazquez Garzon, Jose Joaquin Velasco, Janine N. Post   +3 more
wiley   +1 more source

Active Learning Pipeline for Brain Mapping in a High Performance Computing Environment

, 2020
© 2020 IEEE. This paper describes a scalable active learning pipeline prototype for large-scale brain mapping that leverages high performance computing power. It enables high-throughput evaluation of algorithm results, which, after human review, are used
Chung, Kwanghun, Matthew A. Melton, David Chavez, Michaleas, Adam, Brattain, Laura J., Adam Michaleas, Melton, Matthew A., Webster Guan, Lars A. Gjesteby, Lamb, Damon G., Laura J. Brattain, Snyder, Michael, Guan, Webster, Ash, Meagan, Kamentsky, Lee, Sara N. Burke, Meagan Ash, Damon G. Lamb, Lee Kamentsky, Chavez, David, Burke, Sara N., Kevin J. Otto, Gjesteby, Lars A., Michael Snyder, Otto, Kevin J., Kwanghun Chung   +25 more
core   +1 more source

ET-KAN: an energy-based transformer model with Kolmogorov–Arnold network for image reconstruction

Complex & Intelligent Systems
Transformers models have significantly changed many areas of Machine Learning, due to their structure and extensive number of parameters, which enables them to capture complex patterns in data.
Chiara Marullo, Giuseppe Buonaiuto, Francesco Gargiulo, Massimo Esposito   +3 more
doaj   +1 more source

Conserved binding mode but diverse interfaces of MreC‐PBP2 interactions

FEBS Letters, EarlyView.
The crystal structure of abMreC reveals a conserved two β‐barrel architecture and provides structural insights into its role within the bacterial elongasome. The abMreC–abPBP2 complex model identifies the molecular basis of MreC‐mediated PBP2 recognition, contributing to the regulation of peptidoglycan synthesis.
Hyunseok Jang, Hyo Been Jin, Chang Min Kim, So Yeon Lee, Hyun Ho Park   +4 more
wiley   +1 more source