Current progress and open challenges for applying deep learning across the biosciences
Deep Learning (DL) has recently enabled unprecedented advances in one of the grand
challenges in computational biology: the half-century-old problem of protein structure …
challenges in computational biology: the half-century-old problem of protein structure …
Incorporating machine learning into established bioinformatics frameworks
N Auslander, AB Gussow, EV Koonin - International journal of molecular …, 2021 - mdpi.com
The exponential growth of biomedical data in recent years has urged the application of
numerous machine learning techniques to address emerging problems in biology and …
numerous machine learning techniques to address emerging problems in biology and …
AliSim: a fast and versatile phylogenetic sequence simulator for the genomic era
Sequence simulators play an important role in phylogenetics. Simulated data has many
applications, such as evaluating the performance of different methods, hypothesis testing …
applications, such as evaluating the performance of different methods, hypothesis testing …
[PDF][PDF] Forty years of inferential methods in the Journals of the Society for Molecular Biology and Evolution
CAM Russo, A Eyre-Walker, LA Katz… - Molecular Biology and …, 2024 - academic.oup.com
We are launching a series to celebrate the 40th anniversary of the first issue of Molecular
Biology and Evolution. In 2024, we will publish virtual issues containing selected papers …
Biology and Evolution. In 2024, we will publish virtual issues containing selected papers …
Simulations of sequence evolution: how (un) realistic they are and why
Motivation Simulating multiple sequence alignments (MSAs) using probabilistic models of
sequence evolution plays an important role in the evaluation of phylogenetic inference tools …
sequence evolution plays an important role in the evaluation of phylogenetic inference tools …
Excluding loci with substitution saturation improves inferences from phylogenomic data
The historical signal in nucleotide sequences becomes eroded over time by substitutions
occurring repeatedly at the same sites. This phenomenon, known as substitution saturation …
occurring repeatedly at the same sites. This phenomenon, known as substitution saturation …
Advances in the Applications of Bioinformatics and Chemoinformatics
MA Raslan, SA Raslan, EM Shehata, AS Mahmoud… - Pharmaceuticals, 2023 - mdpi.com
Chemoinformatics involves integrating the principles of physical chemistry with computer-
based and information science methodologies, commonly referred to as “in silico …
based and information science methodologies, commonly referred to as “in silico …
Remarks on phylogeny and molecular variations of criconematid species (Nematoda: Criconematidae) with case studies from Vietnam
The family Criconematidae is a remarkable group of nematodes, containing roughly 600
nominal root-ectoparasitic species, of which many species are known to be significant …
nominal root-ectoparasitic species, of which many species are known to be significant …
Applications of machine learning in phylogenetics
Abstract Machine learning has increasingly been applied to a wide range of questions in
phylogenetic inference. Supervised machine learning approaches that rely on simulated …
phylogenetic inference. Supervised machine learning approaches that rely on simulated …
Human follicular mites: Ectoparasites becoming symbionts
G Smith, A Manzano-Marín… - Molecular Biology …, 2022 - academic.oup.com
Most humans carry mites in the hair follicles of their skin for their entire lives. Follicular mites
are the only metazoans that continuously live on humans. We propose that Demodex …
are the only metazoans that continuously live on humans. We propose that Demodex …