AIMC Topic: Phylogeny
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StomataCounter: a neural network for automatic stomata identification and counting.
The New phytologist
Jul 4, 2019
Stomata regulate important physiological processes in plants and are often phenotyped by researchers in diverse fields of plant biology. Currently, there are no user-friendly, fully automated methods to perform the task of identifying and counting st...
Artificial Neural Networks (ANNs) and Response Surface Methodology (RSM) Approach for Modelling the Optimization of Chromium (VI) Reduction by Newly Isolated Strain NS-MIE from Agricultural Soil.
BioMed research international
May 26, 2019
Numerous technologies and approaches have been used in the past few decades to remove hexavalent chromium (Cr[VI]) in wastewater and the environment. However, these conventional technologies are not economical and efficient in removing Cr(VI) at a ve...
Phy-PMRFI: Phylogeny-Aware Prediction of Metagenomic Functions Using Random Forest Feature Importance.
IEEE transactions on nanobioscience
Apr 24, 2019
High-throughput sequencing techniques have accelerated functional metagenomics studies through the generation of large volumes of omics data. The integration of these data using computational approaches is potentially useful for predicting metagenomi...
Multi-task learning improves ancestral state reconstruction.
Theoretical population biology
Jan 11, 2019
We consider the ancestral state reconstruction problem where we need to infer phenotypes of ancestors using observations from present-day species. For this problem, we propose a multi-task learning method that uses regularized maximum likelihood to e...
OMeta: an ontology-based, data-driven metadata tracking system.
BMC bioinformatics
Jan 7, 2019
BACKGROUND: The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metagenomes, and infectious disease pathogens. Omics studies are enabling genotype-phenotype association stu...
Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase.
BMC evolutionary biology
Dec 22, 2018
BACKGROUND: The family of D-isomer specific 2-hydroxyacid dehydrogenases (2HADHs) contains a wide range of oxidoreductases with various metabolic roles as well as biotechnological applications. Despite a vast amount of biochemical and structural data...
Giardia duodenalis assemblages in cats from Virginia, USA.
Veterinary parasitology, regional studies and reports
Dec 18, 2018
Giardia duodenalis is considered a species complex that is divided into 8 genetically distinct but morphologically identical assemblages (A-H). Assemblages C-H are generally host adapted, while A and B infect both people and animals and are considere...
Molecular phylogenetic investigations of Triops granarius (Lucas, 1864 (Branchiopoda: Notostraca) from the type locality of the former Apus orientalis Tiwari, 1952 and three other localities in the Western Ghats of India.
Zootaxa
Dec 14, 2018
We investigated the phylogenetic position of Triops granarius populations from four localities in the Western Ghats using partial sequences of three mitochondrial genes (COI, 12S rRNA and 16S rRNA) publicly available on the GenBank database. One of t...
Inferring locomotor behaviours in Miocene New World monkeys using finite element analysis, geometric morphometrics and machine-learning classification techniques applied to talar morphology.
Journal of the Royal Society, Interface
Sep 26, 2018
The talus is one of the most commonly preserved post-cranial elements in the platyrrhine fossil record. Talar morphology can provide information about postural adaptations because it is the anatomical structure responsible for transmitting body mass ...
Combinatorial Scoring of Phylogenetic Trees and Networks Based on Homoplasy-Free Characters.
Journal of computational biology : a journal of computational molecular cell biology
Aug 22, 2018
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for tree/netw...
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