Daniel A. Janies

H5N1 Influenza A is now promiscuous in host range and has improved replication in mammals

This study analyzes the spread and adaptation of H5N1 influenza in North America, finding increased host range and improved mammalian replication, with reduced antiviral effectiveness in some isolates.

Adaptive evolution of Plasmodium vivax in Duffy-negative hosts; insights from East African genomes

This study analyzes genome-wide SNPs in Plasmodium vivax isolates from Duffy-negative and Duffy-positive hosts in Ethiopia, identifying genetic adaptations associated with DARC-independent invasion mechanisms.

Large-Scale Computational Modeling of H5 Influenza Variants Against HA1-Neutralizing Antibodies

This study computationally models H5 influenza variants against HA1-neutralizing antibodies, showing weakening antibody binding over time and increased immune evasion risks.

Predicting Antibody and ACE2 Affinity for SARS-CoV-2 BA.2.86 and JN.1 with In Silico Protein Modeling and Docking

This study predicts binding affinity between SARS-CoV-2 variants BA.2.86 and JN.1 and antibodies/ACE2 using in silico modeling, finding minor reductions in affinity but no significant immune escape.

Protein interaction analysis of Plasmodium falciparum circumsporozoite protein variants with human immunoproteins explains RTS,S vaccine efficacy in Ghana

The paper analyzes Plasmodium falciparum CSP variants' interactions with human immunoproteins to explain RTS,S vaccine efficacy in Ghana, finding that peptide length affects binding affinity and immune response.

EchinoDB: An update to the web-based application for genomic and transcriptomic data on Echinoderms.

EchinoDB is updated to include new RNA-seq and genomic data, improved search features, and cloud-based infrastructure for echinoderm genomic and transcriptomic data.

Predictions of the SARS-CoV-2 Omicron Variant (B.1.1.529) Spike Protein Receptor-Binding Domain Structure and Neutralizing Antibody Interactions

This study predicts structural changes in the SARS-CoV-2 Omicron variant's spike protein receptor-binding domain and their impact on neutralizing antibody interactions.

Whole Genome Sequencing of Plasmodium vivax Isolates Reveals Frequent Sequence and Structural Polymorphisms in Erythrocyte Binding Genes

This study analyzes whole genome sequences of Plasmodium vivax isolates from Ethiopia to identify sequence and structural polymorphisms in erythrocyte binding genes, revealing positive selection and gene copy number variations associated with host-parasite interactions.

Active Notch Signaling is Required for Arm Regeneration in a Brittle Star

This study shows Notch signaling is essential for arm regeneration in brittle stars and identifies its role in regulating extracellular matrix, cell migration, and transposable elements.

Ensemble Machine Learning Modeling for the Prediction of Artemisinin Resistance in Malaria

This paper develops ensemble machine learning models to predict Artemisinin resistance and parasite clearance rates in Plasmodium falciparum isolates using transformed data and preprocessing techniques.

Updated phylogeny of Chikungunya virus suggests lineage-specific RNA architecture

The paper updates the phylogeny of Chikungunya virus and identifies lineage-specific RNA architecture in its untranslated regions.

StrainHub: A phylogenetic tool to construct pathogen transmission networks

StrainHub constructs pathogen transmission networks using phylogenetic trees and metadata to identify key nodes for infection control.

Tracking a Serial Killer: Integrating Phylogenetic Relationships, Epidemiology, and Geography for Two Invasive Meningococcal Disease Outbreaks

The paper uses whole genome sequencing and network analysis to study two meningococcal disease outbreaks in NYC, identifying transmission patterns and genomic characteristics.