Investigating differential abundance methods in microbiome data: A benchmark study

M Cappellato, G Baruzzo… - PLoS computational …, 2022 - journals.plos.org
The development of increasingly efficient and cost-effective high throughput DNA
sequencing techniques has enhanced the possibility of studying complex microbial systems …

Duodenum Intestine-Chip for preclinical drug assessment in a human relevant model

M Kasendra, R Luc, J Yin, DV Manatakis, G Kulkarni… - Elife, 2020 - elifesciences.org
Induction of intestinal drug metabolizing enzymes can complicate the development of new
drugs, owing to the potential to cause drug-drug interactions (DDIs) leading to changes in …

[PDF][PDF] Rasusa: Randomly subsample sequencing reads to a specified coverage

MB Hall - Journal of open source software, 2022 - joss.theoj.org
A fundamental requirement for many applications in genomics is the sequencing of genetic
material (DNA/RNA). Different sequencing technologies exist, but all aim to accurately …

[HTML][HTML] Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review

D Rosati, M Palmieri, G Brunelli, A Morrione… - Computational and …, 2024 - Elsevier
In recent years, the role of bioinformatics and computational biology together with omics
techniques and transcriptomics has gained tremendous importance in biomedicine and …

NOTCH signaling pathway is required for bovine early embryonic development

S Li, Y Shi, Y Dang, L Luo, B Hu, S Wang… - Biology of …, 2021 - academic.oup.com
The NOTCH signaling pathway plays an important role in regulating various biological
processes, including lineage specification and apoptosis. Multiple components of the …

Library adaptors with integrated reference controls improve the accuracy and reliability of nanopore sequencing

HM Gunter, SE Youlten, BS Madala, ALM Reis… - Nature …, 2022 - nature.com
Library adaptors are short oligonucleotides that are attached to RNA and DNA samples in
preparation for next-generation sequencing (NGS). Adaptors can also include additional …

Proteomic profiling of IgA nephropathy reveals distinct molecular prognostic subtypes

X Chen, M Li, S Zhu, Y Lu, S Duan, X Wang, Y Wang… - Iscience, 2023 - cell.com
IgA nephropathy (IgAN) is a heterogeneous disease, which poses a series of challenges to
accurate diagnosis and personalized therapy. Herein, we constructed a systematic …

Immune system modulation & virus transmission during parasitism identified by multi-species transcriptomics of a declining insect biocontrol system

SN Inwood, TWR Harrop, MW Shields, SL Goldson… - BMC genomics, 2024 - Springer
Abstract Background The Argentine stem weevil (ASW, Listronotus bonariensis) is a
significant pasture pest in Aotearoa New Zealand, primarily controlled by the parasitoid …

Comparative analysis of rRNA removal methods for RNA-Seq differential expression in halophilic archaea

MM Pastor, S Sakrikar, DN Rodriguez, AK Schmid - Biomolecules, 2022 - mdpi.com
Despite intense recent research interest in archaea, the scientific community has
experienced a bottleneck in the study of genome-scale gene expression experiments by …

Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature

JA Scarborough, SA Eschrich, J Torres-Roca… - NPJ Precision …, 2023 - nature.com
Precision medicine offers remarkable potential for the treatment of cancer, but is largely
focused on tumors that harbor actionable mutations. Gene expression signatures can …