Gene regulatory network inference resources: A practical overview

D Mercatelli, L Scalambra, L Triboli, F Ray… - Biochimica et Biophysica …, 2020 - Elsevier
Transcriptional regulation is a fundamental molecular mechanism involved in almost every
aspect of life, from homeostasis to development, from metabolism to behavior, from reaction …

Discerning molecular interactions: a comprehensive review on biomolecular interaction databases and network analysis tools

SK Miryala, A Anbarasu, S Ramaiah - Gene, 2018 - Elsevier
Computational analysis of biomolecular interaction networks is now gaining a lot of
importance to understand the functions of novel genes/proteins. Gene interaction (GI) …

Map** single-cell atlases throughout Metazoa unravels cell type evolution

AJ Tarashansky, JM Musser, M Khariton, P Li, D Arendt… - Elife, 2021 - elifesciences.org
Comparing single-cell transcriptomic atlases from diverse organisms can elucidate the
origins of cellular diversity and assist the annotation of new cell atlases. Yet, comparison …

Comparative analysis of the transcriptome across distant species

MB Gerstein, J Rozowsky, KK Yan, D Wang, C Cheng… - Nature, 2014 - nature.com
The transcriptome is the readout of the genome. Identifying common features in it across
distant species can reveal fundamental principles. To this end, the ENCODE and …

Comparative analyses of gene co-expression networks: Implementations and applications in the study of evolution

K Ovens, BF Eames, I McQuillan - Frontiers in Genetics, 2021 - frontiersin.org
Similarities and differences in the associations of biological entities among species can
provide us with a better understanding of evolutionary relationships. Often the evolution of …

Expression of immunoproteasome genes is regulated by cell-intrinsic and–extrinsic factors in human cancers

A Rouette, A Trofimov, D Haberl, G Boucher… - Scientific reports, 2016 - nature.com
Based on transcriptomic analyses of thousands of samples from The Cancer Genome Atlas,
we report that expression of constitutive proteasome (CP) genes (PSMB5, PSMB6, PSMB7) …

Evolutionary conservation and divergence of the human brain transcriptome

WG Pembroke, CL Hartl, DH Geschwind - Genome biology, 2021 - Springer
Background Mouse models have allowed for the direct interrogation of genetic effects on
molecular, physiological, and behavioral brain phenotypes. However, it is unknown to what …

How to utilize comparative transcriptomics to dissect morphological diversity in plants

S Li, H Nakayama, NR Sinha - Current Opinion in Plant Biology, 2023 - Elsevier
Comparative transcriptomics has emerged as a powerful approach that allows us to unravel
the genetic basis of organ morphogenesis and its diversification processes during evolution …

Changes in microbiota along the intestine of grass carp (Ctenopharyngodon idella): Community, interspecific interactions, and functions

G Yang, SQ Jian, H Cao, C Wen, B Hu, M Peng, L Peng… - Aquaculture, 2019 - Elsevier
The intestinal microbiota plays crucial roles in the nutrition uptake and metabolism in a
herbivorous fish, the grass carp (Ctenopharyngodon idella). Based on the 16S rRNA …

Molecular ecological network analysis reveals the effects of probiotics and florfenicol on intestinal microbiota homeostasis: an example of sea cucumber

G Yang, M Peng, X Tian, S Dong - Scientific Reports, 2017 - nature.com
Animal gut harbors diverse microbes that play crucial roles in the nutrition uptake,
metabolism, and the regulation of host immune responses. The intestinal microbiota …