Top 10 genomebiology.biomedcentral.com Competitors

biorxiv.org

biorxiv - the preprint server for biology, operated by cold spring harbor laboratory, a research and educational institution

bioconductor.org

Or: how I learned to stop worrying and love the t-SNEs.

genomebiology.com

Background The oocyte-to-embryo transition (OET) converts terminally differentiated gametes into a totipotent embryo and is critically controlled by maternal mRNAs and proteins, while the genome is silent until zygotic genome activation. How the transcriptome, translatome, and proteome are coordinated during this critical developmental window remains poorly understood. Results Utilizing a highly sensitive and quantitative mass spectrometry approach, we obtain high-quality proteome data spanning seven mouse stages, from full-grown oocyte (FGO) to blastocyst, using 100 oocytes/embryos at each stage. Integrative analyses reveal distinct proteome reprogramming compared to that of the transcriptome or translatome. FGO to 8-cell proteomes are dominated by FGO-stockpiled proteins, while the transcriptome and translatome are more dynamic. FGO-originated proteins frequently persist to blastocyst while corresponding transcripts are already downregulated or decayed. Improved concordance between protein and translation or transcription is observed for genes starting translation upon meiotic resumption, as well as those transcribed and translated only in embryos. Concordance between protein and transcription/translation is also observed for proteins with short half-lives. We built a kinetic model that predicts protein dynamics by incorporating both initial protein abundance in FGOs and translation kinetics across developmental stages. Conclusions Through integrative analyses of datasets generated by ultrasensitive methods, our study reveals that the proteome shows distinct dynamics compared to the translatome and transcriptome during mouse OET. We propose that the remarkably stable oocyte-originated proteome may help save resources to accommodate the demanding needs of growing embryos. This study will advance our understanding of mammalian OET and the fundamental principles governing gene expression.

cell.com

publisher of over 50 scientific journals across the life, physical, earth, and health sciences, both independently and in partnership with scientific societies including cell, neuron, immunity, current biology, ajhg, and the trends journals.

davidemms.github.io

In the last tutorial (Running an example OrthoFinder analysis) we downloaded proteomes for 6 model species, pre-processed these files and ran OrthoFinder on them. If you haven’t done these steps yourself you can download the results from here: Results_model_species.tar.gz.

elifesciences.org

eLife reviews research in areas including cell migration, proliferation and differentiation, and inductive and signaling interactions. Learn more about what we review and sign up for the latest research.

frontiersin.org

Our highly competitive publishing fees, charged to authors or institutions enable us to provide industry-leading services for our authors, editors, and readers

embopress.org

embo press is an editorially independent publishing platform for the development of embo scientific publications.

nature.com

Nature is the foremost international weekly scientific journal in the world and is the flagship journal for Nature Portfolio. It publishes the finest ...