Incomplete genomes

Despite the increasing recognition that microbial communities within the human body are linked to health, we have an incomplete understanding of the environmental and molecular interactions that shape the composition of these communities.

13p vibransone 28-03-2024 7 1   Download

The Wiskott–Aldrich syndrome protein (WASp) family of actin-nucleating factors are present in the cytoplasm and in the nucleus. The role of nuclear WASp for T cell development remains incompletely defined. Methods: We performed WASp chromatin immunoprecipitation and deep sequencing (ChIP-seq) in thymocytes and spleen CD4+ T cells.

18p vioraclene 31-03-2024 7 1   Download

Metagenome sampling bias for geographical location and lifestyle is partially responsible for the incomplete catalog of reference genomes of gut microbial species. Thus, genome assembly from currently underrepresented populations may effectively expand the reference gut microbiome and improve taxonomic and functional profiling.

20p vibransone 28-03-2024 4 2   Download

The human gut harbors trillions of microbes that play dynamic roles in health. While the microbiome contributes to many cardiometabolic traits by modulating host inflammation and metabolism, there is an incomplete understanding regarding the extent that and mechanisms by which individual microbes impact risk and development of cardiovascular disease (CVD).

16p vibransone 28-03-2024 8 2   Download

Antimicrobial resistance (AMR) is a major global public health threat, which has been largely driven by the excessive use of antimicrobials. Control measures are urgently needed to slow the trajectory of AMR but are hampered by an incomplete understanding of the interplay between pathogens, AMR encoding genes, and mobile genetic elements at a microbial level.

14p viellison 28-03-2024 2 2   Download

Acute kidney injury (AKI) occurs frequently in critically ill patients and is associated with adverse out‑ comes. Cellular mechanisms underlying AKI and kidney cell responses to injury remain incompletely understood.

18p viellison 28-03-2024 3 2   Download

The incidence of early-onset colorectal cancer (EOCRC; patients < 50 years old) has been rising rapidly, whereas the EOCRC genetic susceptibility remains incompletely investigated. Here, we aimed to systematically identify specific susceptible genetic variants for EOCRC.

19p vicwell 29-02-2024 4 1   Download

Biorepositories archive and distribute well-characterized biospecimens for research to support the development of medical diagnostics and therapeutics. Knowledge of biobanking and associated practices is incomplete in low- and middle-income countries where disease burden is disproportionately high.

10p vicwell 29-02-2024 3 2   Download

Cancer mutations accumulate through replication errors and DNA damage coupled with incomplete repair. Individual mutational processes often show nucleotide sequence and functional region preferences. As a result, some sequence contexts mutate at much higher rates than others, with additional variation found between functional regions.

19p vicwell 29-02-2024 2 1   Download

Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domestication history remain elusive.

16p vigalileogalilei 27-02-2022 11 1   Download

The human reference genome is still incomplete, especially for those population-specific or individual-specific regions, which may have important functions. Here, we developed a HUman Pan-genome ANalysis (HUPAN) system to build the human pan-genome.

11p vielonmusk 30-01-2022 10 0   Download

Diarrhea is the second leading cause of death in children under 5 years of age. Enhanced understanding of causal pathways, pathogenesis, and sequelae of diarrhea is urgently needed. Although the gut microbiota is believed to play a role in susceptibility to diarrheal diseases, our understanding of this association remains incomplete.

16p vielonmusk 30-01-2022 12 0   Download

Single-molecule long-read sequencing has been used to improve mRNA isoform identification. However, not all single-molecule long reads represent full transcripts due to incomplete cDNA synthesis and sequencing length limits.

18p vielonmusk 30-01-2022 6 0   Download

Ciliopathies are clinically diverse disorders of the primary cilium. Remarkable progress has been made in understanding the molecular basis of these genetically heterogeneous conditions; However, our knowledge of their morbid genome, pleiotropy, and variable expressivity remains incomplete.

11p vialfrednobel 29-01-2022 19 0   Download

Gene innovation by duplication is a fundamental evolutionary process but is difficult to study in humans due to the large size, high sequence identity, and mosaic nature of segmental duplication blocks.

16p vialfrednobel 29-01-2022 10 0   Download

Recent technological advances have enabled DNA methylation to be assayed at single-cell resolution. However, current protocols are limited by incomplete CpG coverage and hence methods to predict missing methylation states are critical to enable genome-wide analyses. We report DeepCpG, a computational approach based on deep neural networks to predict methylation states in single cells.

13p vialfrednobel 29-01-2022 20 0   Download

To facilitate indefinite proliferation, stem cells and most cancer cells require the activity of telomerase, which counteracts the successive shortening of telomeres caused by incomplete DNA replication at the very end of each chromosome.

17p viaristotle 29-01-2022 7 0   Download

Long non-coding RNAs (lncRNAs) are increasingly implicated as gene regulators and may ultimately be more numerous than protein-coding genes in the human genome. Despite large numbers of reported lncRNAs, reference annotations are likely incomplete due to their lower and tighter tissue-specific expression compared to mRNAs.

23p viaristotle 29-01-2022 10 0   Download

Understanding the mutational heterogeneity within tumors is a keystone for the development of efficient cancer therapies. Here, we present SCITE, a stochastic search algorithm to identify the evolutionary history of a tumor from noisy and incomplete mutation profiles of single cells.

17p viaristotle 29-01-2022 16 0   Download

Differentiation of lymphocytes is frequently accompanied by cell cycle changes, interplay that is of central importance for immunity but is still incompletely understood. Here, we interrogate and quantitatively model how proliferation is linked to differentiation in CD4+ T cells.

15p viaristotle 29-01-2022 9 0   Download