Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References

DJ Taylor, JM Eizenga, Q Li, A Das… - Annual Review of …, 2024 - annualreviews.org
The Human Genome Project was an enormous accomplishment, providing a foundation for
countless explorations into the genetics and genomics of the human species. Yet for many …

Genomes in clinical care

O Riess, M Sturm, B Menden, A Liebmann… - Npj Genomic …, 2024 - nature.com
In the era of precision medicine, genome sequencing (GS) has become more affordable and
the importance of genomics and multi-omics in clinical care is increasingly being …

Long-read sequencing (method of the year 2022): the way forward for plant omics research

SK Sahu, H Liu - Molecular Plant, 2023 - cell.com
Long-read sequencing (LRS) technology along with the recent development of
computational tools, crowned the ''method of the year 2022''(Marx, 2023), have made it …

Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome

JH Maeng, HJ Jang, AY Du, SC Tzeng… - Genome …, 2023 - genome.cshlp.org
Recent studies have shown that the noncoding genome can produce unannotated proteins
as antigens that induce immune response. One major source of this activity is the aberrant …

Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads

SW Han, S Jewell, A Thomas-Tikhonenko… - Genome …, 2024 - genome.cshlp.org
Mapping transcriptomic variations using either short-or long-read RNA sequencing is a
staple of genomic research. Long reads are able to capture entire isoforms and overcome …

Postmortem Muscle Proteome Characteristics of Silver Carp (Hypophthalmichthys molitrix): Insights from Full-Length Transcriptome and Deep 4D Label-Free …

X Jiao, X Li, N Zhang, W Zhang, B Yan… - Journal of Agricultural …, 2024 - ACS Publications
The coverage of the protein database directly determines the results of shotgun proteomics.
In this study, PacBio single-molecule real-time sequencing technology was performed on …

Structural evidence for MADS‐box type I family expansion seen in new assemblies of Arabidopsis arenosa and A. lyrata

J Bramsiepe, AK Krabberød, KN Bjerkan… - The Plant …, 2023 - Wiley Online Library
Arabidopsis thaliana diverged from A. arenosa and A. lyrata at least 6 million years ago. The
three species differ by genome‐wide polymorphisms and morphological traits. The species …

Pervasive transcription of plant organelle genomes: functional noncoding transcriptomes?

MS Lima, AR Paschoal, DS Domingues… - Trends in Plant Science, 2024 - cell.com
Plant mitochondrial and plastid genomes typically show pervasive, genome-wide
transcription. Little is known, however, about the utility of organelle noncoding RNAs, which …

Genomic structural variation: A complex but important driver of human evolution

DC Soto, JM Uribe‐Salazar, CJ Shew… - American Journal of …, 2023 - Wiley Online Library
Structural variants (SVs)—including duplications, deletions, and inversions of DNA—can
have significant genomic and functional impacts but are technically difficult to identify and …

Causes and Consequences of Varying Transposable Element Activity: An Evolutionary Perspective

AJ Betancourt, KHC Wei, Y Huang… - Annual Review of …, 2024 - annualreviews.org
Transposable elements (TEs) are genomic parasites found in nearly all eukaryotes,
including humans. This evolutionary success of TEs is due to their replicative activity …