Results 51 to 60 of about 9,152,726 (291)

Utility of long-read sequencing for All of Us

Nature Communications, 2023
Abstract The All of Us (AoU) initiative aims to sequence the genomes of over one million Americans from diverse ethnic backgrounds to improve personalized medical care. In a recent technical pilot, we compare the performance of traditional short-read sequencing with long-read sequencing in a small cohort of samples from the HapMap ...
M. Mahmoud, Y. Huang, K. Garimella, P. A. Audano, W. Wan, N. Prasad, R. E. Handsaker, S. Hall, A. Pionzio, M. C. Schatz, M. E. Talkowski, E. E. Eichler, S. E. Levy, F. J. Sedlazeck   +13 more
openaire   +4 more sources

Investigating transcription factor dynamics in health and disease using FRAP

FEBS Letters, EarlyView.
FRAP analysis of GFP‐tagged transcription factors reveals how molecular mobility and target engagement change in response to drug treatment. By combining live‐cell imaging, quantitative model fitting, and statistical analysis, this approach uncovers transcription factor dynamics linked to disease mechanisms, providing a powerful framework for ...
Kannan Govindaraj, Carolina Vazquez Garzon, Jose Joaquin Velasco, Janine N. Post   +3 more
wiley   +1 more source

Opportunities and challenges in long-read sequencing data analysis [PDF]

, 2020
Long-read technologies are overcoming early limitations in accuracy and throughput, broadening their application domains in genomics. Dedicated analysis tools that take into account the characteristics of long-read data are thus required, but the fast ...
Amarasinghe, SL, Zappia, L, Su, S, Ritchie, ME, Gouil, Q, Dong, X   +5 more
core   +1 more source

lra: A long read aligner for sequences and contigs

PLOS Computational Biology, 2021
It is computationally challenging to detect variation by aligning single-molecule sequencing (SMS) reads, or contigs from SMS assemblies. One approach to efficiently align SMS reads is sparse dynamic programming (SDP), where optimal chains of exact matches are found between the sequence and the genome.
Jingwen Ren, Mark J. P. Chaisson
openaire   +5 more sources

Partial depletion of plasminogen activator inhibitor‐1 decreases subcutaneous fat cell hypertrophy and liver cholesterol in high‐fat‐fed female mice

FEBS Letters, EarlyView.
Obesity raises blood levels of PAI‐1, a protein linked to metabolic dysfunction‐associated steatotic liver disease in people with obesity. In female mice fed a high‐fat diet, partially lowering PAI‐1 led to smaller subcutaneous fat cells and lower liver cholesterol, without changing body weight or insulin sensitivity.
Claudia E. Ramirez Bustamante, Robert Sharp, Pradip K. Saha, Elizabeth S. Anaya, Elizabeth L. Lieu, Evelyn L. de Groot, Pooja Patel, Mi Jeong Heo, Aaron R. Cox, Kang Ho Kim, Sean M. Hartig   +10 more
wiley   +1 more source

Synergistic perspectives—How single‐molecule biophysics complement biochemical understanding

FEBS Letters, EarlyView.
In this review, we discuss how ensemble biochemistry and single‐molecule approaches are complementary, outline commonly used single‐molecule techniques, and illustrate their relevance through two representative case studies: chromatin organization by SMC complexes and pathway choice during DNA double‐strand break repair.
Sara De Bragança, Eline L. Jansen, Jorine M. Eeftens   +2 more
wiley   +1 more source

Can long-read sequencing tackle the barriers, which the next-generation could not? A review

Pathology and Oncology Research
The large-scale heterogeneity of genetic diseases necessitated the deeper examination of nucleotide sequence alterations enhancing the discovery of new targeted drug attack points.
Nikolett Szakállas, Barbara K. Barták, Gábor Valcz, Gábor Valcz, Zsófia B. Nagy, István Takács, Béla Molnár   +6 more
doaj   +1 more source

Functional comparison of EncB and EncC cargo proteins in iron storage within the Myxococcus xanthus encapsulin

FEBS Letters, EarlyView.
Encapsulins are protein nanocompartments that play an important role in iron storage. In the Myxococcus xanthus encapsulin system, two cargo proteins called EncB and EncC contribute to iron mineralization. Here, we show that EncB and EncC generate iron‐containing minerals with distinct chemical compositions, suggesting that the composition of stored ...
Harry B. McDowell, Thomas Walther, Egbert Hoiczyk   +2 more
wiley   +1 more source

Comparison of short-read and long-read sequencing of TprK.

, 2020
Comparison of the determination of identical amino acid sequences in each of the variable regions of TprK through short-read (Illumina) and long-read (PacBio CCS) sequencing approaches for A) the initial strain, UW-148B and B) the reinfecting strain, UW ...
Amin Addetia (8201538), Lauren C. Tantalo (8677368), Christina M. Marra (8677374), Hong Xie (133048), Meei-Li Huang (342097), Alexander L. Greninger (8677377), Michelle J. Lin (8677371)   +6 more
core   +1 more source

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing [PDF]

, 2017
Accurate annotation of genes and their transcripts is a foundation of genomics, but currently no annotation technique combines throughput and accuracy.
Abad, Amaya, Barbara Uszczynska-Ratajczak, Thomas R Gingeras, Lagarde, J., Sílvia Pérez-Lluch, Gingeras, Thomas R, Lagarde, Julien, Johnson, R., Jennifer Harrow, Uszczynska-Ratajczak, Barbara, Silvia Carbonell, Guigó Serra, Roderic, Gingeras, T. R., Amaya Abad, Frankish, Adam, Davis, C., Uszczynska-Ratajczak, B., Frankish, A., Carrie Davis, Pérez-Lluch, Sílvia, Gingeras, Thomas R., Adam Frankish, Perez-Lluch, S., Guigo, R., Julien Lagarde, Harrow, J., Carbonell, Silvia, Rory Johnson, Harrow, Jennifer, Davis, Carrie, Johnson, Rory, Guigo, Roderic, Roderic Guigo, Carbonell, S., Davis, Carrie A., Abad, A.   +35 more
core   +3 more sources