Results 61 to 70 of about 283,388 (253)

A comparison of short- and long-read whole-genome sequencing for microbial pathogen epidemiology

mSystems
Whole-genome sequencing provides the highest resolution for characterizing pathogen evolution, epidemiology, and diagnostics. Genome assemblies contain information on the identity and potential phenotypes of a pathogen.
Andrea M. Schiffer, Arafat Rahman, Wendy Sutton, Melodie L. Putnam, Alexandra J. Weisberg   +4 more
doaj   +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

The Shewanella oneidensis Fic enzyme SoFic targets the switch‐I region of EF‐Tu for AMPylation

FEBS Letters, EarlyView.
Fic enzymes mediate diverse post‐translational modifications across all domains of life, including AMPylation. Prokaryotic EF‐Tu can be AMPylated and deAMPylated by the conserved Fic enzyme SoFic. Structural and biochemical approaches were used to characterize the effect of AMPylation on EF‐Tu, SoFic's enzymatic activities, and the enzyme‐target ...
Svenja Runge, Vivian Pogenberg, Alexander Baumgart, Bente Siebels, Hartmut Schlüter, Michael Hecht‐Bucher, Aymelt Itzen   +6 more
wiley   +1 more source

RAPSearch: a fast protein similarity search tool for short reads

BMC Bioinformatics, 2011
Background Next Generation Sequencing (NGS) is producing enormous corpuses of short DNA reads, affecting emerging fields like metagenomics. Protein similarity search--a key step to achieve annotation of protein-coding genes in these short reads, and ...
Choi Jeong-Hyeon, Ye Yuzhen, Tang Haixu
doaj   +1 more source

Fast mapping of short sequences with mismatches, insertions and deletions using index structures. [PDF]

PLoS Computational Biology, 2009
With few exceptions, current methods for short read mapping make use of simple seed heuristics to speed up the search. Most of the underlying matching models neglect the necessity to allow not only mismatches, but also insertions and deletions.
Steve Hoffmann, Christian Otto, Stefan Kurtz, Cynthia M Sharma, Philipp Khaitovich, Jörg Vogel, Peter F Stadler, Jörg Hackermüller   +7 more
doaj   +1 more source

Invisible but not inaccessible—Revealing transient oligomers formed by intrinsically disordered proteins with solution NMR and complementary methods

FEBS Letters, EarlyView.
Transient oligomers formed by intrinsically disordered proteins may be ‘invisible’ to direct detection yet remain accessible to solution NMR through equilibrium‐exchange measurements and pressure‐jump experiments. Complementary methods report on mass, stoichiometry, selected distance distributions, morphology, and internal packing.
Martin D. Gelenter, Ad Bax
wiley   +1 more source

Tumour–host interactions in Drosophila: mechanisms in the tumour micro‐ and macroenvironment

Molecular Oncology, EarlyView.
This review examines how tumour–host crosstalk takes place at multiple levels of biological organisation, from local cell competition and immune crosstalk to organism‐wide metabolic and physiological collapse. Here, we integrate findings from Drosophila melanogaster studies that reveal conserved mechanisms through which tumours hijack host systems to ...
José Teles‐Reis, Tor Erik Rusten
wiley   +1 more source

Mapping short reads, faithfully [PDF]

, 2020
Abstract Mapping is the process of finding the original location of a DNA read in a reference sequence, typically a genome. Short read mappers are software tools used in most applications that involve high-throughput sequencing. As such, they must be continuously improved to keep up with increasing needs.
Zorita, Eduard Valera, Cortini, Ruggero, Filion, Guillaume J.   +2 more
openaire   +1 more source

Transcriptional profiling of circulating extracellular vesicles from prebiopsy prostate cancer patients

Molecular Oncology, EarlyView.
RNA profiling of circulating extracellular vesicles (EVs) from blood samples of men undergoing prostate biopsy identifies transcripts associated with clinically significant prostate cancer. Integrative analysis with public tumor datasets links EV‐derived gene signatures to tumor stage and progression‐free survival, highlighting CASP3, XRCC2, and RIT1 ...
Stefan Werner, Pierre Tennstedt, Randi C. Pose, Christian Müller, Katharina Besler, Svenja Schneegans, Malik Alawi, Marie C. Roesch, Sven Peine, Desiree Bonci, Joanna Budna‐Tukan, Evi Lianidou, Catherine Alix‐Panabières, Derya Tilki, Klaus Pantel   +14 more
wiley   +1 more source

Towards a better understanding of the low recall of insertion variants with short-read based variant callers

BMC Genomics, 2020
Background Since 2009, numerous tools have been developed to detect structural variants using short read technologies. Insertions >50 bp are one of the hardest type to discover and are drastically underrepresented in gold standard variant callsets.
Wesley J. Delage, Julien Thevenon, Claire Lemaitre   +2 more
doaj   +1 more source