Results 61 to 70 of about 393,868 (257)

N-terminal proteomics assisted profiling of the unexplored translation initiation landscape in Arabidopsis thaliana [PDF]

, 2017
Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in ...
Gevaert, Kris, Jonckheere, Veronique, Martens, Lennart, Ndah, Elvis, Stael, Simon, Sticker, Adriaan, Van Breusegem, Frank, Van Damme, Petra, Willems, Patrick   +8 more
core   +1 more source

A Cre‐dependent lentiviral vector for neuron subtype‐specific expression of large proteins

FEBS Letters, EarlyView.
We designed a versatile and modular lentivector comprising a Cre‐dependent switch and self‐cleaving 2A peptide and tested it for co‐expression of GFP and a 2.8 kb gene of interest (GOI) in mouse cortical parvalbumin (PV+) interneurons and midbrain dopamine (TH+) neurons.
Weixuan Xue, Sandrine Picaud, Régine Hepp, Stéphanie Pons, Uwe Maskos, Bertrand Lambolez, Ludovic Tricoire   +6 more
wiley   +1 more source

GOPET: A tool for automated predictions of Gene Ontology terms

BMC Bioinformatics, 2006
Background Vast progress in sequencing projects has called for annotation on a large scale. A Number of methods have been developed to address this challenging task.
Glatting Karl-Heinz, Eils Roland, Schubert Falk, del Val Coral, Vinayagam Arunachalam, Suhai Sándor, König Rainer   +6 more
doaj   +1 more source

By dawn or dusk—how circadian timing rewrites bacterial infection outcomes

FEBS Letters, EarlyView.
The circadian clock shapes immune function, yet its influence on infection outcomes is only beginning to be understood. This review highlights how circadian timing alters host responses to the bacterial pathogens Salmonella enterica, Listeria monocytogenes, and Streptococcus pneumoniae revealing that the effectiveness of immune defense depends not only
Devons Mo, Catherine S. Palmer, Jacqueline M. Kimmey   +2 more
wiley   +1 more source

Improvements in viral gene annotation using large language models and soft alignments

BMC Bioinformatics
Background The annotation of protein sequences in public databases has long posed a challenge in molecular biology. This issue is particularly acute for viral proteins, which demonstrate limited homology to known proteins when using alignment, k-mer, or ...
William L. Harrigan, Barbra D. Ferrell, K. Eric Wommack, Shawn W. Polson, Zachary D. Schreiber, Mahdi Belcaid   +5 more
doaj   +1 more source

Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line

BMC Genomics, 2020
Background The process of identifying all coding regions in a genome is crucial for any study at the level of molecular biology, ranging from single-gene cloning to genome-wide measurements using RNA-seq or mass spectrometry.
Michal Levin, Marion Scheibe, Falk Butter   +2 more
doaj   +1 more source

Molecular bases of circadian magnesium rhythms across eukaryotes

FEBS Letters, EarlyView.
Circadian rhythms in intracellular [Mg2+] exist across eukaryotic kingdoms. Central roles for Mg2+ in metabolism suggest that Mg2+ rhythms could regulate daily cellular energy and metabolism. In this Perspective paper, we propose that ancestral prokaryotic transport proteins could be responsible for mediating Mg2+ rhythms and posit a feedback model ...
Helen K. Feord, Gerben van Ooijen
wiley   +1 more source

Draft genome sequence of Venturia carpophila, the causal agent of peach scab

Standards in Genomic Sciences, 2017
Venturia carpophila causes peach scab, a disease that renders peach (Prunus persica) fruit unmarketable. We report a high-quality draft genome sequence (36.9 Mb) of V.
Chunxian Chen, Clive H. Bock, Bruce W. Wood   +2 more
doaj   +1 more source

Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities. [PDF]

PLoS ONE, 2010
High-throughput Structural Genomics yields many new protein structures without known molecular function. This study aims to uncover these missing annotations by globally comparing select functional residues across the structural proteome.
Eric Venner, Andreas Martin Lisewski, Serkan Erdin, R Matthew Ward, Shivas R Amin, Olivier Lichtarge   +5 more
doaj   +1 more source

Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA). [PDF]

, 2010
Alicyclobacillus acidocaldarius (Darland and Brock 1971) is the type species of the larger of the two genera in the bacillal family 'Alicyclobacillaceae'. A.
Brettin, Thomas, Bristow, Jim, Bruce, David, Chain, Patrick, Chang, Yun-Juan, Chen, Amy, Chen, Feng, Cheng, Jan-Fang, Chertkov, Olga, Copeland, Alex, Detter, John C, Eisen, Jonathan A, Glavina Del Rio, Tijana, Goodwin, Lynne, Göker, Markus, Han, Cliff, Hauser, Loren, Hugenholtz, Philip, Ivanova, Natalia, Jeffries, Cynthia D, Klenk, Hans-Peter, Kyrpides, Nikos C, Land, Miriam, Lapidus, Alla, Lucas, Susan, Markowitz, Victor, Mavromatis, Konstantinos, Meincke, Linda, Nolan, Matt, Ovchinnikova, Galina, Palaniappan, Krishna, Pati, Amrita, Pitluck, Sam, Pukall, Rüdiger, Rohde, Manfred, Sikorski, Johannes, Sims, David, Tice, Hope, Wahrenburg, Claudia   +38 more
core   +2 more sources