A5004385228- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Bacteriophages and microbial interactions
- RNA Research and Splicing
- Microbial Community Ecology and Physiology
- Animal Genetics and Reproduction
- CRISPR and Genetic Engineering
- RNA modifications and cancer
- Genomics and Chromatin Dynamics
- MicroRNA in disease regulation
- Machine Learning in Bioinformatics
- Chromosomal and Genetic Variations
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Sperm and Testicular Function
- Gut microbiota and health
- Vibrio bacteria research studies
- Circular RNAs in diseases
- Antimicrobial Peptides and Activities
- Probiotics and Fermented Foods
- Escherichia coli research studies
- Cancer-related molecular mechanisms research
- Plant Reproductive Biology
- Histone Deacetylase Inhibitors Research
- Bacterial Genetics and Biotechnology
- Protein Hydrolysis and Bioactive Peptides
Ohana Biosciences (United States)
2019-2022
Inserm
2015-2017
Institut Pasteur
2013-2017
Department of Genomes & Genetics
2017
Massachusetts Institute of Technology
2008-2011
Whitehead Institute for Biomedical Research
2008-2010
Howard Hughes Medical Institute
2008
University of California, San Diego
2004-2006
MicroRNAs (miRNAs) are small endogenous RNAs that pair to sites in mRNAs direct post-transcriptional repression. Many match the miRNA seed (nucleotides 2–7), particularly those 3′ untranslated regions (3′UTRs), preferentially conserved. Here, we overhauled our tool for finding preferential conservation of sequence motifs and applied it analysis human 3′UTRs, increasing by nearly threefold detected number conserved target sites. The new more efficiently incorporates genomes completely...
Background. Chronic hepatitis C virus (HCV)–induced liver fibrosis involves upregulation of transforming growth factor (TGF)–β and subsequent hepatic stellate cell (HSC) activation. MicroRNAs (miRNAs) regulate HCV infection HSC Methods. TaqMan miRNA profiling identified 12 families differentially expressed between chronically HCV-infected human livers uninfected controls. To identify pathways affected by miRNAs, we developed a new algorithm (pathway analysis conserved targets), based on the...
Significance Antimicrobial peptides exert antimicrobial, antifungal, antiviral, and antiprotozoan activity. They are expressed at high concentrations the intestinal mucosal surface, where they play a crucial role in homeostasis. Therefore, approaches aiming to boost expression of antimicrobial represent future therapeutic strategy treat infections dysbiosis-driven diseases humans time increasing incidence antibiotic resistance.
Sperm-specific natural selection Sperm cells are genetically haploid, but because of the cytoplasmic bridges that link cells, they can be transcriptionally diploid. However, some gene transcripts not shared. Bhutani et al. sequenced single sperm from mice, cattle, and macaques to determine extent distortion in expression these putatively selfish transcripts, which authors call genoinformative markers (GIMs). Investigating evolutionary pressures on GIMs, found exhibited signatures positive...
Abstract Transmission distorters (TDs) are genetic elements that favor their own transmission to the detriments of others. Slx/Slxl1 (Sycp3-like-X-linked and Slx-like1) Sly (Sycp3-like-Y-linked) TDs, which have been coamplified on X Y chromosomes Mus species. They involved in an intragenomic conflict each favors its transmission, resulting sex ratio distortion progeny when versus copy number is unbalanced. specifically expressed male postmeiotic gametes (spermatids) opposite effects gene...
While eukaryotic noncoding RNAs have recently received intense scrutiny, it is becoming clear that bacterial transcription at least as pervasive. Bacterial small and antisense (sRNAs) are often assumed to be noncoding, due their lack of long open reading frames (ORFs). However, there numerous examples sRNAs encoding for proteins, whether or not they also a regulatory role the RNA level. Here, we apply flexible machine learning techniques based on sequence features comparative genomics...
Many human Gram-negative bacterial pathogens express a Type Three Secretion Apparatus (T3SA), including among the most notorious Shigella spp., Salmonella enterica, Yersinia enterocolitica and enteropathogenic Escherichia coli (EPEC). These bacteria on their surface multiple copies of T3SA that mediate delivery into host cells specific protein substrates critical to pathogenesis. spp. are responsible for bacillary dysentery. The effector function several has largely been studied but...
1 Abstract Mendel’s first law dictates that alleles segregate randomly during meiosis and are distributed to offspring with equal frequency, requiring sperm be functionally independent of their genetic payload. Developing mammalian spermatids have been thought accomplish this by freely sharing RNA from virtually all genes through cytoplasmic bridges, equalizing allelic gene expression across different genotypes. Applying single cell sequencing developing spermatids, we identify a large class...
Abstract Meiosis, recombination, and gametogenesis normally ensure that gametes combine randomly. But in exceptional cases, fertilization depends on the genetics of from both females males. A key question is whether their non-random union results factors intrinsic to oocytes sperm, or interactions with conditions reproductive tracts. To address this question, we used vitro (IVF) a mutant wild-type allele A1cf (APOBEC1 complementation factor) gene mice are otherwise genetically identical. We...
Sequence homologs are an important source of information about proteins. Amino acid profiles, representing the position-specific mutation probabilities found in a richer encoding biological sequences than individual themselves. However, profile comparisons order magnitude slower sequence comparisons, making profiles impractical for large datasets. Also, because they such rich representation, difficult to visualize. To address these problems, we describe method map probabilistic discrete...
While eukaryotic noncoding RNAs have recently received intense scrutiny, it is becoming clear that bacterial transcription at least as pervasive. Bacterial small and antisense (sRNAs) are often assumed to be noncoding, due their lack of long open reading frames (ORFs). However, there numerous examples sRNAs encoding for proteins, whether or not they also a regulatory role the RNA level. Here, we apply flexible machine learning techniques based on sequence features comparative genomics...