Affiliation: Children's Hospital Oakland Research Institute
- Circulating blood leukocyte gene expression profiles: effects of the Ames dwarf mutation on pathways related to immunity and inflammationJoseph Dhahbi
BioMarker Pharmaceuticals Inc, 5941 Optical Court, San Jose, CA 95138, USA
Exp Gerontol 42:772-88. 2007..However, whole leukocytes population represents the function of immune system in these organisms...
- Identification and correction of systematic error in high-throughput sequence dataFrazer Meacham
Department of Mathematics, University of California, Berkeley, 970 Evans Hall 3840, Berkeley, CA 94720, USA
BMC Bioinformatics 12:451. 2011..We describe a new type of systematic error that manifests as statistically unlikely accumulations of errors at specific genome (or transcriptome) locations...
- Deep sequencing reveals novel microRNAs and regulation of microRNA expression during cell senescenceJoseph M Dhahbi
Center for Genetics, Children s Hospital Oakland Research Institute, Oakland, California, United States of America
PLoS ONE 6:e20509. 2011..This result greatly extends existing information on the role of miRNAs in cell senescence and is consistent with miRNAs having a causal role in the process...
- Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation statesDavid I K Martin
Center for Genetics, Children s Hospital Oakland Research Institute, Oakland, California 94609, USA
Genome Res 21:2049-57. 2011..These results provide evidence for epigenetic changes that occur in the germline and distinguish closely related species and suggest that germline epigenetic states might constrain somatic states...
- Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activitySachiko Takayama
Children s Hospital Oakland Research Institute, Oakland, California 94609, USA
Genome Res 24:821-30. 2014..The association of methylation with a lower expression of specific developmental genes at stage 5 raises the possibility that it participates in controlling gene expression during the maternal-zygotic transition. ..
- piRNA-like small RNAs mark extended 3'UTRs present in germ and somatic cellsJennifer Yamtich
Children s Hospital Oakland Research Institute, Oakland, CA, 94609, USA
BMC Genomics 16:462. 2015..We conducted a detailed characterization of piRNAs aligning at or near the 3' UTRs of protein-coding genes in a deep dataset of small RNAs from adult mouse testis...
- Deficiency of MIWI2 (Piwil4) induces mouse erythroleukemia cell differentiation, but has no effect on hematopoiesis in vivoJames E Jacobs
Children s Hospital Oakland Research Institute, Oakland, California, United States of America
PLoS ONE 8:e82573. 2013....
- MetMap enables genome-scale Methyltyping for determining methylation states in populationsMeromit Singer
Computer Science Division, University of California at Berkeley, Berkeley, California, USA
PLoS Comput Biol 6:e1000888. 2010..The combination of MethylSeq and MetMap is a powerful and cost-effective tool for determining genome-scale methyltypes suitable for comparative and association studies...