Osterix is a novel zinc finger-containing transcription factor that is essential for osteoblast differentiation and bone formation. We hypothesized that osterix might have a role in osteosarcoma tumor growth and metastasis. Northern blot analysis showed that the mRNA level of osterix was decreased in two mouse osteosarcoma cell lines compared with its level in normal mouse osteoblasts. Osterix ...

FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the com...

Bone marrow derived human mesenchymal stem cells (MSC) are a great source in bone tissue engineering. However, how to improve the efficiency of MSC osteogenesis remains a big challenge in bone regenerative medicine. Here, we characterized the role of INO80 chromatin remodeling complex in osteogenic differentiation of MSC. We showed that silencing of subunits of INO80 reduced the mineral deposit...

We have developed an ab initio single-particle 3D reconstruction algorithm for cryo-EM that does not rely on contrast enhancement by negative staining, assumptions about particle symmetry, or knowledge about the character of the heterogeneity [1-3]. Here we announce the release of the methods as an open source program package SIMPLE (Single-particle IMage Processing Linux Engine). SIMPLE enable...

New developments in the program package ATSAS (version 2.4) for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described. They include (i) multiplatform data manipulation and display tools, (ii) programs for automated data processing and calculation of overall parameters, (iii) improved usage of high- and low-resolution models from other structural me...

This is an implementation of the R statistical software qvalue package [Dabney et al., 2014], designed for use with large datasets where memory or computation time is limiting. In addition to estimating p values adjusted for multiple testing, the software outputs a script which can be pasted into R to produce diagnostic plots and report parameter estimates. This program runs almost 30 times fas...

Using validated carving techniques, we show that popular operating systems (e.g. Windows, Linux, and OSX) frequently have residual IP packets, Ethernet frames, and associated data structures present in system memory from long-terminated network traffic. Such information is useful for many forensic purposes including establishment of prior connection activity and services used; identification of...

Much of the mammalian skeleton is composed of bones that originate from cartilage templates through endochondral ossification. Elucidating the mechanisms that control endochondral bone development is critical for understanding human skeletal diseases, injury response, and aging. Mouse genetic studies in the past 15 years have provided unprecedented insights about molecules regulating chondrocyt...

We present a new software framework for Markov chain Monte Carlo sampling for simulation, prediction, and inference of protein structure. The software package contains implementations of recent advances in Monte Carlo methodology, such as efficient local updates and sampling from probabilistic models of local protein structure. These models form a probabilistic alternative to the widely used fr...

MOTIVATION Analysis of genomic sequencing data requires efficient, easy-to-use access to alignment results and flexible data management tools (e.g. filtering, merging, sorting, etc.). However, the enormous amount of data produced by current sequencing technologies is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformat...