Bioinformatics

By Paul Nicolaus May 20, 2019 | Researchers at Florida State University have developed a computational model with the potential to change the way researchers approach population genetics and the spread of diseases that evolve quickly in response to different environments. “This method is the first application of fractional calculus to population genetics,” said Florida
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By Benjamin Ross May 16, 2019 | BOSTON—During a panel discussion at the Bio-IT World Conference & Expo, Tanya Cashorali, CEO and Founder of TCB Analytics, Aaron Gardner, Director of Technology at BioTeam, and Eleanor Howe, Founder and CEO of Diamond Age Data Science—three data science consultants—came together to discuss the intricacies of the industry
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Contributed Commentary by Michael B. Lampert and Richard A. Harris II May 15, 2019 | Compliance is foundational—it supports the sustainability of a business model and revenue. Noncompliance can yield assessment of penalties, revocation of licenses, distraction of management, reputational harm and loss of employees. It also can yield erosion of revenue, if the business
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By Bio-IT World Staff May 14, 2019 | Medidata Solutions has launched Acorn AI, a Medidata company dedicated to making “data liquid across the end-to-end lifecycle of a pharmaceutical and life sciences company—from research all the way to development and into post-market,” Sastry Chilukuri, Acorn AI’s president told Bio-IT World. “If you look at any organization, any life
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By Deborah Borfitz May 6, 2019 | The business of research has traditionally focused on producing academic papers, limiting the growth of scientific knowledge to “massive incrementalism” around a succession of magic-bullet solutions—microassays, human genome project, robotics and artificial intelligence and, most recently, open science. Instead of research being translated by the market and compatible
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By Deborah Borfitz May 2, 2019 | Achieving the aims of value-based healthcare presumes the free flow of all kinds of data—including physician free text notes, radiology images and medical journal articles—whenever and wherever they’re needed so providers can deliver personalized, evidence-backed care and patients know their options and can make informed choices. In this
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May 1, 2019 | April featured exciting new, products, and partnerships from around the bio-IT community from innovating companies, organizations, and universities, including Thermo Fisher Scientific, LifeArc, Pure Storage, and more. Researchers and scientists analyzing crystallized protein samples in life sciences and materials research can now benefit from the first commercially released integrated solution for performing
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By Bio-IT World Staff April 29, 2019 | The Michael J. Fox Foundation for Parkinson’s Research (MJFF) and 23andMe today launched the Fox Insight Data Exploration Network (Fox DEN), the data access and analytics platform for Fox Insight, an online clinical study sponsored by MJFF. Fox DEN contains patient-reported outcomes, de-identified genetic data and data exploration
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By Allison Proffitt April 26, 2019 | Pacific Biosciences has launched the Sequel II System. The system includes the new SMRT Cell 8M, as well as chemistry, instrument control software and the SMRT Link software package. Together, the latest product release further reduces project costs and timelines with approximately eight times the data output compared to the previous
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By Benjamin Ross April 26, 2019 | Eugene Koonin, senior investigator at the National Center for Biotechnology Information (NCBI), was honored as the recipient of the 2019 Benjamin Franklin Award for Open Access in the Life Sciences during the Bio-IT World Conference & Expo in Boston. The award, presented annually by Bioinformatics.org, is a humanitarian/bioethics award
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Contributed Commentary By Scott Parker April 25, 2019 | Content and data in the biopharmaceutical industry are complex and growing at an exponential rate. Terabytes from research and development, testing, lab reports, and patients reside in sources such as databases, emails, scientific publications, and medical records. Information that could be crucial to research can be found
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By Deborah Borfitz April 24, 2019 | The human genome is personally unique and identifying—even identical twins are very different genetically—which has created a big privacy problem for researchers. Researchers have shown that research participants can be re-identified using genomic data alongside genealogical databases and public records. An algorithm can literally “pick someone out of
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April 22, 2019 | The Bio-IT World Conference and Expo took over the Boston Seaport area last week, as more than 3,000 researchers, bioinformaticians, and experts converged for conversations around AI, FAIR data, informatics, edge computing, and much more. We are combing through our notebooks, gathering background, and processing all the good information we learned,
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April 18, 2019 | BOSTON—Bio-IT World has announced the winners of the 2019 Innovative Practices Awards. The winners were announced live at the Bio-IT World Conference & Expo. Entries from Abbvie, Novo Nordisk, and Sentieon were honored. Since 2003, Bio-IT World has hosted an elite awards program, highlighting outstanding examples of how technology innovations and strategic
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By Bio-IT World Staff April 17, 2019 | Genomenon announced a partnership with Google to make the company’s genomic mutation data available on Google Cloud Platform. Genomenon’s Cited Variants Reference (CVR) data will be a public dataset available in BigQuery, Google Cloud’s big data and machine learning data warehouse, for use in genomic applications. The Cited
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By Benjamin Ross April 15, 2019 | Othram was awarded a research sequencing grant from Illumina Accelerator after presenting at SXSW for the “Digitizing Biology Through Genomics” session as part of the Energizing Health House program. Founded in 2018, Othram is a new technology company that operates a state-of-the-art forensic DNA sequencing laboratory, focusing on reconstructing
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April 12, 2019 | Like any new technology, blockchain must find its place. Richard Shute believes that one of those places is in the life sciences, where it can benefit researchers and drug companies while protecting patients. Blockchain has great potential within the clinical arena to support enhanced data management at nearly every level, he
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April 11, 2019 | Scientific discovery and innovation is not a solitary undertaking. Advancement depends on the ability to build upon the work of others, and thus it is imperative that experimental data be easily retrievable and of reliable quality. The principles of FAIR data—Findability, Accessibility, Interoperability, and Reusability—seek to improve the way data are collected
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Syntactic and semantic conventions 1. Taxa are models, concepts are mimics. We typically refrain from using the terms “taxon”, “taxa”, or “clade(s)”. We take taxa to constitute evolutionary, causally sustained entities whose members are manifested in the natural realm. The task for systematics is to successively approximate the identities and limits of these entities. Thus,
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Abstract Place cells in the mammalian hippocampus signal self-location with sparse spatially stable firing fields. Based on observation of place cell activity it is possible to accurately decode an animal’s location. The precision of this decoding sets a lower bound for the amount of information that the hippocampal population conveys about the location of the
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The analysis of single-cell RNA sequencing (scRNAseq) data plays an important role in understanding the intrinsic and extrinsic cellular processes in biological and biomedical research. One significant effort in this area is the detection of differentially expressed (DE) genes. scRNAseq data, however, are highly heterogeneous and have a large number of zero counts, which introduces
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Like going from a pinhole camera to a Polaroid, a significant mathematical update to the formula for a popular bioinformatics data visualization method will allow researchers to develop snapshots of single-cell gene expression not only several times faster but also at much higher-resolution. Published in Nature Methods, this innovation by Yale mathematicians will reduce the
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Three-dimensional structure of Mtb-SecBTA in complex with ChAD In contrast with the classical export chaperone SecB, which binds and wraps unfolded presecretory protein substrates and maintains them in an unfolded conformation compatible with translocation through membrane6, previous work revealed that the Mtb-SecBTA chaperone of TAC is capable of binding to its aggregation-prone Mtb-HigA1 antitoxin substrate
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Our methodological pipeline (Fig. 2) is comprised of several steps: (1) numerically represent the genomic contigs using a nucleotide mapping (Table 1). (2) MLBP is used to extract features from these numerical representations. If available, cross-sample coverage information (mean and standard deviation) is extracted separately using Bowtie 233 and can be considered as extra information to be
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Chemicals Paracetamol and paracetamol-D4 internal standard were purchased from Sigma (Sigma-Aldrich Chemie B.V., Zwijndrecht, The Netherlands). UPLC/MS grade MeOH was purchased from Biosolve (Biosolve B.V., Valkenswaard, The Netherlands). Purified water (H2O) was retrieved from PURELAB (Veolia Water Technologies B.V., Ede, The Netherlands). Zebrafish husbandry All experiments were planned and executed in compliance with European regulation6.
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Conversion of 8-mer architecture into 24-mer nanocage As a standard structural component among protein nanocages, ferritin exists ubiquitously in both prokaryotes and eukaryotes. It is a nearly spherical 24-subunits protein with an exterior diameter of about 12 nm and a hollow cavity of 8 nm30,31. Owing to its cage-like morphology and highly symmetrical structure, ferritin has been
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1. Niforou K, Cheimonidou C, Trougakos IP. Molecular chaperones and proteostasis regulation during redox imbalance. Redox Biol. 2014;2:323–32. 2. Powers ET, Balch WE. Diversity in the origins of proteostasis networks–a driver for protein function in evolution. Nat Rev Mol Cell Biol. 2013;14:237–48. 3. Bayer TA. Proteinopathies, a core concept for understanding and ultimately treating degenerative
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The advent of massively parallel sequencing (MPS) technologies in the past decade has revolutionized the field of genomics, enabling fast and cost-effective generation of a large amount of sequence data. This technological innovation leads to the accumulation of vast quantities of genomic data, posing a tremendous challenge to scientists for effective mining of data to
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Identifying and counting individual cells from cell cultures form the basis of numerous biological and biomedical research applications [1, 2]. Determining numbers of cells reflecting the growth, survival, and death of cell populations form the foundations of e.g. basic cancer research and early drug development. Currently, the most commonly used methods for counting cells in
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The analytical approach presented above was implemented using R-shiny. The typical analysis is performed by three interaction steps: i) input of gene lists and modifications, ii) graphical visualization of enriched terms and iii) interactive navigation of the results. A step-by-step user manual is available in Additional file 1. In the first step, the application provides a
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The analytical approach presented above was implemented using R-shiny. The typical analysis is performed by three interaction steps: i) input of gene lists and modifications, ii) graphical visualization of enriched terms and iii) interactive navigation of the results. A step-by-step user manual is available in Additional file 1. In the first step, the application provides a
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1. Hoglinger, GU, G Respondek and GG Kovacs. New classification of tauopathies. Rev Neurol (Paris) 2018. https://doi.org/10.1016/j.neurol.2018.07.001. 2. Lebouvier T, Pasquier F, Buee L. Update on tauopathies. Curr Opin Neurol. 2017;30:589–98. 3. Morris M, Maeda S, Vossel K, Mucke L. The many faces of tau. Neuron. 2011;70:410–26. 4. Höglinger GU, Melhem NM, Dickson DW, et
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Preparing HMEC-1 cells for fluorescence imaging HMEC-1 cells were fixed using 1.7% (w/v) paraformaldehyde (Electron Microscopy Sciences) at room temperature and permeabilized by incubation with 0.02% (w/v) saponin in phosphate-buffered saline (PBS) for 10 min at room temperature. Cells were then preblocked with 3% bovine serum albumin (BSA) in PBS, incubated with anti-Clathrin primary antibody (mouse
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Abstract Next-Generation Sequencing has made available substantial amounts of large-scale Omics data, providing unprecedented opportunities to understand complex biological systems. Specifically, the value of RNA-Sequencing (RNA-Seq) data has been confirmed in inferring how gene regulatory systems will respond under various conditions (bulk data) or cell types (single-cell data). RNA-Seq can generate genome-scale gene expression profiles
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Abstract We seek to characterize the motility of mouse fibroblasts on 2D substrates. Utilizing automated tracking techniques, we find that cell trajectories are super-diffusive, where displacements scale faster than t1/2 in all directions. Two mechanisms have been proposed to explain such statistics in other cell types: run and tumble behavior with Lévy-distributed run times, and
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Abstract We seek to characterize the motility of mouse fibroblasts on 2D substrates. Utilizing automated tracking techniques, we find that cell trajectories are super-diffusive, where displacements scale faster than t1/2 in all directions. Two mechanisms have been proposed to explain such statistics in other cell types: run and tumble behavior with Lévy-distributed run times, and
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