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Platform Agnostic Data Processing Routine for Targeted and Untargeted Metabolite Identification in Drug Discovery
Richard Lee,1 Vitaly Lashin,2 Andrey Paramonov,2 Alexandr Sakharov,2 Alexey Aminov2

A discussion of a new informatics solution that addresses common challenges in metabolite identification and characterization--from LC/MS data processing and metabolites prediction to reporting and databasing of assembled biotransformation knowledge.

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Deep Phenotyping - Harnessing Data Richness for Unsupervised High-Content Analysis
Huang Dong, Wang Yi, Maciej Hermanowicz, Ke Yiping, Maja Choma, Lee Kee Khoon, Frederic Bard

Recognising the key challenges, we develop an end-to-end computational framework for HCA dubbed “Deep Phenotyping” that perform unsupervised analysis to leverage on the data richness for the discovery of unknown sub-phenotypes with minimal labeling cost.

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The Case for CASE: Computer-Assisted Structure Elucidation
ACD/Labs

Modern CASE systems such as Structure Elucidator Suite provide the necessary capability accurately elucidate a novel chemical structure for complex molecules based on readily available NMR data sets. This allows organizations to avoid expensive, labor-intensive, and time-consuming synthetic efforts.

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A Unified Software Platform for Laboratory Informatics
Graham A. McGibbon, Hans de Bie, David Hardy, Ryan Sasaki, Patrick Wheeler, Carol Preisig

Reported here are capabilities in automated workflows involving analytical data with chemical structures. Specifically described is automated homogenization of data from a set of instruments, including NMR structure verification, as one solution.

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Addressing False Positive Variants Arising from Pseudogenes
Risha Govind1,2, Sam Wilkinson1,3, Nicola Whiffin1,2, Shibu John1,2, Rachel J. Buchan1,2, Elizabeth Edwards1,2, Deborah J. Morris-Rosendahl1,3, James S. Ware1,2, P.J. Barton1,2, Stuart A. Cook1,2

Clinical genetic testing has been transformed in recent years by the introduction of Next-Generation Sequencing (NGS).

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PredRet: Prediction of Retention Time by Direct Mapping between Multiple Chromatographic Systems
Jan Stanstrup, Steffen Neumann, Urška Vrhovšek

Retention time (RT) information is under-utilized in LC-MS based metabolomics and sharing of RTs between systems is not currently possible. PredRet is a new system that allows highly accurate mapping and prediction of RTs between LC systems.

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Building a digital pathology ecosystem for education and research
Yves Sucaet, Silke Smeets, Stijn Piessens, Sabrina D'Haese, Chris Groven, Wim Waelput, Peter In't Veld

We wanted to build a core digital pathology infrastructure to support different use cases. Various images platforms needed to be accessible through a single access point, and support different user profiles.

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Predicting Regioselectivityand Labilityof Cytochrome P450 Metabolism using Quantum Mechanical Simulations
Tyzack, Nicholas Foster, Peter Hunt, Matthew Segall

Predicting Regioselectivity and Lability of Cytochrome P450 Metabolism using Quantum Mechanical Simulations

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The Power Decoder simulator for the evaluation of pooled shRNA screen performance
Jesse Stombaugh, Abel Licon, Žaklina Strezoska, Joshua Stahl, Sarah Bael Anderson, Michael Banos, Anja van Brabant Smith, Amanda Birmingham, Annaleen Vermeulen

Power Decoder (written in R and Python) simulates shRNA pooled screening experiments in silico to allow for the estimation of a screen’s statistical power. Populations of shRNAs were engineered in such a way that the magnitude of depletion and enrichment was known, then using the negative binomial distribution, an in silico model was developed to successfully resemble data from an actual laboratory experiment.

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Knockdown of long noncoding RNAs in breast cancer
1 Jennii Luu, 2 Jesper Maag, 1 Yanny Handoko, 3 Richard Redvers, 3,4 Robin L. Anderson, 5 Maren M. Gross , 2 Marcel E. Dinger, and 1,3 Kaylene J. Simpson 1 Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre; 2 Genome Informatics, The Kinghorn Cancer Centre, The Garvan Institute of Medical Research; 3 Metastasis Research Laboratory, Peter MacCallum Cancer Centre, 4 Sir Peter MacCallum Department of Oncology, University of Melbourne;

RNAi global collaboration study using Lincode siRNA in a primary screen of tumor and nontumor breast cell lines. Hundreds of lncRNAs are found to affect viability and cell morphology of breast cancer. Presented at Keystone Symposia on Long Noncoding RNAs: From Evolution to Function, Mar 15 - Mar 20, 2015.

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Scientific News
Personalised Medicine: Dose by Design
Personalised medicine holds the promise of a new approach to healthcare, tailored exactly to our individual needs, as Congenica's Nick Lench discussed on a recent BBC Radio 4 programme.
Expanding Knowledge of Viral Diversity
Environmental datasets help researchers double the number of microbial phyla known to be infected by viruses.
Computers Better Predict Lung Cancer Type, Severity
Study shows automating the analysis of cancer tissue samples increases the accuracy of tumor classification and patient prognoses.
Using Big Data to Discover Potential Cancer Biomarkers
University of Hawai'i Cancer Center researchers used "Big Data" to discover potential cancer biomarkers, a panel of six long intergenic non-coding RNAs (lincRNAs), for the diagnosis of all types of cancers including lung, breast, prostate, liver and ovarian cancers.
Protecting Privacy in Genomic Databases
System helps ensure databases used in medical research will not leak patients’ personal information.
Algorithm To Find Precise Cancer Treatments For Patients Developed
The JAMMIT algorithm could help predict which patients will benefit most from chemotherapy.
Depression Genetics Insight from Crowd-Sourced Data
Genome sites liked to depression have been discovered from data shared by people who had purchased their genetic profiles online.
Detecting Hazardous Chemicals in Complex Mixtures
Researchers are pioneering a new chemical substance analyis software technique that could increase illicit substance detection.
Researchers Develop Software That Could Facilitate Drug Development
AptaTRACE can identify aptamers, potentially speed drug advancement.
Protein Nanocages Could Improve Drug Design and Delivery
HHMI scientists have designed and built 10 large protein icosahedra that are similar to viral capsids that carry viral DNA.
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