"Show me the data!" Practical solutions to interactive visual analysis for big data.

18 Sep 2015 | Contributor(s): Samuel Payne

Nano WG September 10, 2015.Intuitive data visualization is critical for biomedical data analysis; especially essential is the ability for non-computational scientists to productively browse the data and apply their domain knowledge.  We present Active Data Biology, a web-based visual...

CEDAR Making it Easier to Use Ontologies to Author Experimental Metadata

15 Sep 2015 | Contributor(s): Mark Musen

Nano WG September 3, 2015

Screening for Small Molecules: Target Discovery Against miRNAs for Breast Cancer Treatment

18 Aug 2015 | Contributor(s): Odemaris Narvaez del Pilar

Breast cancer is one of the leading causes of cancer related deaths and morbidity among women worldwide. Identifying new targets and developing new therapies is very important in order to improve patient outcomes and minimize this health burden. MicroRNAs, a type of non-coding RNA, are potential...

Drug Selection of γδ T cells using miRNA target sequences

18 Aug 2015 | Contributor(s): Rosa Maria Santana Carrero

Gamma delta T cells constitute a small subset of circulating T lymphocytes in peripheral blood, and recognize antigens in an MHC-independent manner through their γδ T cell receptor. We sought to selectively expand ablatable γδ T cells using an inducible suicide switch,...

ErbB family expression in osteosarcoma

18 Aug 2015 | Contributor(s): Viviana Vidal Anaya

Osteosarcoma (OS) is the most common bone malignancy among children and teenagers. Currently the gold standard treatment is surgery and chemotherapy; however the 5 year survival for these patients remains 60 to 70%. There has being tremendous interest in identifying markers of prognostic and...

Identification of the key node in the expression network of BLM, EXO1, and DNA2 in Homologous Repair mediated DNA damage response

18 Aug 2015 | Contributor(s): Marimar de la Cruz Bonilla

DNA2, EXO1, and BLM are known to be a part of the end resection rate limiting step of the Homologous Recombination (HR) DNA damage repair (DDR) pathway. Inhibition of these three proteins would in effect inhibit the HR repair pathway. In cancer cells where the HR repair pathway is hyperactivated...

An Essential Role for Interleukin 6 in Lung Carcinogenesis

18 Aug 2015 | Contributor(s): Rosa Maria Santana Carrero

Lung cancer is the leading cause of cancer related deaths worldwide. Epidemiological studies have shown that patients with chronic obstructive pulmonary disease (COPD) have a higher risk of developing lung cancer, when compared to smokers without COPD. Moreover, we showed that a bacterial...

MS275 up-regulates Fas expression through down-regulation

14 Aug 2015 | Contributor(s): Vincent Bernard

Despite aggressive chemotherapy treatments, prognosis for patients with lung metastases from osteosarcoma (OS) remains poor. It is thus important to pursue new therapeutic approaches. The ability of osteosarcoma cells to form lung metastases has been inversely correlated to cell surface Fas...

HIF-1α stabilization requires mitochondrial respiration

14 Aug 2015 | Contributor(s): Viviana Vidal Anaya

Hypoxia inducible factors (HIFs) are oxygen sensitive transcription factors that allow adaptation to hypoxic environments by altering their metabolic programming and gene expression. HIF-1 consists of an oxygen-regulated subunit HIF-1α and a constituvely expressed subunit HIF-1β....

Radiation Pneumonitis: Proton Therapy Local Dose Response and Clinical Symptoms

14 Aug 2015 | Contributor(s): Vincent Bernard

Radiation pneumonitis (RP), a major toxicity following thoracic radiotherapy (RT), is expected to diminish with proton therapy. RP due to MV x-ray RT appears on FDG PET imaging as metabolic enhancement within the lungs with a linear dose response. This study evaluates the relationship between...

The Roles of PDGFR-b

14 Aug 2015 | Contributor(s): Sahily Reyes Esteves

After administering a combination of PDGFR agonist with NMDAR antagonist prior to a morphine challenge, we assessed analgesia in rats using a tail-flick latency test. Our results suggest that NMDAR signaling is not downstream of PDGFR signaling in morphine tolerance, as studies in other neural...

Support Access to NPO's Structure and Content

13 Aug 2015 | Contributor(s): Michael Halper, Vladimir Ventura, Yehoshua Perl

•Abstraction Networks (“AbNs”) for Ontologies•Two example AbNs:–Area taxonomy–Partial-area taxonomy•BLUOWL: taxonomy-based software tool•Application to the NPO•Conclusions

Data Readiness Levels

13 Aug 2015

Nanotechnology Signature InitiativeNanotechnology Knowledge Infrastructure (NKI):Enabling National Leadership in Sustainable DesignDraft Discussion Document: May 9, 2013

GDC APIs and Pipelines Presentation

10 Aug 2015 | Contributor(s): Eve R Shalley, Allison Heath

Presentation by Allison Heath for the Cloud Teams.

IHC Template

23 Jul 2015 | Publications | Contributor(s): Kim Jessup

This is an interactive form for entering data about IHC and qIFA assays.    It was created with Larry True's guidance by a group of extramural experts that include a couple of the current members.  The template has 5 sections that describe patient-related information,...

The Good,The Bad and The Ugly for Clinical Markers: Possibilities For the Future

30 Jun 2015 | Presentations | Contributor(s): Kim Jessup

Markers are becoming more important in NCI-supported clinical trials.  These trials are becoming increasingly oriented toward precision medicine. This presentation provides an overview of a database for markers used in NCI Trials as well as definitions of markers and their uses in trials....

Trinity: RNA-Seq De novo Assembly Application

30 Jun 2015 | External Applications | Contributor(s): Grabherr MG, Brian Haas, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, Di Palma F, Birren BW, Nusbaum C, Lindblad-toh K, Friedman N, Regev A

 Quick Guide for the ImpatientTrinity assembles transcript sequences from Illumina RNA-Seq data.Download Trinity here.Build Trinity by typing make : ; in the base installation directory.Assemble RNA-Seq data like so:Trinity --seqType fq --left reads_1.fq --right reads_2.fq...