@article {49608,
	title = {RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder.},
	volume = {19},
	year = {2014},
	month = {2014 Nov},
	pages = {1179-85},
	abstract = {<p>RNA-sequencing (RNA-seq) is a powerful technique to investigate the complexity of gene expression in the human brain. We used RNA-seq to survey the brain transcriptome in high-quality postmortem dorsolateral prefrontal cortex from 11 individuals diagnosed with bipolar disorder (BD) and from 11 age- and gender-matched controls. Deep sequencing was performed, with over 350 million reads per specimen. At a false discovery rate of <5\%, we detected five differentially expressed (DE) genes and 12 DE transcripts, most of which have not been previously implicated in BD. Among these, Prominin 1/CD133 and ATP-binding cassette-sub-family G-member2 (ABCG2) have important roles in neuroplasticity. We also show for the first time differential expression of long noncoding RNAs (lncRNAs) in BD. DE transcripts include those of serine/arginine-rich splicing factor 5 (SRSF5) and regulatory factor X4 (RFX4), which along with lncRNAs have a role in mammalian circadian rhythms. The DE genes were significantly enriched for several Gene Ontology categories. Of these, genes involved with GTPase binding were also enriched for BD-associated SNPs from previous genome-wide association studies, suggesting that differential expression of these genes is not simply a consequence of BD or its treatment. Many of these findings were replicated by microarray in an independent sample of 60 cases and controls. These results highlight common pathways for inherited and non-inherited influences on disease risk that may constitute good targets for novel therapies.</p>},
	keywords = {Adult, Aged, Bipolar Disorder, Circadian Rhythm, Female, Genome-Wide Association Study, GTP Phosphohydrolases, HUMANS, Male, Meta-Analysis as Topic, Microarray Analysis, Middle Aged, Neuronal Plasticity, Polymerase Chain Reaction, Prefrontal Cortex, Principal Component Analysis, Sequence Analysis, RNA, Transcriptome, Young Adult},
	issn = {1476-5578},
	doi = {10.1038/mp.2013.170},
	author = {Akula, N and Barb, J and Jiang, X and Wendland, J R and Choi, K H and Sen, S K and Hou, L and Chen, D T W and Laje, G and Johnson, K and Lipska, B K and Kleinman, J E and Corrada-Bravo, H and Detera-Wadleigh, S and Munson, P J and McMahon, F J}
}
@article {49653,
	title = {Functional genomics of trypanosomatids.},
	journal = {Parasite Immunol},
	volume = {34},
	year = {2012},
	month = {2012 Feb-Mar},
	pages = {72-9},
	abstract = {<p>The decoding of the Tritryp reference genomes nearly 7 years ago provided a first peek into the biology of pathogenic trypanosomatids and a blueprint that has paved the way for genome-wide studies. Although 60-70\% of the predicted protein coding genes in Trypanosoma brucei, Trypanosoma cruzi and Leishmania major remain unannotated, the functional genomics landscape is rapidly changing. Facilitated by the advent of next-generation sequencing technologies, improved structural and functional annotation and genes and their products are emerging. Information is also growing for the interactions between cellular components as transcriptomes, regulatory networks and metabolomes are characterized, ushering in a new era of systems biology. Simultaneously, the launch of comparative sequencing of multiple strains of kinetoplastids will finally lead to the investigation of a vast, yet to be explored, evolutionary and pathogenomic space.</p>},
	keywords = {Animals, Genome, Protozoan, Genomics, HUMANS, Proteome, Protozoan Proteins, Transcriptome, Trypanosomatina},
	issn = {1365-3024},
	doi = {10.1111/j.1365-3024.2011.01347.x},
	author = {Choi, J and El-Sayed, N M}
}
@article {38276,
	title = {Gene expression anti-profiles as a basis for accurate universal cancer signatures},
	journal = {BMC bioinformaticsBMC Bioinformatics},
	volume = {13},
	year = {2012},
	note = {http://www.ncbi.nlm.nih.gov/pubmed/23088656?dopt=Abstract},
	type = {10.1186/1471-2105-13-272},
	abstract = {BACKGROUND: Early screening for cancer is arguably one of the greatest public health advances over the last fifty years. However, many cancer screening tests are invasive (digital rectal exams), expensive (mammograms, imaging) or both (colonoscopies). This has spurred growing interest in developing genomic signatures that can be used for cancer diagnosis and prognosis. However, progress has been slowed by heterogeneity in cancer profiles and the lack of effective computational prediction tools for this type of data. RESULTS: We developed anti-profiles as a first step towards translating experimental findings suggesting that stochastic across-sample hyper-variability in the expression of specific genes is a stable and general property of cancer into predictive and diagnostic signatures. Using single-chip microarray normalization and quality assessment methods, we developed an anti-profile for colon cancer in tissue biopsy samples. To demonstrate the translational potential of our findings, we applied the signature developed in the tissue samples, without any further retraining or normalization, to screen patients for colon cancer based on genomic measurements from peripheral blood in an independent study (AUC of 0.89). This method achieved higher accuracy than the signature underlying commercially available peripheral blood screening tests for colon cancer (AUC of 0.81). We also confirmed the existence of hyper-variable genes across a range of cancer types and found that a significant proportion of tissue-specific genes are hyper-variable in cancer. Based on these observations, we developed a universal cancer anti-profile that accurately distinguishes cancer from normal regardless of tissue type (ten-fold cross-validation AUC > 0.92). CONCLUSIONS: We have introduced anti-profiles as a new approach for developing cancer genomic signatures that specifically takes advantage of gene expression heterogeneity. We have demonstrated that anti-profiles can be successfully applied to develop peripheral-blood based diagnostics for cancer and used anti-profiles to develop a highly accurate universal cancer signature. By using single-chip normalization and quality assessment methods, no further retraining of signatures developed by the anti-profile approach would be required before their application in clinical settings. Our results suggest that anti-profiles may be used to develop inexpensive and non-invasive universal cancer screening tests.},
	keywords = {Area Under Curve, Colonic Neoplasms, Gene Expression Profiling, Genetic Variation, Genomics, HUMANS, Oligonucleotide Array Sequence Analysis, Prognosis, Transcriptome, Tumor Markers, Biological},
	author = {H{\'e}ctor Corrada Bravo and Pihur, Vasyl and McCall, Matthew and Irizarry, Rafael A. and Leek, Jeffrey T.}
}
