Genomes and Genes
Experts and Doctors on gene expression profiling in Berkeley, California, United States
Locale: Berkeley, California, United States
Topic: gene expression profiling
Publications143 found, 100 shown here
- Lapuk A, Marr H, Jakkula L, Pedro H, Bhattacharya S, Purdom E, et al. Exon-level microarray analyses identify alternative splicing programs in breast cancer. Mol Cancer Res. 2010;8:961-74 pubmed publisher..These data also suggest the possibility of reducing the toxicity of protein-targeted breast cancer treatments by targeting protein isoforms that are not present in limiting normal tissues. ..
- Markowitz V, Chen I, Palaniappan K, Chu K, Szeto E, Pillay M, et al. IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res. 2014;42:D560-7 pubmed publisher..jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu). ..
- Yamamoto M, Clark T, Gee S, Kang J, Schweitzer A, Wickrema A, et al. Alternative pre-mRNA splicing switches modulate gene expression in late erythropoiesis. Blood. 2009;113:3363-70 pubmed publisher..Together, these results support the existence of a regulated alternative pre-mRNA splicing program that is critical for late erythroid differentiation...
- Manabe Y, Nafisi M, Verhertbruggen Y, Orfila C, Gille S, Rautengarten C, et al. Loss-of-function mutation of REDUCED WALL ACETYLATION2 in Arabidopsis leads to reduced cell wall acetylation and increased resistance to Botrytis cinerea. Plant Physiol. 2011;155:1068-78 pubmed publisher..There were no obvious morphological or growth differences observed between the wild type and rwa2 mutants. However, both alleles of rwa2 displayed increased tolerance toward the necrotrophic fungal pathogen Botrytis cinerea...
- Dionne M, Skarnes W, Harland R. Mutation and analysis of Dan, the founding member of the Dan family of transforming growth factor beta antagonists. Mol Cell Biol. 2001;21:636-43 pubmed..Mice lacking Dan activity were generated by gene targeting and displayed subtle, background-dependent defects. ..
- Muljo S, Schlissel M. A small molecule Abl kinase inhibitor induces differentiation of Abelson virus-transformed pre-B cell lines. Nat Immunol. 2003;4:31-7 pubmed..This suggests a key role for these factors, and perhaps for c-Abl itself, in the regulated activation of Ig light chain gene rearrangement...
- Fournier M, Fata J, Martin K, Yaswen P, Bissell M. Interaction of E-cadherin and PTEN regulates morphogenesis and growth arrest in human mammary epithelial cells. Cancer Res. 2009;69:4545-52 pubmed publisher..This interaction thus seems to be a critical integrator of proliferative and morphogenetic signaling in breast epithelial cells. ..
- Papatsenko D, Levine M, Goltsev Y. Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles. PLoS Biol. 2011;9:e1000584 pubmed publisher..We propose that gene clustering by local temporal discordance can be used for the de novo identification of the gene batteries underlying morphological diversity...
- Deutschbauer A, Price M, Wetmore K, Shao W, Baumohl J, Xu Z, et al. Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. PLoS Genet. 2011;7:e1002385 pubmed publisher..The approach described here can be applied generally to create large-scale gene-phenotype maps for evidence-based annotation of gene function in prokaryotes. ..
- North M, Steffen J, Loguinov A, Zimmerman G, Vulpe C, Eide D. Genome-wide functional profiling identifies genes and processes important for zinc-limited growth of Saccharomyces cerevisiae. PLoS Genet. 2012;8:e1002699 pubmed publisher..Thus, functional profiling has provided many new insights into genes and processes that are needed for cells to thrive under the stress of zinc deficiency. ..
- Wang N, Li J, Lindow S. RpfF-dependent regulon of Xylella fastidiosa. Phytopathology. 2012;102:1045-53 pubmed publisher..A large number of other RpfF-dependent genes that might contribute to virulence or insect colonization were also identified such as those encoding hemolysin and colicin V, as well as genes with unknown functions. ..
- He S, Ivanova N, Kirton E, Allgaier M, Bergin C, Scheffrahn R, et al. Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites. PLoS ONE. 2013;8:e61126 pubmed publisher..corniger microbiota. These observations are consistent with dietary differences in carbohydrate composition and nutrient contents, but may also reflect the phylogenetic difference between the hosts. ..
- Semeiks J, Rizki A, Bissell M, Mian I. Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features. BMC Bioinformatics. 2006;7:147 pubmed..The results provide information about properties common and unique to subsets of the list and hence insights into the biology of the problem under investigation. ..
- Osterhout R, Figueroa I, Keasling J, Arkin A. Global analysis of host response to induction of a latent bacteriophage. BMC Microbiol. 2007;7:82 pubmed..Overall, we observe that prophage induction has a surprisingly low impact on host physiology. This study provides the first global dynamic picture of how host processes respond to lambda phage induction. ..
- Hutchison E, Brown S, Tian C, Glass N. Transcriptional profiling and functional analysis of heterokaryon incompatibility in Neurospora crassa reveals that reactive oxygen species, but not metacaspases, are associated with programmed cell death. Microbiology. 2009;155:3957-70 pubmed publisher..These data indicate that PCD during HI occurs via a novel and possibly fungal-specific mechanism, making this pathway an attractive drug target for control of fungal infections. ..
- Chandran D, Inada N, Hather G, Kleindt C, Wildermuth M. Laser microdissection of Arabidopsis cells at the powdery mildew infection site reveals site-specific processes and regulators. Proc Natl Acad Sci U S A. 2010;107:460-5 pubmed publisher..This suggests that, by increasing gene copy number, localized endoreduplication serves as a mechanism to meet the enhanced metabolic demands imposed by the fungus, which acquires all its nutrients from the plant host. ..
- Cheong Y, Sung S, Kim B, Pandey G, Cho J, Kim K, et al. Constitutive overexpression of the calcium sensor CBL5 confers osmotic or drought stress tolerance in Arabidopsis. Mol Cells. 2010;29:159-65 pubmed publisher..Furthermore, overexpression of CBL5 alters the gene expression of stress gene markers, such as RD29A, RD29B and Kin1 etc. These results suggest that CBL5 may function as a positive regulator of salt or drought responses in plants. ..
- Wang D, Huang J, Hu Z. RNA helicase DDX5 regulates microRNA expression and contributes to cytoskeletal reorganization in basal breast cancer cells. Mol Cell Proteomics. 2012;11:M111.011932 pubmed publisher..Our results reveal a new functional role of DDX5 in breast cancer via the DDX5?miR-182?actin cytoskeleton pathway, and suggest the potential clinical utility of DDX5 and its downstream MicroRNAs in the theranostics of breast cancer. ..
- Coleman Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genet. 2012;8:e1002988 pubmed publisher..We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes...
- Roberts A, Pachter L. Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Methods. 2013;10:71-3 pubmed publisher..We demonstrate its use on RNA-seq data and show that eXpress achieves greater efficiency than other quantification methods. ..
- Attanasio C, Nord A, Zhu Y, Blow M, Li Z, Liberton D, et al. Fine tuning of craniofacial morphology by distant-acting enhancers. Science. 2013;342:1241006 pubmed publisher..These results demonstrate that enhancers are involved in craniofacial development and suggest that enhancer sequence variation contributes to the diversity of human facial morphology. ..
- Hu P, Brodie E, Suzuki Y, McAdams H, Andersen G. Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus. J Bacteriol. 2005;187:8437-49 pubmed..Several differentially regulated transcripts from regions previously not known to encode proteins were identified, demonstrating the advantage of evaluating the transcriptome by using whole-genome microarrays. ..
- Fournier M, Martin K, Kenny P, Xhaja K, Bosch I, Yaswen P, et al. Gene expression signature in organized and growth-arrested mammary acini predicts good outcome in breast cancer. Cancer Res. 2006;66:7095-102 pubmed..This study represents a novel unsupervised approach to identifying breast cancer markers that may be of use clinically. ..
- Cacheaux L, Ivens S, David Y, Lakhter A, Bar Klein G, Shapira M, et al. Transcriptome profiling reveals TGF-beta signaling involvement in epileptogenesis. J Neurosci. 2009;29:8927-35 pubmed publisher..Our present data identifies the TGF-beta pathway as a novel putative epileptogenic signaling cascade and therapeutic target for the prevention of injury-induced epilepsy. ..
- Moustakas J, Smith K, Hlusko L. Evolution and development of the mammalian dentition: insights from the marsupial Monodelphis domestica. Dev Dyn. 2011;240:232-9 pubmed publisher..We show that the tooth germs of M. domestica express fibroblast growth factor (FGF) genes and Sprouty genes in a manner similar to wild-type mouse molar germs, but with a few key differences...
- Mueller R, Dill B, Pan C, Belnap C, Thomas B, Verberkmoes N, et al. Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community. Environ Microbiol. 2011;13:2279-92 pubmed publisher..These findings provide unprecedented insight into the physiological changes that may result from competitive interactions within communities in natural environments...
- Znameroski E, Coradetti S, Roche C, Tsai J, Iavarone A, Cate J, et al. Induction of lignocellulose-degrading enzymes in Neurospora crassa by cellodextrins. Proc Natl Acad Sci U S A. 2012;109:6012-7 pubmed publisher..Thus, the ability to induce cellulase gene expression using a common and soluble carbon source simplifies enzyme production and characterization, which could be applied to other cellulolytic filamentous fungi. ..
- Boonyaratanakornkit B, Cordova J, Park C, Clark D. Pressure affects transcription profiles of Methanocaldococcus jannaschii despite the absence of barophilic growth under gas-transfer limitation. Environ Microbiol. 2006;8:2031-5 pubmed..Potential high-pressure adaptation of a barophilic organism can thus occur at the transcriptional level, even though the cells are stressed by low substrate availability and do not exhibit accelerated growth. ..
- Lowe X, Lu X, Marchetti F, Wyrobek A. The expression of Troponin T1 gene is induced by ketamine in adult mouse brain. Brain Res. 2007;1174:7-17 pubmed..Our findings suggest that the induction of Tnnt1 gene expression in adult mouse brains by ketamine may illustrate the genes involved in the metabolic syndromes observed in neuropsychiatric disorders. ..
- Kizer L, Pitera D, Pfleger B, Keasling J. Application of functional genomics to pathway optimization for increased isoprenoid production. Appl Environ Microbiol. 2008;74:3229-41 pubmed publisher..This work demonstrates the utility of using transcriptomic and metabolomic methods to optimize synthetic biological systems. ..
- Jo W, Kim J, Oh E, Jaramillo D, Holman P, Loguinov A, et al. Novel insights into iron metabolism by integrating deletome and transcriptome analysis in an iron deficiency model of the yeast Saccharomyces cerevisiae. BMC Genomics. 2009;10:130 pubmed publisher..This should be taken into consideration when designing and analyzing data from these type of studies. We used this and other published data to develop a molecular interaction network of iron metabolism in yeast. ..
- Sun J, Tian C, Diamond S, Glass N. Deciphering transcriptional regulatory mechanisms associated with hemicellulose degradation in Neurospora crassa. Eukaryot Cell. 2012;11:482-93 pubmed publisher..This systematic analysis illustrates the similarities and differences in regulation of hemicellulose degradation among filamentous fungi. ..
- Hockett K, Burch A, Lindow S. Thermo-regulation of genes mediating motility and plant interactions in Pseudomonas syringae. PLoS ONE. 2013;8:e59850 pubmed publisher..This work highlights the importance of temperature in the biology of P. syringae, as many genes encoding traits important for plant-microbe interactions were thermo-regulated...
- Snijders A, Liu Y, Su L, Huang Y, Mao J. Expression profiling reveals transcriptional regulation by Fbxw7/mTOR pathway in radiation-induced mouse thymic lymphomas. Oncotarget. 2015;6:44794-805 pubmed publisher..These results provide novel insights into the role of FBXW7 in tumor development and have identified a number of potential targets for therapeutic intervention. ..
- Visser J, Cheng Y, Perry S, Chastain A, Parsa B, Masri S, et al. An extracellular biochemical screen reveals that FLRTs and Unc5s mediate neuronal subtype recognition in the retina. elife. 2015;4:e08149 pubmed publisher..These data suggest a single molecular mechanism may have been co-opted by synaptic partners to ensure joint laminar restriction. ..
- Session A, Uno Y, Kwon T, Chapman J, Toyoda A, Takahashi S, et al. Genome evolution in the allotetraploid frog Xenopus laevis. Nature. 2016;538:336-343 pubmed publisher..The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression. ..
- de Rie D, Abugessaisa I, Alam T, Arner E, Arner P, Ashoor H, et al. An integrated expression atlas of miRNAs and their promoters in human and mouse. Nat Biotechnol. 2017;35:872-878 pubmed publisher..We thus provide a broad atlas of miRNA expression and promoters in primary mammalian cells, establishing a foundation for detailed analysis of miRNA expression patterns and transcriptional control regions. ..
- Ziegelbauer J, Wei J, Tjian R. Myc-interacting protein 1 target gene profile: a link to microtubules, extracellular signal-regulated kinase, and cell growth. Proc Natl Acad Sci U S A. 2004;101:458-63 pubmed..Taken together, our studies suggest that MIZ-1 regulates a specific set of genes that includes LDLR and that the ERK pathway plays a role in the activation of target promoters by MIZ-1. ..
- Stathopoulos A, Levine M. Whole-genome expression profiles identify gene batteries in Drosophila. Dev Cell. 2002;3:464-5 pubmed
- Tian C, Kasuga T, Sachs M, Glass N. Transcriptional profiling of cross pathway control in Neurospora crassa and comparative analysis of the Gcn4 and CPC1 regulons. Eukaryot Cell. 2007;6:1018-29 pubmed..The 32-gene conserved regulon comprises mostly amino acid biosynthetic genes. The comparison of regulatory networks in species with clear orthology among genes sheds light on how gene interaction networks evolve. ..
- Szpara M, Vranizan K, Tai Y, Goodman C, Speed T, Ngai J. Analysis of gene expression during neurite outgrowth and regeneration. BMC Neurosci. 2007;8:100 pubmed..This suggests that the genes identified in this in vitro study may represent new candidates worthy of further study for potential roles in the therapeutic regrowth of neuronal connections. ..
- Weigelt B, Kreike B, Reis Filho J. Metaplastic breast carcinomas are basal-like breast cancers: a genomic profiling analysis. Breast Cancer Res Treat. 2009;117:273-80 pubmed publisher..The reported poorer response to chemotherapeutic agents in patients with MBCs may stem from downregulated DNA damage response pathways, PTEN and TOP2A. ..
- Gong H, Vu G, Bai Y, Yang E, Liu F, Lu S. Differential expression of Salmonella type III secretion system factors InvJ, PrgJ, SipC, SipD, SopA and SopB in cultures and in mice. Microbiology. 2010;156:116-27 pubmed publisher..Our results suggest that differential expression of these proteins may be important for tissue-specific aspects of bacterial pathogenesis such as gastroenterititis in the ileum and systemic infection in the liver. ..
- Wang D, Bodovitz S. Single cell analysis: the new frontier in 'omics'. Trends Biotechnol. 2010;28:281-90 pubmed publisher..As described in this review, single cell analysis is the new frontier in omics, and single cell omics has the potential to transform systems biology through new discoveries derived from cellular heterogeneity. ..
- Fletcher R, Prasol M, Estrada J, Baudhuin A, Vranizan K, Choi Y, et al. p63 regulates olfactory stem cell self-renewal and differentiation. Neuron. 2011;72:748-59 pubmed publisher..These results provide critical insight into the genetic regulation of the olfactory stem cell in vivo and more generally provide an entrée toward understanding the coordination of stem cell self-renewal and differentiation...
- Twumasi Boateng K, Shapira M. Dissociation of immune responses from pathogen colonization supports pattern recognition in C. elegans. PLoS ONE. 2012;7:e35400 pubmed publisher..In the absence of orthologs of known pattern recognition receptors, C. elegans may rely on novel mechanisms, thus holding the potential to advance our understanding of evolutionarily conserved strategies for pathogen recognition. ..
- De Freitas J, Kim J, Poynton H, Su T, Wintz H, Fox T, et al. Exploratory and confirmatory gene expression profiling of mac1Delta. J Biol Chem. 2004;279:4450-8 pubmed..New or additional support for a role in copper and iron homeostasis is provided in this study for the gene products of AKR1, MRS4, PCA1, SSU1, TIS11, YBR047W, YHL035C, YHR045W, YLR047C, YLR126C, and YTP1. ..
- Collier J, Selmin O, Johnson P, Runyan R. Trichloroethylene effects on gene expression during cardiac development. Birth Defects Res A Clin Mol Teratol. 2003;67:488-95 pubmed
- Liu K, Harland R. Cloning and characterization of Xenopus Id4 reveals differing roles for Id genes. Dev Biol. 2003;264:339-51 pubmed..Id4 is able to inhibit the activity all these bHLH molecules, Id2 inhibits MyoD and neuroD, while Id3 blocks only neuroD activity in our assays. ..
- Price M, Huang K, Alm E, Arkin A. A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res. 2005;33:880-92 pubmed
- Price M, Arkin A, Alm E. OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments. BMC Bioinformatics. 2006;7:19 pubmed..Although microarray data can contain large amounts of systematic error, operons provide an external standard and allow for reasonable estimates of significance. OpWise is available at http://microbesonline.org/OpWise. ..
- Papatsenko D. Stripe formation in the early fly embryo: principles, models, and networks. Bioessays. 2009;31:1172-80 pubmed publisher..The current model analysis emphasizes the role of spatial information flow in development. Discussion is given on frequent network motifs, pointing to spatial stripe formation solutions...
- Bengtsson H, Neuvial P, Speed T. TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. BMC Bioinformatics. 2010;11:245 pubmed publisher..A bounded-memory implementation is available in the open-source and cross-platform R package aroma.cn, which is part of the Aroma Project (http://www.aroma-project.org/). ..
- Kim K, Yang E, Vu G, Gong H, Su J, Liu F, et al. Mass spectrometry-based quantitative proteomic analysis of Salmonella enterica serovar Enteritidis protein expression upon exposure to hydrogen peroxide. BMC Microbiol. 2010;10:166 pubmed publisher..These results suggest a possible role of SipC and other regulated proteins in supporting survival and replication of Salmonella under oxidative stress and during its systemic infection in vivo. ..
- Burch A, Shimada B, Browne P, Lindow S. Novel high-throughput detection method to assess bacterial surfactant production. Appl Environ Microbiol. 2010;76:5363-72 pubmed publisher..Additionally, measurements of the transcription of the syringafactin biosynthetic cluster in the mutants, the principal biosurfactant known to be produced by B728a, revealed novel regulators of this pathway. ..
- Brooks A, Yang L, Duff M, Hansen K, Park J, Dudoit S, et al. Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res. 2011;21:193-202 pubmed publisher..This observation suggests that the regulatory codes of individual RNA binding proteins may be nearly immutable, yet the regulatory modules controlled by these proteins are highly evolvable. ..
- Lombardi L, Ellahi A, Rine J. Direct regulation of nucleosome density by the conserved AAA-ATPase Yta7. Proc Natl Acad Sci U S A. 2011;108:E1302-11 pubmed publisher..Further, local loss of Yta7 activity at a long inducible gene resulted in accumulation of H3 at the 3' end upon transcriptional activation, implying Yta7 may regulate H3 cotranscriptionally. ..
- Risso D, Schwartz K, Sherlock G, Dudoit S. GC-content normalization for RNA-Seq data. BMC Bioinformatics. 2011;12:480 pubmed publisher..Such results are crucial for the biological interpretation of RNA-Seq experiments, where downstream analyses can be sensitive to the supplied lists of genes. ..
- Padmanabhan P, Babaoğlu M, Terry N. A comparative transcriptomic analysis of the extremely boron tolerant plant Puccinellia distans with the moderately boron tolerant Gypsophila arrostil. Plant Cell Rep. 2012;31:1407-13 pubmed publisher..The molecular basis of boron tolerance of two plant species (Puccinellia distans and Gypsophila arrostil) that differ greatly in their boron tolerance was studied in this manuscript. ..
- Price M, Deutschbauer A, Skerker J, Wetmore K, Ruths T, Mar J, et al. Indirect and suboptimal control of gene expression is widespread in bacteria. Mol Syst Biol. 2013;9:660 pubmed publisher..Because genes that have closely related functions can have dissimilar expression patterns, regulation may be suboptimal in the wild as well as in the laboratory. ..
- Stern Ginossar N, Ingolia N. Ribosome Profiling as a Tool to Decipher Viral Complexity. Annu Rev Virol. 2015;2:335-49 pubmed publisher..Ribosome profiling in other viruses will likely expand further our understanding of viral gene regulation and the proteome. ..
- Qin L, Wu V, Glass N. Deciphering the Regulatory Network between the SREBP Pathway and Protein Secretion in Neurospora crassa. MBio. 2017;8: pubmed publisher..These findings have implications for our understanding of the cross talk of the SREBP and UPR pathways in other organisms and will guide the rational engineering of fungal strains to improve cellulolytic enzyme production. ..
- Armendariz A, Gonzalez M, Loguinov A, Vulpe C. Gene expression profiling in chronic copper overload reveals upregulation of Prnp and App. Physiol Genomics. 2004;20:45-54 pubmed..The genes that encode for the prion protein and the amyloid-beta precursor protein, two known copper-binding proteins, are upregulated in both cell lines. ..
- Rosenblum E, Stajich J, Maddox N, Eisen M. Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis. Proc Natl Acad Sci U S A. 2008;105:17034-9 pubmed publisher..Finally we discuss the challenges inherent in developing a molecular toolkit for chytrids, a basal fungal lineage separated by vast phylogenetic distance from other well characterized fungi...
- Bánfai B, Jia H, Khatun J, Wood E, Risk B, Gundling W, et al. Long noncoding RNAs are rarely translated in two human cell lines. Genome Res. 2012;22:1646-57 pubmed publisher..We conclude that with very few exceptions, ribosomes are able to distinguish coding from noncoding transcripts and, hence, that ectopic translation and cryptic mRNAs are rare in the human lncRNAome. ..
- Wintz H, Yoo L, Loguinov A, Wu Y, Steevens J, Holland R, et al. Gene expression profiles in fathead minnow exposed to 2,4-DNT: correlation with toxicity in mammals. Toxicol Sci. 2006;94:71-82 pubmed..We present possible modes of action of 2,4-DNT toxicity and suggest that fathead minnow cDNA microarrays can be useful to identify mechanisms of toxicity in fish and as a predictive tool for toxicity in mammals. ..
- Hutchison E, Glass N. Meiotic regulators Ndt80 and ime2 have different roles in Saccharomyces and Neurospora. Genetics. 2010;185:1271-82 pubmed publisher..Our data indicate that the IME2/NDT80 pathway is not involved in meiosis in N. crassa, but rather regulates the formation of female reproductive structures. ..
- Chang H, Fontenay G, Han J, Cong G, Baehner F, Gray J, et al. Morphometic analysis of TCGA glioblastoma multiforme. BMC Bioinformatics. 2011;12:484 pubmed publisher..Accordingly, we have identified a subtype that is a predictor of the outcome as a result of a therapeutic regime. Computed representation has become publicly available through our Web site. ..
- Tepperman J, Hwang Y, Quail P. phyA dominates in transduction of red-light signals to rapidly responding genes at the initiation of Arabidopsis seedling de-etiolation. Plant J. 2006;48:728-42 pubmed
- Weber G, Rübel O, Huang M, DePace A, Fowlkes C, Keränen S, et al. Visual exploration of three-dimensional gene expression using physical views and linked abstract views. IEEE/ACM Trans Comput Biol Bioinform. 2009;6:296-309 pubmed publisher..Using linking, these selected cells can be viewed in multiple representations. We describe PCX as a 3D gene expression visualization tool and provide examples of how it has been used by BDTNP biologists to generate new hypotheses. ..
- Martínez García J, Huq E, Quail P. Direct targeting of light signals to a promoter element-bound transcription factor. Science. 2000;288:859-63 pubmed
- Tepperman J, Hudson M, Khanna R, Zhu T, Chang S, Wang X, et al. Expression profiling of phyB mutant demonstrates substantial contribution of other phytochromes to red-light-regulated gene expression during seedling de-etiolation. Plant J. 2004;38:725-39 pubmed
- Grate L. Many accurate small-discriminatory feature subsets exist in microarray transcript data: biomarker discovery. BMC Bioinformatics. 2005;6:97 pubmed..We also find small gene sets that distinguish leukemia subtypes in the large pediatric acute lymphoblastic leukemia cancer set of Yeoh et al. ..
- McHale C, Zhang L, Lan Q, Li G, Hubbard A, Forrest M, et al. Changes in the peripheral blood transcriptome associated with occupational benzene exposure identified by cross-comparison on two microarray platforms. Genomics. 2009;93:343-9 pubmed publisher..The two-platform approach allows for robust changes in the PBMC transcriptome of benzene-exposed individuals to be identified. ..
- Roberts A, Trapnell C, Donaghey J, Rinn J, Pachter L. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol. 2011;12:R22 pubmed publisher..We find improvements in expression estimates as measured by correlation with independently performed qRT-PCR and show that correction of bias leads to improved replicability of results across libraries and sequencing technologies. ..
- ORDINARIO E, Han H, Furuta S, Heiser L, Jakkula L, Rodier F, et al. ATM suppresses SATB1-induced malignant progression in breast epithelial cells. PLoS ONE. 2012;7:e51786 pubmed publisher..These data indicate a novel role for ATM as a suppressor of SATB1-induced malignancy in breast epithelial cells, but also raise a cautionary note that phenotypic drift could lead to dramatically different functional outcomes. ..
- Schraiber J, Mostovoy Y, Hsu T, Brem R. Inferring evolutionary histories of pathway regulation from transcriptional profiling data. PLoS Comput Biol. 2013;9:e1003255 pubmed publisher..We anticipate that our pathway-based phylogenetic approach will be of broad utility in the search to understand the evolutionary relevance of regulatory change. ..
- Anderton B, Camarda R, Balakrishnan S, Balakrishnan A, Kohnz R, Lim L, et al. MYC-driven inhibition of the glutamate-cysteine ligase promotes glutathione depletion in liver cancer. EMBO Rep. 2017;18:569-585 pubmed publisher..Our results identify new metabolic pathways deregulated in primary MYC tumors and implicate a role for MYC in regulating a major antioxidant pathway downstream of glutamine. ..
- Chiou S, Yoo J, Loh K, Guzman R, Gopinath G, Rajkumar L, et al. Identification of rat mammary tumor-1 gene (RMT-1), which is highly expressed in rat mammary tumors. Cancer Lett. 2001;174:45-55 pubmed..However, whether or not RMT-1 gene has a functional role in these processes remains to be investigated. ..
- Kim K, Zhang S, Jiang K, Cai L, Lee I, Feldman L, et al. Measuring similarities between gene expression profiles through new data transformations. BMC Bioinformatics. 2007;8:29 pubmed..Our method should provide new insights in analyzing gene expression data. The clustering algorithms are available upon request. ..
- Sharp J, Sales C, LeBlanc J, Liu J, Wood T, Eltis L, et al. An inducible propane monooxygenase is responsible for N-nitrosodimethylamine degradation by Rhodococcus sp. strain RHA1. Appl Environ Microbiol. 2007;73:6930-8 pubmed..These results demonstrate that propane monooxygenase is responsible for NDMA degradation by RHA1 and explain the enhanced cometabolic degradation of NDMA in the presence of propane. ..
- Killiny N, Almeida R. Host structural carbohydrate induces vector transmission of a bacterial plant pathogen. Proc Natl Acad Sci U S A. 2009;106:22416-20 pubmed publisher..A better understanding of how vector-borne pathogens transition from host to vector, and vice versa, may lead to previously undiscovered disease-control strategies. ..