Genomes and Genes
Affiliation: Mount Sinai School of Medicine
- flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak findingYongchao Ge
Department of Neurology and Center of Translational System Biology, Mount Sinai School of Medicine, New York, NY 10029, USA
Bioinformatics 28:2052-8. 2012..The latter approach cannot be applied directly to high-dimensional data as the computational time and memory become unmanageable and the estimated histogram is unreliable. An algorithm without these two problems would be very useful...
- Bioconductor: open software development for computational biology and bioinformaticsRobert C Gentleman
Department of Biostatistical Science, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
Genome Biol 5:R80. 2004..We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples...
- Multiple testing and its applications to microarraysYongchao Ge
Department of Neurology and Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, NY 10029, USA
Stat Methods Med Res 18:543-63. 2009..The advantages and disadvantages of these methods are discussed. These methods are applied to gene expression data from two microarray studies and the properties of these multiple testing procedures are compared...
- Role of CpG context and content in evolutionary signatures of brain DNA methylationYurong Xin
Department of Psychiatry, Columbia University and the New York State Psychiatric Institute, New York, NY, USA
Epigenetics 6:1308-18. 2011..We identify key genomic features that can be targeted for identification of epigenetic loci that may be developmentally and evolutionarily conserved and wherein aberrations in DNA methylation patterns can confer risk for disease...
- MethylomeDB: a database of DNA methylation profiles of the brainYurong Xin
Department of Psychiatry, Columbia University and the New York State Psychiatric Institute, New York, NY 10032, USA
Nucleic Acids Res 40:D1245-9. 2012....
- Localized mucosal response to intranasal live attenuated influenza vaccine in adultsMaría Inés Barría
Department of Microbiology, Mount Sinai School of Medicine, New York, New York 10029, USA
J Infect Dis 207:115-24. 2013..The measure of successful vaccination with the inactivated vaccine is a systemic rise in immunoglobulin G (IgG) level, but for the LAIV no such correlate has been established...
- Development of a novel peptide microarray for large-scale epitope mapping of food allergensJing Lin
Pediatric Allergy and Immunology, Mount Sinai School of Medicine, New York, NY 10029 6574, USA
J Allergy Clin Immunol 124:315-22, 322.e1-3. 2009..The peptide microarray is a novel assay that facilitates high-throughput screening of peptides with a small quantity of sample...
- Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional networkYen Sin Ang
Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, NY 10029, USA
Cell 145:183-97. 2011..We propose an integrated model of transcriptional and epigenetic control, mediated by select trxG members, for the maintenance of ES cell self-renewal and somatic cell reprogramming...
- A comprehensive evaluation of human plasmacytoid dendritic cells using small volumes of human bloodHannah Phipps-Yonas
Department of Microbiology, Mount Sinai School of Medicine, New York, New York, USA
J Interferon Cytokine Res 28:501-7. 2008..In addition, we have used multiplex enzyme-linked immunosorbent assays to measure secreted proteins. We demonstrate the validity of this technique and document its potential for use with blood from human study populations...
- Single-cell analysis shows that paracrine signaling by first responder cells shapes the interferon-β response to viral infectionSonali Patil
Department of Neurology and Center for Translational Systems Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Sci Signal 8:ra16. 2015..Integration of simulations and experiments identified the role of paracrine signaling in increasing the number of cells that express Ifnb1 over time and in calibrating the immune response to viral infection. ..
- Human cytomegalovirus modulates monocyte-mediated innate immune responses during short-term experimental latency in vitroVanessa M Noriega
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
J Virol 88:9391-405. 2014..The modulation of innate immune responses is likely a viral evasion strategy contributing to viral dissemination and pathogenesis in the host...
- Coregulation mapping based on individual phenotypic variation in response to virus infectionGerman Nudelman
Center for Translational Systems Biology and Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA
Immunome Res 6:2. 2010..CONCLUSIONS: MDS mapping based on correlation in conjunction with TF enrichment analysis represents a useful computational method to generate predictions underlying gene coregulation across a population...
- Gene expression changes in areas of focal loss of retinal ganglion cells in the retina of DBA/2J miceLampros Panagis
Departments of Ophthalmology, Mount Sinai School of Medicine, New York, New York, USA
Invest Ophthalmol Vis Sci 51:2024-34. 2010....
- Peripheral blood cytokine profiling during pregnancy and post-partum periodsThomas A Kraus
Department of Obstetrics, Gynecology and Reproductive Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
Am J Reprod Immunol 64:411-26. 2010..This immunologic adaptation may contribute to pregnancy-related alterations in disease susceptibility and severity of infections from viral pathogens such as influenza virus...
- Low-variance RNAs identify Parkinson's disease molecular signature in bloodMaria D Chikina
Departments of Neurology and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
Mov Disord 30:813-21. 2015..We identify whole-blood mRNA signatures correlating with LRRK2 genotype and with PD disease state. This approach may provide insight into pathogenesis and a route to early disease detection...
- Methyl-Analyzer--whole genome DNA methylation profilingYurong Xin
Department of Psychiatry, Columbia University and New York State Psychiatric Institute, New York, NY 10032, USA
Bioinformatics 27:2296-7. 2011..Methyl-Analyzer processes and integrates sequencing reads from methylated and unmethylated compartments and estimates CpG methylation probabilities at single base resolution...
- Involvement of histone demethylase LSD1 in short-time-scale gene expression changes during cell cycle progression in embryonic stem cellsVenugopalan D Nair
Department of Neurology, Mount Sinai School of Medicine, New York, New York, USA
Mol Cell Biol 32:4861-76. 2012..Taken together, these results suggest that cell cycle-dependent association and dissociation of LSD1 with chromatin mediates short-time-scale gene expression changes during embryonic stem cell cycle progression...
- Compensatory redistribution of neuroligins and N-cadherin following deletion of synaptic β1-integrinSteven Mortillo
Department of Neuroscience, Friedman Brain Institute, Mount Sinai School of Medicine, New York, New York, USA
J Comp Neurol 520:2041-52. 2012..Together, our findings demonstrate unequivocally that β1-integrin is an integral synaptic adhesion protein, and suggest that adhesive function at the synapse reflects a cooperative and dynamic network of multiple CAM families...
- Noise propagation and scaling in regulation of gonadotrope biosynthesisFrederique Ruf
Department of Neurology, Mount Sinai School of Medicine, New York, New York, USA
Biophys J 93:4474-80. 2007..These results explain the basis for variation in cellular responses in an important mammalian signaling pathway leading to gene induction...
- Patient-specific induced pluripotent stem-cell-derived models of LEOPARD syndromeXonia Carvajal-Vergara
Department of Gene and Cell Medicine, Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, New York 10029, USA
Nature 465:808-12. 2010..These features correlate with a potential hypertrophic state. We also provide molecular insights into signalling pathways that may promote the disease phenotype...