Matteo Pellegrini

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae
    Hung Pham
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
    Mol Syst Biol 3:153. 2007
  2. pmc Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana
    Yana V Bernatavichute
    Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS ONE 3:e3156. 2008
  3. pmc Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa
    Kelly Vining
    Department of Forest Ecosystems and Society, 321 Richardson Hall, Corvallis, OR, USA
    BMC Plant Biol 13:92. 2013
  4. pmc Bio-crude transcriptomics: gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa)
    Istvan Molnar
    Natural Products Center, School of Natural Resources and the Environment, The University of Arizona, Tucson, 85739, USA
    BMC Genomics 13:576. 2012
  5. pmc Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression
    Kelly J Vining
    Department of Forest Ecosystems and Society, Oregon State University, Corvallis, 97331, USA
    BMC Genomics 13:27. 2012
  6. pmc Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana
    Xiaoyu Zhang
    Department of Plant Biology, University of Georgia, Green Street, Athens, GA 30602, USA
    Genome Biol 10:R62. 2009
  7. pmc Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways
    David M Levine
    Rosetta Inpharmatics LLC, Merck and Co, Inc, Terry Avenue North, Seattle, WA 98109, USA
    Genome Biol 7:R93. 2006
  8. pmc Expression profile of CREB knockdown in myeloid leukemia cells
    Matteo Pellegrini
    Department of Molecular, Cellular, and Developmental Biology, University of California, Los Angeles, USA
    BMC Cancer 8:264. 2008
  9. doi request reprint Using phylogenetic profiles to predict functional relationships
    Matteo Pellegrini
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
    Methods Mol Biol 804:167-77. 2012
  10. doi request reprint Epigenetic analysis: ChIP-chip and ChIP-seq
    Matteo Pellegrini
    Department of Molecular, Cell and Developmental, University of California, Los Angeles, CA, USA
    Methods Mol Biol 802:377-87. 2012

Detail Information

Publications73

  1. pmc Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae
    Hung Pham
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
    Mol Syst Biol 3:153. 2007
    ..We validate the model, both computationally and experimentally, to demonstrate that it yields accurate predictions of these regulatory mechanisms...
  2. pmc Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana
    Yana V Bernatavichute
    Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS ONE 3:e3156. 2008
    ..These results suggest a complex interplay between H3K9m2 and different types of DNA methylation and suggest that distinct mechanisms control H3K9m2 in different compartments of the genome...
  3. pmc Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa
    Kelly Vining
    Department of Forest Ecosystems and Society, 321 Richardson Hall, Corvallis, OR, USA
    BMC Plant Biol 13:92. 2013
    ..A fuller understanding of how 5mC changes during in vitro manipulation may aid the development of methods for reducing or amplifying the mutagenic and epigenetic effects of in vitro culture and plant transformation...
  4. pmc Bio-crude transcriptomics: gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa)
    Istvan Molnar
    Natural Products Center, School of Natural Resources and the Environment, The University of Arizona, Tucson, 85739, USA
    BMC Genomics 13:576. 2012
    ....
  5. pmc Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression
    Kelly J Vining
    Department of Forest Ecosystems and Society, Oregon State University, Corvallis, 97331, USA
    BMC Genomics 13:27. 2012
    ..However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylation among specialized tissues and its relationship to gene expression is poorly understood...
  6. pmc Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana
    Xiaoyu Zhang
    Department of Plant Biology, University of Georgia, Green Street, Athens, GA 30602, USA
    Genome Biol 10:R62. 2009
    ..In plants, methylation of histone H3 lysine 4 (H3K4me) is associated with genes and required for normal plant development...
  7. pmc Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways
    David M Levine
    Rosetta Inpharmatics LLC, Merck and Co, Inc, Terry Avenue North, Seattle, WA 98109, USA
    Genome Biol 7:R93. 2006
    ..Although many methods for measuring pathway expression have been proposed, a systematic analysis of the performance of multiple methods over multiple independent data sets has not previously been reported...
  8. pmc Expression profile of CREB knockdown in myeloid leukemia cells
    Matteo Pellegrini
    Department of Molecular, Cellular, and Developmental Biology, University of California, Los Angeles, USA
    BMC Cancer 8:264. 2008
    ..CREB knockdown inhibits leukemic cell proliferation in vitro and in vivo, but does not affect long-term hematopoietic reconstitution...
  9. doi request reprint Using phylogenetic profiles to predict functional relationships
    Matteo Pellegrini
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
    Methods Mol Biol 804:167-77. 2012
    ..We discuss a set of these implementations and present the software and databases that are available to perform phylogenetic profiling...
  10. doi request reprint Epigenetic analysis: ChIP-chip and ChIP-seq
    Matteo Pellegrini
    Department of Molecular, Cell and Developmental, University of California, Los Angeles, CA, USA
    Methods Mol Biol 802:377-87. 2012
    ..Here, we present a data analysis pipeline for processing ChIP-seq data, and discuss the limitations and idiosyncrasies of these approaches...
  11. pmc Systems and trans-system level analysis identifies conserved iron deficiency responses in the plant lineage
    Eugen I Urzica
    Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
    Plant Cell 24:3921-48. 2012
    ..CGLD27/At5g67370 is a highly conserved, presumed chloroplast-localized pioneer protein and is important for growth of Arabidopsis thaliana in low iron...
  12. pmc Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps
    Michael Strong
    Howard Hughes Medical Institute, University of California at Los Angeles, Box 951570, Los Angeles, CA 90095 1570, USA
    Nucleic Acids Res 31:7099-109. 2003
    ....
  13. pmc MORC family ATPases required for heterochromatin condensation and gene silencing
    Guillaume Moissiard
    Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Terasaki Life Sciences Building, 610 Charles Young Drive East, Los Angeles, CA 90095 723905, USA
    Science 336:1448-51. 2012
    ..Knockdown of the single MORC homolog in Caenorhabditis elegans also impairs transgene silencing. We propose that the MORC ATPases are conserved regulators of gene silencing in eukaryotes...
  14. pmc Identifying cognate binding pairs among a large set of paralogs: the case of PE/PPE proteins of Mycobacterium tuberculosis
    Robert Riley
    Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS Comput Biol 4:e1000174. 2008
    ....
  15. pmc The proteome of copper, iron, zinc, and manganese micronutrient deficiency in Chlamydomonas reinhardtii
    Scott I Hsieh
    Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
    Mol Cell Proteomics 12:65-86. 2013
    ....
  16. pmc Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency
    Rupa Sridharan
    University of California Los Angeles, David Geffen School of Medicine, Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, Bioinformatics Interdepartmental Degree Program, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Los Angeles, California 90095, USA
    Nat Cell Biol 15:872-82. 2013
    ..Together, our findings demonstrate that Cbx3 and H3K9 methylation restrict late reprogramming events, and suggest that a marked change in global chromatin character constitutes an epigenetic roadblock for reprogramming. ..
  17. pmc Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis
    Xiaoyu Zhang
    Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS Biol 5:e129. 2007
    ..The results suggest that different mechanisms may underlie the establishment and spreading of H3K27me3 in plants and animals...
  18. pmc Zinc deficiency impacts CO2 assimilation and disrupts copper homeostasis in Chlamydomonas reinhardtii
    Davin Malasarn
    Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
    J Biol Chem 288:10672-83. 2013
    ..We suggest that zinc-deficient cells sequester copper in a biounavailable form, perhaps to prevent mismetallation of critical zinc sites...
  19. pmc Relationship between nucleosome positioning and DNA methylation
    Ramakrishna K Chodavarapu
    Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA
    Nature 466:388-92. 2010
    ..DNA methylation is also enriched on exons, consistent with the targeting of DNA methylation to nucleosomes, and suggesting a role for DNA methylation in exon definition...
  20. pmc Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation
    Shaun D Fouse
    Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Cell Stem Cell 2:160-9. 2008
    ..Our data suggest that in mES cells promoter methylation represents a unique epigenetic program that complements other regulatory mechanisms to ensure appropriate gene expression...
  21. ncbi request reprint Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis
    Xiaoyu Zhang
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
    Cell 126:1189-201. 2006
    ....
  22. pmc Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
    Shawn J Cokus
    Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
    Nature 452:215-9. 2008
    ....
  23. pmc Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas
    Nanette R Boyle
    Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
    J Biol Chem 287:15811-25. 2012
    ....
  24. pmc SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation
    Lianna M Johnson
    1 Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA 2
    Nature 507:124-8. 2014
    ....
  25. pmc Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival
    Deqiang Duanmu
    Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
    Proc Natl Acad Sci U S A 110:3621-6. 2013
    ..Our studies also suggest that bilins trigger critical metabolic pathways to detoxify molecular oxygen produced by photosynthesis, thereby permitting survival and phototrophic growth during the light period...
  26. pmc Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data
    David Lopez
    Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, USA
    BMC Bioinformatics 12:282. 2011
    ..Due to renewed interest in algae as potential sources of biofuels and the emergence of multiple algal genome sequences, a significant need has arisen for such a database to process the growing compendiums of algal genomic data...
  27. doi request reprint Determining DNA methylation profiles using sequencing
    Suhua Feng
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
    Methods Mol Biol 733:223-38. 2011
    ..We also describe the specialized protocol for mapping bisulfite converted reads. These approaches allow one to determine the methylation state of each cytosine in the genome...
  28. pmc Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression
    Einat Sprinzak
    UCLA DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA, USA
    BMC Syst Biol 3:115. 2009
    ..However, this type of coordinated regulation between whole complexes is difficult to detect by existing methods for analyzing mRNA co-expression. We propose a new methodology that is able to detect such higher order relationships...
  29. pmc Identification of genes required for de novo DNA methylation in Arabidopsis
    Maxim V C Greenberg
    Department of Molecular, Cell and Developmental Biology, University of California Davis, USA
    Epigenetics 6:344-54. 2011
    ..Mutations were mapped and genes cloned by both traditional and whole genome sequencing approaches. The methodologies and the mutant alleles discovered will be instrumental in further studies of de novo DNA methylation...
  30. pmc Identification of novel targets of CSL-dependent Notch signaling in hematopoiesis
    Habib Hamidi
    Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS ONE 6:e20022. 2011
    ..Time course analysis of hematopoietic development revealed that cells with Notch 1 overexpression mimic miRNA expression of cells in a less mature stage, which is consistent with our previous biological characterization...
  31. pmc Stage-specific roles for tet1 and tet2 in DNA demethylation in primordial germ cells
    John J Vincent
    Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Cell Stem Cell 12:470-8. 2013
    ..Instead, Tet1 and Tet2 have a locus-specific role in shaping the PGC epigenome during subsequent development...
  32. pmc Unraveling inflammatory responses using systems genetics and gene-environment interactions in macrophages
    Luz D Orozco
    Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Cell 151:658-70. 2012
    ..We have created a public database where the data presented here can be used as a resource for understanding many common inflammatory traits that are modeled in the mouse and for the dissection of regulatory relationships between genes...
  33. pmc Reorganization of the host epigenome by a viral oncogene
    Roberto Ferrari
    Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
    Genome Res 22:1212-21. 2012
    ..The strategic redistribution of H3K18ac by e1a highlights the importance of this modification for transcriptional activation and cellular transformation as well as functional differences between the RB-family member proteins...
  34. pmc Transcriptome and methylome interactions in rice hybrids
    Ramakrishna K Chodavarapu
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 109:12040-5. 2012
    ..We conclude that much of the misinheritance of expression levels is likely caused by epimutations and trans effects...
  35. pmc A comparative analysis of DNA methylation across human embryonic stem cell lines
    Pao Yang Chen
    Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
    Genome Biol 12:R62. 2011
    ..It had previously been shown that HESC lines had significantly higher non-CG methylation than differentiated cells, and we therefore asked whether these sites were conserved across cell lines...
  36. pmc Epigenetic reprogramming by adenovirus e1a
    Roberto Ferrari
    Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA
    Science 321:1086-8. 2008
    ..The temporal order of e1a binding requires its interactions with p300/CBP and RB proteins. Our data uncover a defined epigenetic reprogramming leading to cellular transformation...
  37. pmc Conservation and divergence of methylation patterning in plants and animals
    Suhua Feng
    Howard Hughes Medical Institute, Department of Molecular, Cell and Developmental Biology, and Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 107:8689-94. 2010
    ..In addition, the Dnmt1 cofactor Uhrf1 has a conserved function in maintaining CG methylation in both transposons and gene bodies in the mouse, Arabidopsis, and zebrafish genomes...
  38. pmc Prolinks: a database of protein functional linkages derived from coevolution
    Peter M Bowers
    Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
    Genome Biol 5:R35. 2004
    ..The Prolinks database and the Proteome Navigator tool are available for use online at http://dip.doe-mbi.ucla.edu/pronav...
  39. pmc AID-induced genotoxic stress promotes B cell differentiation in the germinal center via ATM and LKB1 signaling
    Mara H Sherman
    Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Mol Cell 39:873-85. 2010
    ..Combined, our data show that CRTC2 inactivation, via physiologic DNA damage response signaling, promotes B cell differentiation in response to genotoxic stress...
  40. pmc Plants regenerated from tissue culture contain stable epigenome changes in rice
    Hume Stroud
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
    elife 2:e00354. 2013
    ..These changes in methylation may explain a component of somaclonal variation, a phenomenon in which plants derived from tissue culture manifest phenotypic variability. DOI:http://dx.doi.org/10.7554/eLife.00354.001...
  41. pmc Impact of oxidative stress on ascorbate biosynthesis in Chlamydomonas via regulation of the VTC2 gene encoding a GDP-L-galactose phosphorylase
    Eugen I Urzica
    Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
    J Biol Chem 287:14234-45. 2012
    ....
  42. pmc An improved method for identifying functionally linked proteins using phylogenetic profiles
    Shawn Cokus
    Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095 1606, USA
    BMC Bioinformatics 8:S7. 2007
    ..We hypothesize that profiles with many runs are more likely to involve functionally related proteins than profiles in which all the matches are concentrated in one interval of the tree...
  43. pmc Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps
    Madeli Castruita
    Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
    Plant Cell 23:1273-92. 2011
    ..Forty percent of the targets are previously uncharacterized proteins, indicating considerable potential for new discovery in the biology of copper...
  44. pmc Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae
    Shawn Cokus
    Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, USA
    BMC Bioinformatics 7:381. 2006
    ..In contrast, here we focus on reverse-engineering the network of relationships among transcription factors that regulate the cell cycle in S. cerevisiae...
  45. pmc Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization
    Matthew Denholtz
    Department of Biological Chemistry at the David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
    Cell Stem Cell 13:602-16. 2013
    ....
  46. ncbi request reprint Determining the conservation of DNA methylation in Arabidopsis
    Nicolas Widman
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095 1606, USA
    Epigenetics 4:119-24. 2009
    ..Despite this observation, we find that methylated cytosines are less often paired with other nucleotides than non-methylated cytosines within gene bodies indicating that they may play an important functional role...
  47. pmc BS Seeker: precise mapping for bisulfite sequencing
    Pao Yang Chen
    Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, USA
    BMC Bioinformatics 11:203. 2010
    ..It uses sequence tags to reduce mapping ambiguity. Post-processing of the alignments removes non-unique and low-quality mappings...
  48. pmc Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells
    Weilong Guo
    Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing 100084, China, Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA, LMAM, School of Mathematical Sciences, Peking University, Beijing 100871, China, Center for Theoretical Biology, Peking University, Beijing 100871, China and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
    Nucleic Acids Res 42:3009-16. 2014
    ..Together, the divide-and-compare strategy leads us to identify regions with strand-specific distributions of non-CpG methylation in humans. ..
  49. pmc SINGLET OXYGEN RESISTANT 1 links reactive electrophile signaling to singlet oxygen acclimation in Chlamydomonas reinhardtii
    Beat B Fischer
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 109:E1302-11. 2012
    ..RES can be formed after singlet oxygen-induced lipid peroxidation, indicating that RES-stimulated and SOR1-mediated responses of detoxification genes are part of the singlet oxygen-induced acclimation process in C. reinhardtii...
  50. pmc Lethal iron deprivation induced by non-neutralizing antibodies targeting transferrin receptor 1 in malignant B cells
    Jose A Rodriguez
    Molecular Biology Institute, David Geff en School of Medicine, University of California, Los Angeles, CA 90095 1782, USA
    Leuk Lymphoma 52:2169-78. 2011
    ..These findings are expected to facilitate the rational design and clinical use of therapeutic agents targeting iron import via TfR1 in hematopoietic malignancies...
  51. pmc Copy number variation influences gene expression and metabolic traits in mice
    Luz D Orozco
    Department of Human Genetics, UCLA, Los Angeles, CA, USA
    Hum Mol Genet 18:4118-29. 2009
    ..Our results suggest that CNVs have a significant impact on gene expression and that CNVs may be playing a role in the mechanisms underlying metabolic traits in mice...
  52. ncbi request reprint Nkx2-5 suppresses the proliferation of atrial myocytes and conduction system
    Yasuhiro Nakashima
    From the Department of Molecular Cell and Developmental Biology Y N, D A Y, H N, A J, M P, A N, Departments of Pediatrics and Molecular Cell and Integrative Physiology, David Geffen School of Medicine M T, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research H N, M P, A N, Department of Physiology, David Geffen School of Medicine M C J, K P R, Molecular Biology Institute M P, Institute of Genomics and Proteomics M P, and Jonsson Comprehensive Cancer Center A N, University of California, Los Angeles, Los Angeles, CA
    Circ Res 114:1103-13. 2014
    ....
  53. pmc Genome-wide evaluation of histone methylation changes associated with leaf senescence in Arabidopsis
    Judy A Brusslan
    Department of Biological Sciences, California State University Long Beach, Long Beach, California, United States of America
    PLoS ONE 7:e33151. 2012
    ..Two of these genes, SAG12 and At1g73220, display strong senescence up-regulation without the activating H3K4me3 histone modification. This study provides an initial epigenetic framework for the developmental transition into senescence...
  54. pmc Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa
    Eran Elhaik
    Children s Hospital Los Angeles, Keck School of Medicine, University of Southern California, 4650 Sunset Blvd, Los Angeles, CA 90027, USA
    BMC Bioinformatics 15:23. 2014
    ..We thus designed a model to predict methylation in Oryza sativa based on genomic sequence features and gene expression data...
  55. pmc Bioinformatic challenges for the next decade(s)
    David Eisenberg
    Howard Hughes Medical Institute UCLA DOE Institute for Genomics and Proteomics Box 951570 UCLA, Los Angeles, CA 90095 1570, USA
    Philos Trans R Soc Lond B Biol Sci 361:525-7. 2006
    ..We here give a consideration of some of the key problems of bioinformatics in the coming decade, and perhaps longer...
  56. pmc Insights into the mechanism of cell death induced by saporin delivered into cancer cells by an antibody fusion protein targeting the transferrin receptor 1
    Tracy R Daniels-Wells
    Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
    Toxicol In Vitro 27:220-31. 2013
    ..1Av/b-SO6 is not toxic to normal human hematopoietic stem cells suggesting that this critical cell population would be preserved in therapeutic interventions using this immunotoxin...
  57. pmc Scl represses cardiomyogenesis in prospective hemogenic endothelium and endocardium
    Ben Van Handel
    Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Cell 150:590-605. 2012
    ..These results reveal unexpected plasticity in embryonic endothelium such that loss of a single master regulator can induce ectopic cardiomyogenesis from endothelial cells...
  58. pmc Regulation of the yeast metabolic cycle by transcription factors with periodic activities
    Aliz R Rao
    Bioinformatics Interdepartmental Program, University of California, Los Angeles, USA
    BMC Syst Biol 5:160. 2011
    ..Knowing the transcription factors involved in the yeast metabolic cycle is helpful for determining the cascade of regulatory events that cause these patterns...
  59. pmc Nonsense-mediated mRNA decay mutes the splicing defects of spliceosome component mutations
    Tadashi Kawashima
    Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095 1569, USA
    RNA 15:2236-47. 2009
    ....
  60. pmc Novel stem/progenitor cell population from murine tracheal submucosal gland ducts with multipotent regenerative potential
    Ahmed E Hegab
    Department of Pediatrics, David Geffen School of Medicine at University of California Los Angeles, University of California Los Angeles School of Medicine, Los Angeles, California, USA
    Stem Cells 29:1283-93. 2011
    ....
  61. pmc Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli
    Shota Atsumi
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
    Mol Syst Biol 6:449. 2010
    ..Interestingly, improved isobutanol tolerance did not increase the final titer of isobutanol production...
  62. pmc Systems-level analysis of nitrogen starvation-induced modifications of carbon metabolism in a Chlamydomonas reinhardtii starchless mutant
    Ian K Blaby
    Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
    Plant Cell 25:4305-23. 2013
    ....
  63. pmc BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data
    Weilong Guo
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
    BMC Genomics 14:774. 2013
    ..Libraries such as whole genome bisulfite sequencing (WGBS) and reduced represented bisulfite sequencing (RRBS) are widely used for generating DNA methylomes, demanding efficient and versatile tools for aligning bisulfite sequencing data...
  64. pmc The ontogeny of cKIT+ human primordial germ cells proves to be a resource for human germ line reprogramming, imprint erasure and in vitro differentiation
    Sofia Gkountela
    Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA
    Nat Cell Biol 15:113-22. 2013
    ..Taken together, our study creates a resource of human germ line ontogeny that is essential for future studies aimed at in vitro differentiation and unveiling the mechanisms necessary to pass human DNA from one generation to the next...
  65. pmc New transgenic reporters identify somatosensory neuron subtypes in larval zebrafish
    Ana Marie S Palanca
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles 90095, USA
    Dev Neurobiol 73:152-67. 2013
    ..The new transgenes created in this study will be powerful tools for further characterizing the molecular, morphological, and developmental diversity of larval somatosensory neurons...
  66. pmc Mef2C is a lineage-restricted target of Scl/Tal1 and regulates megakaryopoiesis and B-cell homeostasis
    Christos Gekas
    Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
    Blood 113:3461-71. 2009
    ..In summary, this work identifies Mef2C as an integral member of hematopoietic transcription factors with distinct upstream regulatory mechanisms and functional requirements in megakaryocyte and B-lymphoid lineages...
  67. pmc Hybrid mouse diversity panel: a panel of inbred mouse strains suitable for analysis of complex genetic traits
    Anatole Ghazalpour
    Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
    Mamm Genome 23:680-92. 2012
    ..In this essay, we review our experience with the HMDP, describe various ongoing projects, and discuss how the HMDP may fit into the larger picture of common diseases and different approaches...
  68. pmc X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations
    Yin Shen
    Department of Human Genetics, Geffen School of Medicine, and Departments of Pathology and Laboratory Medicine and Molecular Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 105:4709-14. 2008
    ....
  69. pmc Molecular analyses of human induced pluripotent stem cells and embryonic stem cells
    Mark H Chin
    Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
    Cell Stem Cell 7:263-9. 2010
    ....
  70. pmc Genomewide clonal analysis of lethal mutations in the Drosophila melanogaster eye: comparison of the X chromosome and autosomes
    Gerald B Call
    Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095, USA
    Genetics 177:689-97. 2007
    ..The data reveal the surprising result that the X chromosome has almost twice the frequency of essential genes involved in eye development as that found on the autosomes...
  71. pmc Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach
    Michael Strong
    Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095 1570, USA
    Genome Biol 4:R59. 2003
    ....
  72. pmc A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii
    Janette Kropat
    Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 1569, USA
    Plant J 66:770-80. 2011
    ..Fe and Zn deficiency also induced TAG accumulation, as suggested by Nile Red staining. This approach can be used to efficiently optimize culture conditions for other algal species to improve growth and to assay cell physiology...
  73. pmc Global phosphoproteomics reveals crosstalk between Bcr-Abl and negative feedback mechanisms controlling Src signaling
    Liudmilla Rubbi
    Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
    Sci Signal 4:ra18. 2011
    ..The identified Bcr-Abl-activated SFK regulatory mechanisms are candidates for dysregulation during leukemia progression and acquisition of SFK-mediated drug resistance...