Publications

Acknowledgements

StemCore Laboratories undergoes annual evaluation based, in part, upon its ability to provide access to research enabling genomic technology platforms that are critical to scientific success, but difficult to manage within the context of an individual laboratory. One tangible demonstration of StemCore’s utility is the use of data generated within our laboratories in peer-reviewed publications. We therefore would appreciate the inclusion of a statement in manuscripts accepted for publication to acknowledge StemCore’s contribution to your research. We would also be very pleased to receive notification of such manuscripts when they are accepted for publication. Thank you for your ongoing support and use of StemCore’s facilities.

Selected Publications

 

2015 1-4              

 

1.   Yamak, A.  et al.  Novel Exons in the Tbx5 Gene Locus Generate Protein Isoforms with Distinct Expression Domains and Function.  Journal of Biological Chemistry   290 , 6844-6856 (2015).

2.   Smid, J.K., Faulkes, S. & Rudnicki, M.A. Periostin Induces Pancreatic Regeneration.  Endocrinology   156 , 824-836 (2015).

3.   Jones, A.  et al.  Wnt/beta-catenin controls follistatin signalling to regulate satellite cell myogenic potential.  Skeletal Muscle   5 , 14 (2015).

4.   Baldwin, R.M.  et al.  Protein arginine methyltransferase 7 promotes breast cancer cell invasion through the induction of MMP9 expression.  Oncotarget   6 , 3013-3032 (2015).

 

2014

 

5.   Sikora, D., Rocheleau, L., Brown, E.G. & Pelchat, M. Deep sequencing reveals the eight facets of the influenza A/HongKong/1/1968 (H3N2) virus cap-snatching process.  Scientific Reports   4 , 1-10 (2014).

6.   Price, F.D.  et al.  Inhibition of JAK-STAT signaling stimulates adult satellite cell function.  Nat Med   20 , 1174-1181 (2014).

7.   Palii, Carmen G.  et al.  Trichostatin A Enhances Vascular Repair by Injected Human Endothelial Progenitors through Increasing the Expression of TAL1-Dependent Genes.  Cell Stem Cell   14 , 644-657 (2014).

8.   Muharemagic, D.  et al.  Aptamer-facilitated Protection of Oncolytic Virus from Neutralizing Antibodies.  Mol Ther Nucleic Acids   3 , e167 (2014).

9.   Karapetis, C.S.  et al.  PIK3CA, BRAF, and PTEN Status and Benefit from Cetuximab in the Treatment of Advanced Colorectal Cancer—Results from NCIC CTG/AGITG CO.17.  Clinical Cancer Research   20 , 744-753 (2014).

10.   Gallagher, J.M.  et al.  Carboxy terminus of GATA4 transcription factor is required for its cardiogenic activity and interaction with CDK4.  Mechanisms of Development   134 , 31-41 (2014).

11.   Coulombe, J.  et al.  Loss of UCHL1 promotes age-related degenerative changes in the enteric nervous system.  Frontiers in Aging Neuroscience   6 , 129 (2014).

12.   Aries, A.  et al.  Caspase-1 cleavage of transcription factor GATA4 and regulation of cardiac cell fate.  Cell Death Dis   5 , e1566 (2014).

 

2013

 

13.   Yin, H., Price, F. & Rudnicki, M.A. Satellite cells and the muscle stem cell niche.  physiological Reviews   93 , 23-67 (2013).

14.   Yin, H.  et al.  MicroRNA-133 controls brown adipose determination in skeletal muscle satellite cells by targeting Prdm16.  Cell Metabolism   5 , 210-24 (2013).

15.   Ward, T., Hosid, S., Ioshikhes, I. & Altosaar, I. Human milk metagenome: a functional capacity analysis.  BMC Microbiology   13 , 116 (2013).

16.   Price, F.D.  et al.  Canonical Wnt signaling induces a primitive endoderm metastable state in mouse embryonic stem cells.  Stem Cells.   31 , 752-764 (2013).

17.   Patrick, C.  et al.  Promotion of Autoimmune Diabetes by Cereal Diet in the Presence or Absence of Microbes Associated With Gut Immune Activation, Regulatory Imbalance, and Altered Cathelicidin Antimicrobial Peptide.  Diabetes   62 , 2036-2047 (2013).

18.   Melanson, B.D.  et al.  A novel cis-acting element from the 3′UTR of DNA damage-binding protein 2 mRNA links transcriptional and post-transcriptional regulation of gene expression.  Nucleic Acids Research  (2013).

19.   Greco-Stewart, V.S.  et al.  Biofilm formation by Staphylococcus capitis strains isolated from contaminated platelet concentrates.  Journal of Medical Microbiology   62 , 1051-1059 (2013).

20.   Dankar, S.  et al.  Influenza A/Hong Kong/156/1997(H5N1) virus NS1 gene mutations F103L and M106I both increase IFN antagonism, virulence and cytoplasmic localization but differ in binding to RIG-I and CPSF30.  Virology Journal   10 , 243 (2013).

21.   Dalby, S.J. & Bonen, L. Impact of low temperature on splicing of atypical group II introns in wheat mitochondria.  Mitochondrion   13 , 647-655 (2013).

22.   Campbell, P.A. & Rudnicki, M.A. Oct4 interaction with Hmgb2 regulates Akt signaling and pluripotency.  Stem Cells   31 , 1107-1120 (2013).

23.   Andrade-Navarro, M.A.  et al.  A method for cell type marker discovery by high-throughput gene expression analysis of mixed cell populations.  BMC Biotechnology   13 , 80-80 (2013).

 

2012

 

24.   Wan, S., Johnson, A.M. & Altosaar, I. Expression of nitrous oxide reductase from Pseudomonas stutzeri in transgenic tobacco roots using the root-specific rolD promoter from Agrobacterium rhizogenes.  Ecology and Evolution   2 , 286-297 (2012).

25.   Soleimani, V.D.  et al.  Snail regulates MyoD binding-site occupancy to direct enhancer switching and differentiation-specific transcription in myogenesis.  Molecular Cell.  47 , 457-68 (2012).

26.   Soleimani, V.D.  et al.  Transcriptional dominance of Pax7 in adult myogenesis is due to high-affinity recognition of homeodomain motifs.  Developmental Cell   22 , 1208-20 (2012).

27.   Pasut, A., Oleynik, P. & Rudnicki, M.A. Isolation of muscle stem cells by fluorescence activated cell sorting cytometry.  Methods in Molecular Biology  798 , 53-64 (2012).

28.   Liu, Q.C.  et al.  Comparative expression profiling identifies differential roles for Myogenin and p38α MAPK signaling in myogenesis.  Journal of Molecular Cell Biology   4 , 386-97 (2012).

29.   Howe, G.A. & Addison, C.L. β1 integrin: an emerging player in the modulation of tumorigenesis and response to therapy.  Cell Adhesion and Migration   6 , 71-7 (2012).

30.   Ho, S., S.J.,  et al.  The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons.  Nucleic Acids Research   40 , D984-91 (2012).

31.   Gamwell, L.F., Collins, O. & Vanderhyden, B.C. The Mouse Ovarian Surface Epithelium Contains a Population of LY6A (SCA-1) Expressing Progenitor Cells That Are Regulated by Ovulation-Associated Factors.  Biology of Reproduction   87 , 80, 1-10 (2012).

32.   Duarte-Guterman, P., Ryan, M.J., Hogan, N.S. & Trudeau, V.L. Developmental profiles and thyroid hormone regulation of brain transcripts in frogs: a species comparison with emphasis on Physalaemus pustulosus.  Brain Behavior Evolution   79 , 98-112 (2012).

33.   Daneshmand, M.  et al.  Detection of PIK3CA Mutations in Breast Cancer Bone Metastases.  ISRN Oncology   2012 , 8 (2012).

 

2011

 

34.   Yan, D.  et al.  Differential Signaling of Cysteinyl Leukotrienes and a Novel Cysteinyl Leukotriene Receptor 2 (CysLT2) Agonist, N-Methyl-Leukotriene C4, in Calcium Reporter and β Arrestin Assays.  Molecular Pharmacology   79 , 270-278 (2011).

35.   Swist, E.  et al.  Excess dietary iodine differentially affects thyroid gene expression in diabetes, thyroiditis-prone versus -resistant BioBreeding (BB) rats.  Molecular Nutrition & Food Research   55 , 1875-86 (2011).

36.   Palii, C.G.  et al.  Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages.  The EMBO Journal   30 , 494-509 (2011).

37.   Melanson, B.D.  et al.  The role of mRNA decay in p53-induced gene expression.  RNA   17 , 2222-34 (2011).

38.   Dankar, S.K.  et al.  Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence.  Virology Journal   8 , 13 (2011).

39.   Chen, Q.  et al.  Dietary fructooligosaccharides and wheat bran elicit specific and dose-dependent gene expression profiles in the proximal colon epithelia of healthy Fischer 344 rats.  Journal of Nutrition   141 , 790-7 (2011).

 

2010

 

40.   Li, L.  et al.  A unique interplay between Rap1 and E-cadherin in the endocytic pathway regulates self-renewal of human embryonic stem cells.  Stem Cells.  28 , 247-57 (2010 ).

41.   Xuefang, X.  et al.  MHC class I Dk expression in hematopoietic and nonhematopoietic cells confers natural killer cell resistance to murine cytomegalovirus.  Proceedings of the National Academy of Sciences   107 , 8754–87 59 (2010).

42.   Tomlinson, J.J.  et al.  Insulin sensitization of human preadipocytes through glucocorticoid hormone induction of forkhead transcription factors.  Molecular Endocrinology   24 , 104-13 (2010).

43.   Scimè, A.  et al.  Transcriptional profiling of skeletal muscle reveals factors that are necessary to maintain satellite cell integrity during ageing.  Mechanisms of Ageing and Development   131 , 9-20 (2010).

44.   Schnerch, A., Cerdan, C. & Bhatia, M. Distinguishing between mouse and human pluripotent stem cell regulation: the best laid plans of mice and men.  Stem Cells  (2010).

45.   Sasawatari, S.  et al.  The Ly49Q receptor plays a crucial role in neutrophil polarization and migration by regulating raft trafficking.  Immunity   32 , 200-13 (2010).

46.   Ping, J.  et al.  PB2 and hemagglutinin mutations are major determinants of host range and virulence in mouse-adapted influenza A virus.  Journal of Virology   84 , 10606-18 (2010).

47.   Patel, R., Bélanger, S., Tai, L.H., Troke, A.D. & Makrigiannis, A.P. Effect of Ly49 haplotype variance on NK cell function and education.  The Journal of Immunology   185 , 4783-92 (2010).

48.   Pardo, M.  et al.  An expanded Oct4 interaction network: implications for stem cell biology, development, and disease.  Cell Stem Cell   6 , 382-95 (2010).

49.   Miura, P.  et al.  The utrophin A 5'-UTR drives cap-independent translation exclusively in skeletal muscles of transgenic mice and interacts with eEF1A2.  Human Molecular Genetics   19 , 1211-20 (2010).

50.   Lim, S.J., Tan, T.W. & Tong, J.C. Computational Epigenetics: the new scientific paradigm.  Bioinformation   4 , 331-7 (2010).

51.   Li, L.  et al.  Individual cell movement, asymmetric colony expansion, rho-associated kinase, and E-cadherin impact the clonogenicity of human embryonic stem cells.  Biophysical Journal  98 , 2442-51 (2010).

52.   Lewis, J.M., Hori, T.S., Rise, M.L., Walsh, P.J. & Currie, S.  Transcriptome responses to heat stress in the nucleated red blood cells of the rainbow trout (Oncorhynchus mykiss) , 361-373 (2010).

53.   Hayashi, M.  et al.  Ly49Q, an ITIM-bearing NK receptor, positively regulates osteoclast differentiation.  Biochemical and Biophysical Research Communications   393 , 432-8 (2010).

54.   Benveniste, P.  et al.  Intermediate-term hematopoietic stem cells with extended but time-limited reconstitution potential.  Cell Stem Cell   6 , 48-58 (2010).

 

2009

 

55.   Werbowetski-Ogilvie, T.E.  et al.  Characterization of human embryonic stem cells with features of neoplastic progression.  Nature Biotechnology   27 , 91-7 (2009).

56.   Savage, J., Conley, A.J., Blais, A. & Skerjanc, I.S. SOX15 and SOX7 differentially regulate the myogenic program in P19 cells.  Stem Cells   27 , 1231-43 (2009).

57.   Sandie, R.  et al.  Recent developments in StemBase: a tool to study gene expression in human and murine stem cells.  BMC Research Notes   2 , 39 (2009).

58.   Ross, P.J., Kennedy, M.A. & Parks, R.J. Host Cell Detection of Noncoding Stuffer DNA Contained in Helper-Dependent Adenovirus Vectors Leads to Epigenetic Repression of Transgene Expression.  Journal of Virology   83 , 8409-8417 (2009).

59.   Pratt, M.A.  et al.  The canonical NF-kappaB pathway is required for formation of luminal mammary neoplasias and is activated in the mammary progenitor population.  Oncogene.  28 , 2710-22 (2009).

60.   Natale, D.R., Hemberger, M., Hughes, M. & Cross, J.C. Activin promotes differentiation of cultured mouse trophoblast stem cells towards a labyrinth cell fate.  Developmental Biology   335 , 120-31 (2009).

61.   Muro, E.M., McCann, J.A., Rudnicki, M.A. & Andrade-Navarro, M.A. Use of SNP-arrays for ChIP assays: computational aspects.  Methods in Molecular Biology   567 , 145-54 (2009).

62.   Le Grand, F., Jones, A.E., Seale, V., Scime, A. & Rudnicki, M.A. Wnt7a activates the planar cell polarity pathway to drive the symmetric expansion of satellite stem cells.  Cell Stem Cell   4 , 535-47 (2009).

63.   Hu, G.  et al.  A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal.  Genes & Development   23 , 837-848 (2009).

64.   Haddon, D.J.  et al.  Prion protein expression and release by mast cells after activation.  The Journal of Infectious Diseases   200 , 827-31 (2009).

65.   Doyle, P.J.  et al.  Intracellular Expression of a Single Domain Antibody Reduces Cytotoxicity of 15-Acetyldeoxynivalenol in Yeast.  Journal of Biological Chemistry   284 , 35029-35039 (2009).

 

2008

 

66.   Wang, S.  et al.  Simplified recombinational approach for influenza A virus reverse genetics.  Journal of Virological Methods   151 , 74-8 (2008).

67.   Tam, W.-L.  et al.  T-Cell Factor 3 Regulates Embryonic Stem Cell Pluripotency and Self-Renewal by the Transcriptional Control of Multiple Lineage Pathways.  STEM CELLS   26 , 2019-2031 (2008).

68.   Raouf, A.  et al.  Transcriptome analysis of the normal human mammary cell commitment and differentiation process.  Cell Stem Cell   3 , 109-18 (2008).

69.   Pineault, N.  et al.  Characterization of the effects and potential mechanisms leading to increased megakaryocytic differentiation under mild hyperthermia.  Stem Cells and Development   17 , 483-93 (2008).

70.   McKinnell, I.W.  et al.  Pax7 activates myogenic genes by recruitment of a histone methyltransferase complex.  Nature Cell Biology   10 , 77-84 (2008).

71.   Lee, R.E., Puente, L.G., Kaern, M. & Megeney, L.A. A non-death role of the yeast metacaspase: Yca1p alters cell cycle dynamics.  PLoS One   3 , e2956 (2008).

72.   Goulet, I., Boisvenue, S., Mokas, S., Mazroui, R. & Cote, J. TDRD3, a novel Tudor domain-containing protein, localizes to cytoplasmic stress granules.  Human Molecular Genetics   17 , 3055-74 (2008).

73.   Calixte, S. & Bonen, L. Developmentally-specific transcripts from the ccmFN-rps1 locus in wheat mitochondria.  Molecular Genetics and Genomics   280 , 419-26 (2008).

74.   Baldwin, R.M., Parolin & Lorimer, A.J. Regulation of glioblastoma cell invasion by PKCι and RhoB.  Oncogene  27 , 3587-3595 (2008).

75.   Bakkar, N.  et al.  IKK/NF-kappaB regulates skeletal myogenesis via a signaling switch to inhibit differentiation and promote mitochondrial biogenesis.  The Journal of Cell Biology   180 , 787-802 (2008).

76.   Archer, S.L.  et al.  Mitochondrial metabolism, redox signaling, and fusion: a mitochondria-ROS-HIF-1alpha-Kv1.5 O2-sensing pathway at the intersection of pulmonary hypertension and cancer.  American Journal of Physiology - Heart and Circulatory Physiology   294 , H570-8 (2008).

 

2007

 

77.   zur Nieden, N.I., Price, F.D., Davis, L.A., Everitt, R.E. & Rancourt, D.E. Gene profiling on mixed embryonic stem cell populations reveals a biphasic role for beta-catenin in osteogenic differentiation.  Journal of Molecular Endocrinology   21 , 674-85 (2007).

78.   Smith, J.M., Stubbert, L.J., Hamill, J.D. & McKay, B.C. The Contribution of Transactivation Subdomains 1 and 2 to p53-Induced Gene Expression Is Heterogeneous But Not Subdomain-Specific.  Neoplasia.  9 , 1057-1065 (2007).

79.   Power, A.T.  et al.  Carrier cell-based delivery of an oncolytic virus circumvents antiviral immunity.  Molecular Therapy   15 , 123-30 (2007).

80.   Porter, C.J.  et al.  StemBase: A resource for the analysis of stem cell gene expression data.  Methods in Molecular Biology   407 , 137-48 (2007).

81.   McCann, J.A.  et al.  ChIP on SNP-chip for genome-wide analysis of human histone H4 hyperacetylation.  BMC Genomics   8 , 322 (2007).

82.   Kuang, S., Kuroda, K., Le Grand, F. & Rudnicki, M.A. Asymmetric self-renewal and commitment of satellite stem cells in muscle.  Cell   129 , 999-1010 (2007).

83.   Holterman, C.E., Le Grand, F., Kuang, S., Seale, P. & Rudnicki, M.A. Megf10 regulates the progression of the satellite cell myogenic program.  The Journal of Cell Biology   179 , 911-22 (2007).

84.   Hailesellasse Sene, K.  et al.  Gene function in early mouse embryonic stem cell differentiation.  BMC Genomics   8 , 85 (2007).

85.   Grenier, G.  et al.  Resident endothelial precursors in muscle, adipose, and dermis contribute to postnatal vasculogenesis.  Stem Cells   25 , 3101-10 (2007).

86.   Goulet, I., Gauvin, G., Boisvenue, S. & Cote, J. Alternative splicing yields protein arginine methyltransferase 1 isoforms with distinct activity, substrate specificity, and subcellular localization.  The Journal of Biological Chemistry   282 , 33009-21 (2007).

87.   Campbell, P.A., Perez-Iratxeta, C., Andrade-Navarro, M.A. & Rudnicki, M.A. Oct4 targets regulatory nodes to modulate stem cell function.  PLoS One   2 , e553 (2007).

 

2006

 

88.   Puente, L.G., Voisin, S., Lee, R.E. & Megeney, L.A. Reconstructing the regulatory kinase pathways of myogenesis from phosphopeptide data.  Molecular & Cellular Proteomics   5 , 2244-51 (2006).

89.   Puente, L.G., Borris, D.J., Carrière, J.-F., Kelly, J.F. & Megeney, L.A. Identification of Candidate Regulators of Embryonic Stem Cell Differentiation by Comparative Phosphoprotein Affinity Profiling.  Molecular & Cellular Proteomics  5 , 57-67 (2006).

90.   Palidwor, G., Reynaud, E.G. & Andrade-Navarro, M.A. Taxonomic colouring of phylogenetic trees of protein sequences.  BMC Bioinformatics  7 (2006).

91.   Muro, E.M., Perez-Iratxeta, C. & Andrade-Navarro, M.A. Amplification of the Gene Ontology annotation of Affymetrix probe sets.  BMC Bioinformatics   7 , 159 (2006).

92.   Bonnet, S.  et al.  An abnormal mitochondrial-hypoxia inducible factor-1alpha-Kv channel pathway disrupts oxygen sensing and triggers pulmonary arterial hypertension in fawn hooded rats: similarities to human pulmonary arterial hypertension.  Circulation   113 , 2630-41 (2006).

93.   Baldwin, R.M.  et al.  Protection of glioblastoma cells from cisplatin cytotoxicity via protein kinase Ciota-mediated attenuation of p38 MAP kinase signaling.  Oncogene   25 , 2909-19 (2006).

 

2005

 

94.   Xia, X. & Palidwor, G. Genomic adaptation to acidic environment: evidence from Helicobacter pylori.  The American Naturalist   166 , 776-84 (2005).

95.   Suomela, B.P. & Andrade, M.A. Ranking the whole MEDLINE database according to a large training set using text indexing.  BMC Bioinformatics   6 (2005).

96.   Scimè, A.  et al.  Rb and p107 regulate preadipocyte differentiation into white versus brown fat through repression of PGC-1alpha.  Cell Metabolism  2 , 283-95 (2005).

97.   Savchenko, A., ,   et al.  The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism.  The Journal of Biological Chemistry   280 , 19213-20 (2005).

98.   Reynaud, E.G.  et al.  Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization.  BMC Biology  3 (2005).

99.   Perez-Iratxeta, C., Wjst, M., Bork, P. & Andrade, M.A. G2D: a tool for mining genes associated with disease.  BMC Genetics   6 , 45 (2005).

100.   Perez-Iratxeta, C.  et al.  Study of stem cell function using microarray experiments.  FEBS Letters   579 , 1795-1801 (2005).

101.   Perez-Iratxeta, C. & Andrade, M.A. Inconsistencies over time in 5% of NetAffx probe-to-gene annotations.  BMC Bioinformatics   6 , 183 (2005).

102.   Korbel, J.O.  et al.  Systematic association of genes to phenotypes by genome and literature mining.  PLoS Biology   3 , e134 (2005).

103.   Kendal, W.S. & Suomela, B.P. Large-scale genomic correlations in Arabidopsis thaliana relate to chromosomal structure.  BMC Genomics   6 , 82 (2005).

104.   Fernando, P.  et al.  Active kinase proteome screening reveals novel signal complexity in cardiomyopathy.  Molecular & Cellular Proteomics   4 , 673-82 (2005).

 

2004

 

105.   Yauk, C.L., Berndt, M.L., Williams, A. & Douglas, G.R. Comprehensive comparison of six microarray technologies.  Nucleic Acids Research  32 , e124 (2004).

106.   Seale, P., Holtreman, C. & Rudnick, i.M.A. Muscle satellite cell-specific genes identified by genetic profiling of MyoD-deficient myogenic cell.  Developmental Biology   275 (2004).

107.   Puente, L.G., Carrière, J.F., Kelly, J.F. & Megeney, L.A. Comparative analysis of phosphoprotein-enriched myocyte proteomes reveals widespread alterations during differentiation.  FEBS Letters   574 , 138-44 (2004).

 

2003

 

108.   Polesskaya, A., Seale, P. & Rudnicki, M.A. Wnt signaling induces the myogenic specification of resident CD45+ adult stem cells during muscle regeneration.  Cell   113 , 841-52 (2003).

 

2002

 

109.   Hierlihy, A.M., Seale, P., Lobe, C.G., Rudnicki, M.A. & Megeney, L.A. The post-natal heart contains a myocardial stem cell population.  FEBS Letters   530 , 239-43 (2002).