Mark Bieda

Scientist

Publications



Note: some publications show up multiple times due to fitting in several categories.

Neuroscience and Neurogenomics-related Publications

Yoo S, Bieda MC. (2014) Differences among brain tumor stem cell types and fetal neural stem cells in focal regions of histone modifications and DNA methylation, broad regions of modifications, and bivalent promoters. BMC Genomics 15:72. Pubmed

Padmanabhan N, Jia D, Geary-Joo C, Wu X, Ferguson-Smith AC, Fung E, Bieda MC, Snyder FF, Gravel RA, Cross JC, Watson ED. (2013) Mutation in folate metabolism causes epigenetic instability and transgenerational effects on development. Cell 155(1):81-93. Pubmed

Bieda MC, Su H, MacIver MB (2009) Anesthetics discriminate between tonic and phasic gamma-aminobutyric acid receptors on hippocampal CA1 neurons. Anesth Analgesia 108:484. Pubmed

Yasui DH, Peddada S, Bieda M, Thatcher K, Vallero R, Farnham PJ, LaSalle J (2007) Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes. Proceedings of the National Academy of Science (USA) 104:19146. Pubmed

Bieda MC, MacIver MB (2004) A major role for tonic GABAA conductances in anesthetic suppression of intrinsic neuronal excitability. Journal of Neurophysiology 92:1658. Pubmed

Bieda MC, Copenhagen DR (2004) N-type and L-type calcium channels mediate glycinergic synaptic inputs to retinal ganglion cells. Visual Neuroscience 21:545-550. Pubmed

Bieda MC, Copenhagen DR (2000) Inhibition is not required for the production of transient spiking responses from retinal ganglion cells. Visual Neuroscience 17:243-254. Pubmed

Bieda MC, Copenhagen DR (1999) Sodium action potentials are not required for light-evoked release of GABA or glycine from retinal amacrine cells. Journal of Neurophysiology 81:3092-3095. Pubmed

Dixon DB, Takahashi K-I, Bieda M, Copenhagen DR (1996) Quinine, intracellular pH and modulation of hemi-gap junctions in catfish horizontal cells. Vision Research 36:3925-3931. Pubmed

Rogawski MA, Yamaguichi S, Blake PA, Jones SM, Bieda MC, de Costa BR, Thurkauf A (1992) Anticonvulsant 1-Phenylcycloalkylamine analogs: uncompetitive NMDA antagonists with low motor toxicity. In: Multiple Sigma and PCP Receptor Ligands: Mechanisms for Neuromodulation and Neuroprotection? (Kamenka J-M, Domino EF, eds), pp 747-758. Ann Arbor, MI: NPP Books.

Genomics/Bioinformatics-related Publications

Leigh R, Mostafa MM, King EM, Rider CF, Shah S, Dumonceaux C, Traves SL, McWhae A, Kolisnik T, Kooi C, Slater DM, Kelly MM, Bieda M, Miller-Larsson A, Newton R. (2016) An inhaled dose of budesonide induces genes involved in transcription and signaling in the human airways: Enhancement of anti- and pro-inflammatory effector genes. Pharma Res Per 4:e00243 doi: 10.1002/prp2.243 Link

Cormier N, Kolisnik T, Bieda MC. (2016) Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis. BMC Bioinformatics 17:270. Pubmed

McPhillips T, Song T, Kolisnik T, Aulenbach S, Belhajjame K, Bocinsky RK, Cao Y, Cheney J, Chirigati F, Dey S, Freire J, Jones C, Hanken J, Kintigh KW, Kohler TA, Koop D, Macklin JA, Missier P, Schildhauer M, Schwalm C, Wei Y, Bieda MC, Ludäscher B. (2015) YesWorkflow: A User-Oriented, Language-Independent Tool for Recovering Workflow Information from Scripts. IJDC 10:298-313. Link

Yoo S, Bieda MC. (2014) Differences among brain tumor stem cell types and fetal neural stem cells in focal regions of histone modifications and DNA methylation, broad regions of modifications, and bivalent promoters. BMC Genomics 15:72. Pubmed

Padmanabhan N, Jia D, Geary-Joo C, Wu X, Ferguson-Smith AC, Fung E, Bieda MC, Snyder FF, Gravel RA, Cross JC, Watson ED. (2013) Mutation in folate metabolism causes epigenetic instability and transgenerational effects on development. Cell 155(1):81-93. Pubmed

Bieda M. (2012) Kepler for ‘Omics Bioinformatics. Procedia Computer Science 9:1635–1638. PDF

Stropp T, McPhillips T, Ludaescher B, Bieda M. (2012) Workflows for Microarray Data Processing in the Kepler Environment. BMC Bioinformatics 13:102. Pubmed

Acevedo LG*, Bieda M*, Green R, Farnham PJ (2008) Analysis of the mechanisms mediating tumor-specific changes in gene expression in human liver tumors. Cancer Res 68:2641. * denotes co-first authors Pubmed

Johnson et al. (2008) Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res. 18: 393. Pubmed

Xu S, Bieda MC, Jin VX, Rabinovitch A, Farnham PJ (2007) A comprehensive ChIP–chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Research 17:550. Pubmed

Yasui DH, Peddada S, Bieda M, Thatcher K, Vallero R, Farnham PJ, LaSalle J (2007) Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes. Proceedings of the National Academy of Science (USA) 104:19146. Pubmed

The ENCODE Project Consortium (2007) The ENCODE pilot project: Identification and analysis of functional elements in 1% of the human genome. Nature 447:799. Pubmed

Krig SR, Jin VX, Bieda MC, O’Geen H, Yaswen P, Green R, Farnham PJ (2007) Identification of genes directly regulated by the oncogene ZNF217 in ChIP-chip assays. Journal of Biological Chemistry 282:9703. Pubmed

Bieda M, Xu X, Singer M, Green R, Farnham PJ (2006) Unbiased location Analysis of E2F1-binding sites suggests a widespread role for E2F1 in the Human Genome. Genome Research, 16:595. Pubmed

Faculty of 1000 Biology: evaluations for Bieda M et al Genome Res 2006 May 16 (5) :595-605 Link

Bieda MC, Webb CT (2004) Distribution and patterns of CNSs in a Caenorhabditis gene family. published in SFI Working Papers Series Link

Cancer Biology-related Publications

Yoo S, Bieda MC. (2014) Differences among brain tumor stem cell types and fetal neural stem cells in focal regions of histone modifications and DNA methylation, broad regions of modifications, and bivalent promoters. BMC Genomics 15:72. Pubmed

Acevedo LG*, Bieda M*, Green R, Farnham PJ (2008) Analysis of the mechanisms mediating tumor-specific changes in gene expression in human liver tumors. Cancer Res 68:2641. * denotes co-first authors Pubmed

Xu S, Bieda MC, Jin VX, Rabinovitch A, Farnham PJ (2007) A comprehensive ChIP–chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Research 17:550. Pubmed

The ENCODE Project Consortium (2007) The ENCODE pilot project: Identification and analysis of functional elements in 1% of the human genome. Nature 447:799. Pubmed

Krig SR, Jin VX, Bieda MC, O’Geen H, Yaswen P, Green R, Farnham PJ (2007) Identification of genes directly regulated by the oncogene ZNF217 in ChIP-chip assays. Journal of Biological Chemistry 282:9703. Pubmed

Bieda M, Xu X, Singer M, Green R, Farnham PJ (2006) Unbiased location Analysis of E2F1-binding sites suggests a widespread role for E2F1 in the Human Genome. Genome Research, 16:595. Pubmed

Faculty of 1000 Biology: evaluations for Bieda M et al Genome Res 2006 May 16 (5) :595-605 Link