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jacobian163

Interested in Bioinformatics, Tutoring, Science Writing, etc.

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Location: Escondido, United States

Member since: May 2012

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Portfolio

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Résumé

Experience

Postdoctoral Researcher

Sep 2011 - Present (2 years)

Salk Institute for Biological Studies

Bioinformatics Analysis and Bio-Programming in the field of Aging and Cancer Research

Graduate Student/Research Associate

Jan 2006 - Aug 2011 (5 years)

UW Madison, Department of Biochemistry

o Chromatin immunoprecipitation on microarrays (ChIP-chip) with small-molecule kinase inhibition<br />o Various applications of standard procedures, including: EMSA, in vitro kinase assays, western blotting, qPCR, microarray hybridization, and bacterial, yeast, and mammalian cell culture, and photolithographic synthesis of DNA-based microarrays<br />o Extensive bioinformatics analysis using R programming, PERL, and various software, including: TIGR mev, Osprey, Cytoscape, SignalMap and NimbleScan

Undergraduate Student Researcher

Feb 2005 - May 2005 (3 months)

UCR, Department of Environmental Sciences

o Worked with a graduate student (Gyorgyi Nyerges) on ammonia oxidation and methane reduction in methanotrophic bacteria.

Chemical engineering Intern/Consultant

May 2004 - Jun 2005 (1 year)

Sierra Aluminum Company

o Extruded Aluminum Quenching Process Testing<br /><br />o Nitriding Process Optimization<br /><br />o SOP Manual Revision for Riverside and Fontana Facility Operations<br /><br />o Facility Expansion Planning

Undergraduate Student Researcher

Feb 2004 - Nov 2004 (9 months)

UCR, Department of Chemical/Environmental Engineering

o Performed enzyme purification and activity assays for the detection and degradation of organophosphate nerve agents.

Undergraduate Student Research

Jun 2001 - Oct 2002 (1 year)

UCR, Bourns College of Engineering Center for Environmental Research and Technology (CE-CERT)

o Performed on-site recording and measurement of vehicle emissions, traffic patterns, and traffic vehicle composition across the South Coast Air Basin.

Education

Doctor of Philosophy in Microbiology

University of Wisconsin-Madison

2005-2011

Bachelor of Science, Chemical Engineering with concentration in Biochemistry

University of California, Riverside

2001-2005

Bachelor of Science, Mathematics with concentration in Applied Mathematics/Chemistry

University of California, Riverside

2001-2005

Publications

Emerging Views on the CTD Code

Genetics Research International

Abstract:<br />The C-terminal domain (CTD) of RNA polymerase II (Pol II) consists of conserved heptapeptide repeats that function as a binding platform for different protein complexes involved in transcription, RNA processing, export, and chromatin remodeling. The CTD repeats are subject to sequential waves of posttranslational modifications during specific stages of the transcription cycle. These patterned modifications have led to the postulation of the "CTD code" hypothesis, where stage-specific

Jarid2 (Jumonji, AT rich interactive domain 2) regulates NOTCH1 expression via histone modification in the developing heart

Journal of Biological Chemistry

Abstract: Jarid2/Jumonji, the founding member of the Jmj factor family, critically regulates various developmental processes, including cardiovascular development. The Jmj family was identified as histone demethylases, indicating epigenetic regulation by Jmj proteins. Deletion of Jarid2 in mice resulted in cardiac malformation and increased endocardial Notch1 expression during development. Although Jarid2 has been shown to occupy the Notch1 locus in the developing heart, the precise molecular role of Jarid2

Sequence-specificity and energy landscapes of DNA-binding molecules

Methods in Enzymology

Abstract: A central goal of biology is to understand how transcription factors target and regulate specific genes and networks to control cell fate and function. An equally important goal of synthetic biology, chemical biology, and personalized medicine is to devise molecules that can regulate genes and networks in a programmable manner. To achieve these goals, it is necessary to chart the sequence specificity of natural and engineered DNA-binding molecules. Cognate site identification (CSI) is now achieved

Chemical-genomic dissection of the CTD code

Nature Structural and Molecular Biology

Abstract: Sequential modifications of the RNA polymerase II (Pol II) C-terminal domain (CTD) coordinate the stage-specific association and release of cellular machines during transcription. Here we examine the genome-wide distributions of the 'early' (phospho-Ser5 (Ser5-P)), 'mid' (Ser7-P) and 'late' (Ser2-P) CTD marks. We identify gene class-specific patterns and find widespread co-occurrence of the CTD marks. Contrary to its role in 3'-processing of noncoding RNA,

The origin recognition complex interacts with a subset of metabolic genes tightly linked to origins of replication

PLoS Genetics

Abstract: The origin recognition complex (ORC) marks chromosomal sites as replication origins and is essential for replication initiation. In yeast, ORC also binds to DNA elements called silencers, where its primary function is to recruit silent information regulator (SIR) proteins to establish transcriptional silencing. Indeed, silencers function poorly as chromosomal origins. Several genetic, molecular, and biochemical studies of HMR-E have led to a model proposing that when ORC becomes limiting in the ce

TFIIH kinase places bivalent marks on the carboxy-terminal domain of RNA polymerase II

Molecular Cell

Abstract: Posttranslational modifications of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) specify a molecular recognition code that is deciphered by proteins involved in RNA biogenesis. The CTD is comprised of a repeating heptapeptide (Y(1)S(2)P(3)T(4)S(5)P(6)S(7)). Recently, phosphorylation of serine 7 was shown to be important for cotranscriptional processing of two snRNAs in mammalian cells. Here we report that Kin28/Cdk7, a subunit of the evolutionarily conserve

Quantitative microarray profiling of DNA-binding molecules

Journal of the American Chemical Society

Abstract: A high-throughput Cognate Site Identity (CSI) microarray platform interrogating all 524 800 10-base pair variable sites is correlated to quantitative DNase I footprinting data of DNA binding pyrrole-imidazole polyamides. An eight-ring hairpin polyamide programmed to target the 5 bp sequence 5'-TACGT-3' within the hypoxia response element (HRE) yielded a CSI microarray-derived sequence motif of 5'-WWACGT-3' (W = A,T). A linear beta-linked polyamide programmed to target a (GA