Christopher Burge

Last updated
Chris Burge
Born
Christopher Boyce Burge

(1968-05-26) May 26, 1968 (age 56) [1]
Alma mater Stanford University
Known for GENSCAN [2] [3]
Awards Overton Prize [4]
Searle Scholar Award [5]
Scientific career
Institutions Massachusetts Institute of Technology
Thesis Identification of genes in human genomic DNA  (1997)
Doctoral advisor Samuel Karlin [6]
Website genes.mit.edu/burgelab/cburge.html

Christopher Boyce Burge is Professor of Biology and Biological Engineering at Massachusetts Institute of Technology.

Contents

Education

Burge completed his Bachelor of Science at Stanford University in 1990, and continued graduate studies in computational biology at Stanford University, gaining his PhD [7] in 1997 [1] under the supervision of Samuel Karlin. [2] [3] During his time at Stanford he was responsible for developing algorithms for GENSCAN used in gene prediction for example the initial analysis of the Human Genome Project. [8] His PhD thesis was titled Identification of genes in human genomic DNA.

Research

From 1997 to 1999 Burge worked as a postdoc in the laboratory of Phillip Allen Sharp, working in the fields of RNA splicing and molecular evolution. [9] Burge joined the Massachusetts Institute of Technology in 1999 as a Bioinformatics Fellow. He became Assistant Professor in 2002, Associate Professor in 2004, was tenured in 2006, and was promoted to full Professor in 2010. He has been an Associate Member of the Broad Institute since 2004. [1] His current research interests include genomics, RNA splicing and microRNA [10] regulation. [11] [12] [13] [14]

Burge has also served on the editorial boards of the academic journals RNA , PLOS Computational Biology , BMC Bioinformatics and BMC Genomics. [1]

Awards

In 2001 he was awarded the Overton Prize [4] for Computational Biology by the International Society for Computational Biology. He was awarded a Searle Scholar Award in 2003 for his research in the computational biology of gene expression. [5] In 2007 he was awarded the Schering-Plough Research Institute Award (now known as the ASBMB Young Investigator Award) by the American Society for Biochemistry and Molecular Biology for his outstanding research contributions to biochemistry and molecular biology. [15]

Related Research Articles

microRNA Small non-coding ribonucleic acid molecule

Micro ribonucleic acid are small, single-stranded, non-coding RNA molecules containing 21–23 nucleotides. Found in plants, animals, and even some viruses, miRNAs are involved in RNA silencing and post-transcriptional regulation of gene expression. miRNAs base-pair to complementary sequences in messenger RNA (mRNA) molecules, then silence said mRNA molecules by one or more of the following processes:

<span class="mw-page-title-main">Gene expression</span> Conversion of a genes sequence into a mature gene product or products

Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, proteins or non-coding RNA, and ultimately affect a phenotype. These products are often proteins, but in non-protein-coding genes such as transfer RNA (tRNA) and small nuclear RNA (snRNA), the product is a functional non-coding RNA. The process of gene expression is used by all known life—eukaryotes, prokaryotes, and utilized by viruses—to generate the macromolecular machinery for life.

<span class="mw-page-title-main">Regulation of gene expression</span> Modifying mechanisms used by cells to increase or decrease the production of specific gene products

Regulation of gene expression, or gene regulation, includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products. Sophisticated programs of gene expression are widely observed in biology, for example to trigger developmental pathways, respond to environmental stimuli, or adapt to new food sources. Virtually any step of gene expression can be modulated, from transcriptional initiation, to RNA processing, and to the post-translational modification of a protein. Often, one gene regulator controls another, and so on, in a gene regulatory network.

RNA silencing or RNA interference refers to a family of gene silencing effects by which gene expression is negatively regulated by non-coding RNAs such as microRNAs. RNA silencing may also be defined as sequence-specific regulation of gene expression triggered by double-stranded RNA (dsRNA). RNA silencing mechanisms are conserved among most eukaryotes. The most common and well-studied example is RNA interference (RNAi), in which endogenously expressed microRNA (miRNA) or exogenously derived small interfering RNA (siRNA) induces the degradation of complementary messenger RNA. Other classes of small RNA have been identified, including piwi-interacting RNA (piRNA) and its subspecies repeat associated small interfering RNA (rasiRNA).

mir-160 microRNA precursor family

In molecular biology, mir-160 is a microRNA that has been predicted or experimentally confirmed in a range of plant species including Arabidopsis thaliana and Oryza sativa (rice). miR-160 is predicted to bind complementary sites in the untranslated regions of auxin response factor genes to regulate their expression. The hairpin precursors are predicted based on base pairing and cross-species conservation; their extents are not known. In this case, the mature sequence is excised from the 5' arm of the hairpin.

mir-2 microRNA precursor Type of RNA

The mir-2 microRNA family includes the microRNA genes mir-2 and mir-13. Mir-2 is widespread in invertebrates, and it is the largest family of microRNAs in the model species Drosophila melanogaster. MicroRNAs from this family are produced from the 3' arm of the precursor hairpin. Leaman et al. showed that the miR-2 family regulates cell survival by translational repression of proapoptotic factors. Based on computational prediction of targets, a role in neural development and maintenance has been suggested.

<span class="mw-page-title-main">ZCCHC6</span> Protein-coding gene in the species Homo sapiens

Terminal uridylyltransferase 7 (TUT7), also known as "zinc finger, CCHC domain containing 6", is an enzyme that in humans is encoded by the ZCCHC6 gene located on chromosome 9. The ZCCHC6 protein mediates the terminal uridylation of RNA transcripts with short poly-A tails and is involved in mRNA and microRNA degradation

Samuel Karlin was an American mathematician at Stanford University in the late 20th century.

Post-transcriptional regulation is the control of gene expression at the RNA level. It occurs once the RNA polymerase has been attached to the gene's promoter and is synthesizing the nucleotide sequence. Therefore, as the name indicates, it occurs between the transcription phase and the translation phase of gene expression. These controls are critical for the regulation of many genes across human tissues. It also plays a big role in cell physiology, being implicated in pathologies such as cancer and neurodegenerative diseases.

In bioinformatics, GENSCAN is a program to identify complete gene structures in genomic DNA. It is a GHMM-based program that can be used to predict the location of genes and their exon-intron boundaries in genomic sequences from a variety of organisms. The GENSCAN Web server can be found at MIT.

This microRNA database and microRNA targets databases is a compilation of databases and web portals and servers used for microRNAs and their targets. MicroRNAs (miRNAs) represent an important class of small non-coding RNAs (ncRNAs) that regulate gene expression by targeting messenger RNAs.

<span class="mw-page-title-main">Aviv Regev</span> Bioinformatician

Aviv Regev is a computational biologist and systems biologist and Executive Vice President and Head of Genentech Research and Early Development in Genentech/Roche. She is a core member at the Broad Institute of MIT and Harvard and professor at the Department of Biology of the Massachusetts Institute of Technology. Regev is a pioneer of single cell genomics and of computational and systems biology of gene regulatory circuits. She founded and leads the Human Cell Atlas project, together with Sarah Teichmann.

MicroRNA sequencing (miRNA-seq), a type of RNA-Seq, is the use of next-generation sequencing or massively parallel high-throughput DNA sequencing to sequence microRNAs, also called miRNAs. miRNA-seq differs from other forms of RNA-seq in that input material is often enriched for small RNAs. miRNA-seq allows researchers to examine tissue-specific expression patterns, disease associations, and isoforms of miRNAs, and to discover previously uncharacterized miRNAs. Evidence that dysregulated miRNAs play a role in diseases such as cancer has positioned miRNA-seq to potentially become an important tool in the future for diagnostics and prognostics as costs continue to decrease. Like other miRNA profiling technologies, miRNA-Seq has both advantages and disadvantages.

David P. Bartel is an American molecular biologist best known for his work on microRNAs. Bartel is a Professor of Biology at the Massachusetts Institute of Technology, Member of the Whitehead Institute, and investigator of the Howard Hughes Medical Institute (HHMI).

In bioinformatics, TargetScan is a web server that predicts biological targets of microRNAs (miRNAs) by searching for the presence of sites that match the seed region of each miRNA. For many species, other types of sites, known as 3'-compensatory sites are also identified. These miRNA target predictions are regularly updated and improved by the laboratory of David Bartel in conjunction with the Whitehead Institute Bioinformatics and Research Computing Group.

<span class="mw-page-title-main">Debora Marks</span> Computational biologist

Debora S. Marks is a researcher in computational biology and a Professor of Systems Biology at Harvard Medical School. Her research uses computational approaches to address a variety of biological problems.

<span class="mw-page-title-main">Hanah Margalit</span>

Hanah Margalit is a Professor in the faculty of medicine at the Hebrew University of Jerusalem. Her research combines bioinformatics, computational biology and systems biology, specifically in the fields of gene regulation in bacteria and eukaryotes.

Anindya Dutta is an Indian-born American biochemist and cancer researcher, a Chair of the Department of Genetics at the University of Alabama at Birmingham School of Medicine since 2021, who has served as Chair of the Department of Biochemistry and Molecular Genetics at the University of Virginia School of Medicine in 2011–2021. Dutta's research has focused on the mammalian cell cycle with an emphasis on DNA replication and repair and on noncoding RNAs. He is particularly interested in how de-regulation of these processes promote cancer progression. For his accomplishments he has been elected a Fellow of the American Association for the Advancement of Science, received the Ranbaxy Award in Biomedical Sciences, the Outstanding Investigator Award from the American Society for Investigative Pathology, the Distinguished Scientist Award from the University of Virginia and the Mark Brothers Award from the Indiana University School of Medicine.

References

  1. 1 2 3 4 http://genes.mit.edu/burgelab/CBurgeCV.pdf Archived 2011-08-17 at the Wayback Machine Christopher Burge CV
  2. 1 2 Burge, Christopher; Karlin, Samuel (1997). "Prediction of complete gene structures in human genomic DNA" (PDF). Journal of Molecular Biology. 268 (1): 78–94. doi:10.1006/jmbi.1997.0951. PMID   9149143. Archived from the original (PDF) on 2015-06-20.
  3. 1 2 Burge, C.; Karlin, S. (1998). "Finding the genes in genomic DNA". Current Opinion in Structural Biology. 8 (3): 346–354. doi: 10.1016/S0959-440X(98)80069-9 . PMID   9666331.
  4. 1 2 "Overton Prize". www.iscb.org. Retrieved 23 May 2021.
  5. 1 2 "Searle Scholars Program: Christopher Burge (2003)". Archived from the original on 5 September 2015. Retrieved 10 August 2015.
  6. ↑ Christopher Burge at the Mathematics Genealogy Project
  7. ↑ Burge, Christopher Boyce (2012). Identification of genes in human genomic DNA (PhD thesis). Stanford University. ProQuest   304386368.
  8. ↑ Lander, E. S.; Linton, M.; Birren, B.; Nusbaum, C.; Zody, C.; Baldwin, J.; Devon, K.; Dewar, K.; Doyle, M.; Fitzhugh, W.; Funke, R.; Gage, D.; Harris, K.; Heaford, A.; Howland, J.; Kann, L.; Lehoczky, J.; Levine, R.; McEwan, P.; McKernan, K.; Meldrim, J.; Mesirov, J. P.; Miranda, C.; Morris, W.; Naylor, J.; Raymond, C.; Rosetti, M.; Santos, R.; Sheridan, A.; et al. (Feb 2001). "Initial sequencing and analysis of the human genome" (PDF). Nature. 409 (6822): 860–921. Bibcode:2001Natur.409..860L. doi: 10.1038/35057062 . ISSN   0028-0836. PMID   11237011.
  9. ↑ Burge, C.; Padgett, R.; Sharp, P. (1998). "Evolutionary fates and origins of U12-type introns". Molecular Cell. 2 (6): 773–785. doi: 10.1016/S1097-2765(00)80292-0 . PMID   9885565.
  10. ↑ Rhoades, M. W.; Reinhart, B. J.; Lim, L. P.; Burge, C. B.; Bartel, B.; Bartel, D. P. (2002). "Prediction of Plant MicroRNA Targets". Cell. 110 (4): 513–520. doi: 10.1016/S0092-8674(02)00863-2 . PMID   12202040.
  11. ↑ Christopher Burge's publications indexed by the Scopus bibliographic database. (subscription required)
  12. ↑ http://www.biomedexperts.com/Profile.bme/172484/Christopher_B_Burge Archived 2012-03-21 at the Wayback Machine Chris Burge profile in BiomedExperts
  13. ↑ Lewis, B. P.; Burge, C. B.; Bartel, D. P. (2005). "Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets". Cell. 120 (1): 15–20. doi: 10.1016/j.cell.2004.12.035 . PMID   15652477.
  14. ↑ Lewis, B. P.; Shih, I. H.; Jones-Rhoades, M. W.; Bartel, D. P.; Burge, C. B. (2003). "Prediction of Mammalian MicroRNA Targets". Cell. 115 (7): 787–98. doi: 10.1016/S0092-8674(03)01018-3 . PMID   14697198.
  15. ↑ "ASBMB Young Investigator Award formerly the ASBMB Schering-Plough Research Institute Award" . Retrieved 10 August 2015.
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