Christopher Burge

Last updated
Chris Burge
Born
Christopher Boyce Burge

(1968-05-26) May 26, 1968 (age 53) [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

Bioinformatics Computational analysis of large, complex sets of biological data

Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for in silico analyses of biological queries using mathematical and statistical techniques.

microRNA Small non-coding ribonucleic acid molecule

A microRNA is a small single-stranded non-coding RNA molecule found in plants, animals and some viruses, that functions in RNA silencing and post-transcriptional regulation of gene expression. miRNAs function via base-pairing with complementary sequences within mRNA molecules. As a result, these mRNA molecules are silenced, by one or more of the following processes: (1) Cleavage of the mRNA strand into two pieces, (2) Destabilization of the mRNA through shortening of its poly(A) tail, and (3) Less efficient translation of the mRNA into proteins by ribosomes.

Non-coding RNA Class of ribonucleic acid that is not translated into proteins

A non-coding RNA (ncRNA) is an RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-coding RNAs include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), as well as small RNAs such as microRNAs, siRNAs, piRNAs, snoRNAs, snRNAs, exRNAs, scaRNAs and the long ncRNAs such as Xist and HOTAIR.

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 highly conserved in 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

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.

RAD52

RAD52 homolog , also known as RAD52, is a protein which in humans is encoded by the RAD52 gene.

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.

miR-138

miR-138 is a family of microRNA precursors found in animals, including humans. MicroRNAs are typically transcribed as ~70 nucleotide precursors and subsequently processed by the Dicer enzyme to give a ~22 nucleotide product. The excised region or, mature product, of the miR-138 precursor is the microRNA mir-138.

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.

In molecular biology mir-241 microRNA is a short RNA molecule. MicroRNAs function to regulate the expression levels of other genes by several mechanisms.

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.

Debora Marks Computational biologist

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

Hanah Margalit

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.

C7orf50

C7orf50 is a gene in humans that encodes a protein known as C7orf50. This gene is ubiquitously expressed in the kidneys, brain, fat, prostate, spleen, among 22 other tissues and demonstrates low tissue specificity. C7orf50 is conserved in chimpanzees, Rhesus monkeys, dogs, cows, mice, rats, and chickens, along with 307 other organisms from mammals to fungi. This protein is predicted to be involved with the import of ribosomal proteins into the nucleus to be assembled into ribosomal subunits as a part of rRNA processing. Additionally, this gene is predicted to be a microRNA (miRNA) protein coding host gene, meaning that it may contain miRNA genes in its introns and/or exons.

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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