Jim Kent

Last updated
Jim Kent
Jim Kent.JPG
Photo courtesy of Jim Kent.
Born (1960-02-10) February 10, 1960 (age 59)
Nationality United States
Alma mater University of California, Santa Cruz
Awards Overton Prize
Benjamin Franklin Award (Bioinformatics)
Scientific career
Thesis Patching and painting the working draft of the human genome  (2002)
Doctoral advisor Alan M Zahler
Other academic advisors David Haussler [1]
Website www.soe.ucsc.edu/~kent

William James Kent (born February 10, 1960) is an American research scientist and computer programmer. He has been a contributor to genome database projects and the 2003 winner of the Benjamin Franklin Award.

United States Federal republic in North America

The United States of America (USA), commonly known as the United States or America, is a country composed of 50 states, a federal district, five major self-governing territories, and various possessions. At 3.8 million square miles, the United States is the world's third or fourth largest country by total area and is slightly smaller than the entire continent of Europe's 3.9 million square miles. With a population of over 327 million people, the U.S. is the third most populous country. The capital is Washington, D.C., and the largest city by population is New York City. Forty-eight states and the capital's federal district are contiguous in North America between Canada and Mexico. The State of Alaska is in the northwest corner of North America, bordered by Canada to the east and across the Bering Strait from Russia to the west. The State of Hawaii is an archipelago in the mid-Pacific Ocean. The U.S. territories are scattered about the Pacific Ocean and the Caribbean Sea, stretching across nine official time zones. The extremely diverse geography, climate, and wildlife of the United States make it one of the world's 17 megadiverse countries.

Genome entirety of an organisms hereditary information; genome of organism (encoded by the genomic DNA) is the (biological) information of heredity which is passed from one generation of organism to the next; is transcribed to produce various RNAs

In the fields of molecular biology and genetics, a genome is the genetic material of an organism. It consists of DNA. The genome includes both the genes and the noncoding DNA, as well as mitochondrial DNA and chloroplast DNA. The study of the genome is called genomics.

Benjamin Franklin Award (Bioinformatics)

The Benjamin Franklin Award is an award for Open Access in the Life Sciences presented by Bioinformatics.org.

Contents

Early life

Kent was born in Hawaii and grew up in San Francisco, California, United States.

Hawaii State of the United States of America

Hawaii is the 50th and most recent state to have joined the United States, having received statehood on August 21, 1959. Hawaii is the only U.S. state located in Oceania, the only U.S. state located outside North America, and the only one composed entirely of islands. It is the northernmost island group in Polynesia, occupying most of an archipelago in the central Pacific Ocean.

Computer Animation

Kent began his programming career in 1983 with Island Graphics Inc. where he wrote the Aegis Animator program for the Amiga home computer. This program combined polygon tweening in 3D with simple 2D cel-based animation. In 1985 he founded and ran a software company, Dancing Flame, which adapted the Aegis Animator to the Atari ST, [2] and created Cyber Paint [3] for that machine. Cyber Paint was a 2D animation program that brought together a wide variety of animation and paint functionality and the delta-compressed animation format developed for CAD-3D. The user could move freely between animation frames and paint arbitrarily, or utilize various animation tools for automatic tweening movement across frames. Cyber Paint was one of the first, if not the first, consumer program that enabled the user to paint across time in a compressed digital video format. Later he developed a similar program, the Autodesk Animator for PC compatibles, where the image compression improved to the point it could play off of hard disk, and one could paint using "inks" that performed algorithmic transformations such as smoothing, transparency, and tiled patterns. The Autodesk Animator was used to create artwork for a wide variety of video games. [4]

Amiga family of personal computers sold by Commodore

The Amiga is a family of personal computers introduced by Commodore in 1985. The original model was part of a wave of 16- and 32-bit computers that featured 256 KB or more of RAM, mouse-based GUIs, and significantly improved graphics and audio over 8-bit systems. This wave included the Atari ST—released the same year—Apple's Macintosh, and later the Apple IIGS. Based on the Motorola 68000 microprocessor, the Amiga differed from its contemporaries through the inclusion of custom hardware to accelerate graphics and sound, including sprites and a blitter, and a pre-emptive multitasking operating system called AmigaOS.

Atari ST home computer

The Atari ST is a line of home computers from Atari Corporation and the successor to the Atari 8-bit family. The initial ST model, the 520ST, saw limited release in April–June 1985 and was widely available in July. The Atari ST is the first personal computer to come with a bitmapped color GUI, using a version of Digital Research's GEM released in February 1985. The 1040ST, released in 1986, is the first personal computer to ship with a megabyte of RAM in the base configuration and also the first with a cost-per-kilobyte of less than US$1.

Autodesk Animator software

Autodesk Animator, also known as Ani Pro, PJ Paint, PJ, was a 2D computer animation and painting program in 1989 for PC with MS-DOS. The program was considered to be groundbreaking in the field of computer animation when it was initially released, and was very popular in the late 1980s and the early 1990s.

Involvement with the Human Genome Project

In 2000, he wrote a program, GigAssembler, [5] that allowed the publicly funded Human Genome Project to assemble and publish the first human genome sequence. His efforts were motivated by the research needs of himself and his colleagues, but also out of concern that the data might be made proprietary via patents by Celera Genomics. [6] In their close race with Celera, Kent and the UCSC Professor David Haussler quickly built a modest cluster of 50 commodity personal computers running the Linux operating system to run the software. In contrast, Celera was using what was thought then to be one of the most powerful civilian supercomputers in the world. Kent's first assembly on the human genome was released on June 22. Celera finished its assembly three days later on June 25, and the dual results were announced at the White House on June 26. On July 7, 2000, the Santa Cruz data was made publicly available on the World Wide Web while the research paper describing this publicly funded genome was published in February 2001 special issue of Nature , [7] in parallel with Celera's results in the journal Science . [8] In 2002 Tim O'Reilly described Kent's work as "the most significant work of open source development in the past year". While all of Kent's genomics software is open source in the sense that the source code can be downloaded and read for free, and all of the software can be freely used for academic, nonprofit, and personal use, some of it requires a license, either from UCSC or from Kent Informatics Inc., for commercial use. [9]

Human Genome Project Research program for sequencing the human genome

The Human Genome Project (HGP) was an international scientific research project with the goal of determining the sequence of nucleotide base pairs that make up human DNA, and of identifying and mapping all of the genes of the human genome from both a physical and a functional standpoint. It remains the world's largest collaborative biological project. After the idea was picked up in 1984 by the US government when the planning started, the project formally launched in 1990 and was declared complete on April 14, 2003. Funding came from the US government through the National Institutes of Health (NIH) as well as numerous other groups from around the world. A parallel project was conducted outside government by the Celera Corporation, or Celera Genomics, which was formally launched in 1998. Most of the government-sponsored sequencing was performed in twenty universities and research centers in the United States, the United Kingdom, Japan, France, Germany and China.

David Haussler bioengineering scientist

David Haussler is an American bioinformatician known for his work leading the team that assembled the first human genome sequence in the race to complete the Human Genome Project and subsequently for comparative genome analysis that deepens understanding the molecular function and evolution of the genome. He is a Howard Hughes Medical Institute Investigator, professor of biomolecular engineering and director of the Center for Biomolecular Science and Engineering at the University of California, Santa Cruz, director of the California Institute for Quantitative Biosciences (QB3) on the UC Santa Cruz campus, and a consulting professor at the Stanford University School of Medicine and the UC San Francisco Biopharmaceutical Sciences Department.

Personal computer Computer intended for use by an individual person

A personal computer (PC) is a multi-purpose computer whose size, capabilities, and price make it feasible for individual use. Personal computers are intended to be operated directly by an end user, rather than by a computer expert or technician. Unlike large costly minicomputer and mainframes, time-sharing by many people at the same time is not used with personal computers.

After GigAssembler, Kent went on to write BLAT (BLAST-like alignment tool) [10] and the UCSC Genome Browser [11] to help analyze important genome data. Kent continues to work at UCSC primarily on web tools to help understand the human genome. He helps maintain and upgrade the browser, and has worked on comparative genomics, [12] Parasol, a job control management software for the UCSC kilocluster, and the ENCODE Project.

BLAT is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the human genome. It was designed primarily to decrease the time needed to align millions of mouse genomic reads and expressed sequence tags against the human genome sequence. The alignment tools of the time were not capable of performing these operations in a manner that would allow a regular update of the human genome assembly. Compared to pre-existing tools, BLAT was ~500 times faster with performing mRNA/DNA alignments and ~50 times faster with protein/protein alignments.

ENCODE research consortium investigating functional elements in human and model organism DNA

The Encyclopedia of DNA Elements (ENCODE) is a public research project which aims to identify functional elements in the human genome.

Related Research Articles

Ensembl genome database project gene sequence database

Ensembl genome database project is a joint scientific project between the European Bioinformatics Institute and the Wellcome Trust Sanger Institute, which was launched in 1999 in response to the imminent completion of the Human Genome Project. Ensembl aims to provide a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other vertebrates and model organisms. Ensembl is one of several well known genome browsers for the retrieval of genomic information.

Ewan Birney English biologist and bioinformatician

John Frederick William Birney is joint director with Rolf Apweiler of the European Bioinformatics Institute (EBI), part of the European Molecular Biology Laboratory (EMBL) in Hinxton, Cambridgeshire. He also serves as non-executive director of Genomics England, chair of the Global Alliance for Genomics and Health (GA4GH) and honorary professor of Bioinformatics at the University of Cambridge. Birney has made significant contributions to genomics. Through his development of innovative bioinformatics and computational biology tools, researchers around the world are able to predict and annotate regions of interest in DNA with speed and confidence. He was previously an associate faculty member at the Wellcome Trust Sanger Institute..

Boreoeutheria magnorder of mammals

Boreoeutheria is a clade (magnorder) of placental mammals which is composed of the sister taxa Laurasiatheria and Euarchontoglires (Supraprimates). It is now well supported by DNA sequence analyses, as well as retrotransposon presence or absence data. Placental mammals outside of this clade are the clades Xenarthra and Afrotheria.

Galaxy (computational biology) workflow system in the biology field

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience. Although it was initially developed for genomics research, it is largely domain agnostic and is now used as a general bioinformatics workflow management system.

BBS5 protein-coding gene in the species Homo sapiens

Bardet-Biedl syndrome 5 protein is a protein that in humans is encoded by the BBS5 gene.

DGLUCY protein-coding gene in the species Homo sapiens

DGLUCY is a protein that in humans is encoded by the DGLUCY gene.

The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC). It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. The Browser is a graphical viewer optimized to support fast interactive performance and is an open-source, web-based tool suite built on top of a MySQL database for rapid visualization, examination, and querying of the data at many levels. The Genome Browser Database, browsing tools, downloadable data files, and documentation can all be found on the UCSC Genome Bioinformatics website.

UCbase is a database of ultraconserved sequences that were first described by Bejerano, G. et al. in 2004. They are highly conserved genome regions that share 100% identity among human, mouse and rat. UCRs are 481 sequences longer than 200 bases. They are frequently located at genomic regions involved in cancer, differentially expressed in human leukemias and carcinomas and in some instances regulated by microRNAs. The first release of UCbase was published by Taccioli, C. et al. in 2009. Recent updates include new annotation based on hg19 Human genome, information about disorders related to the chromosome coordinates using the SNOMED CT classification, a query tool to search for SNPs, and a new text box to directly interrogate the database using a MySQL interface. Moreover, a sequence comparison tool allows the researchers to match selected sequences against ultraconserved elements located in genomic regions involved in specific disorders. To facilitate the interactive, visual interpretation of UCR chromosomal coordinates, the authors have implemented the graph visualization feature of UCbase creating a link to UCSC genome browser. UCbase 2.0 does not provide microRNAs (miRNAs) information anymore focusing only on UCRs. The official release of UCbase 2.0 was published in 2014 and is accessible at http://ucbase.unimore.it

De novo transcriptome assembly is the de novo sequence assembly method of creating a transcriptome without the aid of a reference genome.

Adam C. Siepel bioinformatician

Adam C. Siepel is an American computational biologist known for his research in comparative genomics and population genetics, particularly the development of statistical methods and software tools for identifying evolutionarily conserved sequences. Siepel is currently Chair of the Simons Center for Quantitative Biology and Professor in the Watson School for Biological Sciences at Cold Spring Harbor Laboratory.

GenomeSpace is an environment for genomics software tools and applications. It helps users manage their analysis workflows involving multiple diverse tools, including web applications and desktop tools and facilitates the transfer of data between tools via automatic format conversion. Analyses can use data from local or cloud-based stores.

Transmembrane Protein 205 protein-coding gene in the species Homo sapiens

Transmembrane Protein 205 (TMEM205) is a protein encoded on chromosome 19 by the TMEM205 gene.

Scaffolding (bioinformatics)

Scaffolding is a technique used in bioinformatics. It is defined as follows:

Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length. The sequences that are linked are typically contiguous sequences corresponding to read overlaps.

Mathieu Daniel Blanchette is a computational biologist and Associate Professor in the School of Computer Science at McGill University. His research focuses on developing new algorithms for the detection of functional regions in DNA sequences.

De novo sequence assemblers are a type of program that assembles short nucleotide sequences into longer ones without the use of a reference genome. These are most commonly used in bioinformatic studies to assemble genomes or transcriptomes. Two common types of de novo assemblers are greedy algorithm assemblers and De Bruijn graph assemblers.

References

  1. Gitschier, J. (2013). "Life, the Universe, and Everything: An Interview with David Haussler". PLoS Genetics. 9 (1): e1003282. doi:10.1371/journal.pgen.1003282. PMC   3561096 . PMID   23382705.
  2. "Aegis Animator ST and Art Pak ST". Atarimagazines.com. Retrieved 2016-10-21.
  3. "Cyber Paint". Ataricq.org. 2009-05-23. Retrieved 2016-10-21.
  4. Breton Slivka (2009-05-08). "Busting at the Seams: Autodesk Animator". Bustingseams.blogspot.com. Retrieved 2016-10-21.
  5. Kent WJ, Haussler D (2001). "Assembly of the Working Draft of the Human Genome with GigAssembler". Genome Research. 11 (9): 1461–2. doi:10.1101/gr.183201. PMC   311095 . PMID   11544197.
  6. "Archived copy". Archived from the original on 2012-03-20. Retrieved 2010-09-19.CS1 maint: Archived copy as title (link)
  7. International Human Genome Sequencing Consortium (2001). "Initial sequencing and analysis of the human genome" (PDF). Nature. 409 (6822): 860–921. Bibcode:2001Natur.409..860L. doi:10.1038/35057062. PMID   11237011.
  8. Venter, JC; et al. (2001). "The sequence of the human genome" (PDF). Science. 291 (5507): 1304–1351. Bibcode:2001Sci...291.1304V. doi:10.1126/science.1058040. PMID   11181995.
  9. "Index of /~kent/src". Hgwdev.cse.ucsc.edu. Retrieved 2016-10-21.
  10. Kent, W. J. (2002). "BLAT---The BLAST-Like Alignment Tool". Genome Research. 12 (4): 656–664. doi:10.1101/gr.229202. PMC   187518 . PMID   11932250.
  11. Kent, W. J.; Sugnet, C. W.; Furey, T. S.; Roskin, K. M.; Pringle, T. H.; Zahler, A. M.; Haussler, A. D. (2002). "The Human Genome Browser at UCSC". Genome Research. 12 (6): 996–1006. doi:10.1101/gr.229102. PMC   186604 . PMID   12045153.
  12. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D (2003). "Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes". Proc Natl Acad Sci U S A. 100 (20): 11484–9. Bibcode:2003PNAS..10011484K. doi:10.1073/pnas.1932072100. PMC   208784 . PMID   14500911.