CosmosID | Date: 2012-09-25
MULTIPLE CHARACTERISTIC COMPUTER SOFTWARE FOR USE IN DOING PROBABILISTIC MATCHING OF DNA SEQUENCED NUCLEOTIDE READ LENGTHS AGAINST REFERENCE WHOLE GENOME DATABASES.
CosmosID | Date: 2012-12-04
SCIENTIFIC APPARATUS, INSTRUMENTS, SOFTWARE AND INTEGRATED CIRCUITS INCORPORATING ALGORITHMS, AND SOFTWARE, ALL FOR MEASURING DNA AND RNA AND MEASURING THE IDENTITY OF THE RELATED ORGANISMS WITH PROBABILISTIC AND STATISTICAL METHODS.
CosmosID | Date: 2014-05-30
The present invention belongs to the field of genomics and nucleic acid sequencing. It involves a novel method of sequencing biological material and real-time probabilistic matching of short strings of sequencing information to identify all species present in said biological material. It is related to real-time probabilistic matching of sequence information, and more particular to comparing short strings of a plurality of sequences of single molecule nucleic acids, whether amplified or unamplied, whether chemically synthesized or physically interrogated, as fast as the sequence information is generated and in parallel with continuous sequence information generation or collection.
CosmosID | Date: 2013-07-02
The present invention relates to systems and methods capable of characterizing populations of organisms within a sample. The characterization may utilize probabilistic matching of short strings of sequencing information to identify genomes from a reference genomic database to which the short strings belong. The characterization may include identification of the microbial community of the sample to the species and/or sub-species and/or strain level with their relative concentrations or abundance. In addition, the system and methods may enable rapid identification of organisms including both pathogens and commensals in clinical samples, and the identification may be achieved by a comparison of many (e.g., hundreds to millions) metagenomic fragments, which have been captured from a sample and sequenced, to many (e.g., millions or billions) of archived sequence information of genomes (i.e., reference genomic databases).
Our annual list of 35 innovators under the age of 35 inevitably arouses this objection: “Do you really believe older people aren’t innovative?” Of course they are. We write about the young because we want to introduce you to promising researchers and entrepreneurs. But older people are as capable of new thinking as young ones. Below are seven innovators over the age of 70, still working. 1. Shirley Ann Jackson, 70, is the 18th president of Rensselaer Polytechnic Institute. A theoretical physicist, she was the first African-American woman to be awarded a doctorate from MIT, and she is widely admired for making Rensselaer into a major center of research. She has served on a bewildering number of public committees, including President Obama’s Intelligence Advisory Board, where she is cochair, and the Nuclear Regulatory Commission, which she chaired from 1995 to 1999. 2. Research conducted and startups founded by the computer scientist Michael Stonebraker, who is 71, led directly to the relational databases used everywhere today. He worked for many years at UC Berkeley and in Silicon Valley; and as an adjunct professor at MIT and an entrepreneur, he continues to cofound a new company every couple of years, commercializing his breakthroughs in database management. In 2014, he received the Turing Award. 3. The philosopher Derek Parfit, born in 1942, published Reasons and Persons in 1984 to immense acclaim. Using thought experiments borrowed from science fiction, including speculations about teleportation, the book exploded ideas about the persistence of identity and our duties to future generations. There followed a 37-year near silence, while a monumental unfinished work was circulated in manuscript amongst philosophers and reading groups. In 2011, Parfit finally published On What Matters. It reconciles rules-based, consequentialist, and contractualist conceptions of morality, which Parfit says are “climbing the same mountain on different sides.” 4. Matthew Carter, 78, is one of the most prolific type designers in history. More than anyone else, Carter is responsible for translating classic type to digital uses. His fonts include Georgia, designed to be legible even on very small or low-resolution screens and included in the “core fonts for the Web” bundled with Internet Explorer 4.0. His greatest typefaces, including Miller, Verdana, and Walker, are displayed in the permanent collection of MOMA. 5. Donald Knuth, also 78, is a professor emeritus at Stanford University and the author of the influential multivolume The Art of Computer Programming. It was initially conceived as a single book of 12 chapters in 1962, but Knuth retired from teaching in 1990 in order to complete the series, whose Volume 4, Fascicle 6 (on “Satisfiability”), was released in December of last year. 6. The environmental microbiologist Rita Colwell, born in 1934, was the director of the National Science Foundation from 1998 to 2004 and is now a professor at the University of Maryland and Johns Hopkins University, chairman emeritus of Canon U.S. Life Sciences, and CEO of CosmosID, a genomics company using data analysis to identify microörganisms for diagnostics, public health, and drug discovery. In 2006, Colwell was awarded the National Medal of Science. 7. Ruzena Bajcsy is a roboticist who is still actively publishing at the age of 83. Born and educated in Czechoslovakia (where the Nazis killed most of her relatives, orphaning her at 11), she was a professor of electrical engineering at the University of Pennsylvania, led the Computer and Information Science and Engineering Directorate of the National Science Foundation with its $500 million budget, and is today a professor at UC Berkeley, where she is also director emerita of the Center for Information Technology Research in the Interest of Society. Her current research focuses on AI, computational biology, and biosystems. Last year, she cowrote three papers about using Microsoft Kinect to improve the lives of older adults or people with muscular dystrophy.