G. Gonnet - Academia.edu (original) (raw)

Papers by G. Gonnet

Research paper thumbnail of The Darwin Manual c

Research paper thumbnail of of Special Issue of Annals of Mathematics and Artificial Intelligence, Vol. 38, No. 1-3, May 2003, Kluwer Academic Publisher, ISSN 1012-2443

Research paper thumbnail of b ma Algonthmlca

Research paper thumbnail of Organizing the Protein-Sequence Data-Base

Research paper thumbnail of On Boyer-Moore Automata

Research paper thumbnail of Testing in large-scale scientific computation: the short circuit method

Research paper thumbnail of Main Routines

Maple V Library Reference Manual, 1991

Research paper thumbnail of Operators

Maple V Language Reference Manual, 1991

Research paper thumbnail of Probing protein function using a combination of gene knockout and proteome analysis by mass spectrometry

Electrophoresis, 1997

Probing protein function using a combination of gene knockout and proteome analysis by mass spect... more Probing protein function using a combination of gene knockout and proteome analysis by mass spectrometry Recently the determination of the genome sequences of three procaryotes (Haemophilus influenzae, Methanococcus ,jannaschii and Mycoplasma genitahum) as well as the first eucaryotic genome (Saccharomyces cerevisiae) were completed. Between 40-60% of the genes were found to code for proteins to which no function could be assigned. We describe an approach which con?bines proteome analysis (mapping of expressed proteins isolated by twodimensional polyacrylamide gel electrophoresis to the genome) with genetic manipulations to study the complex pattern of protein regulation occurring in Escherichia coli in response to sulfate starvation. We have previously described the upregulation of eight spots on two-dimensional (2-D) gels in response to sulfate starvation and the assignment of six of these to entries in the E. coli genome sequence (Quadroni et al., Eur. J. Biochem. 1996, 239, 773-781). Here we describe the identification of the remaining two proteins which are encoded in a sulfate-controlled operon in the 21.5' region of the E. colr genome. Upregulated protein spots were cut from multiple 2-D gels collected and run on a modified funnel gel to concentrate the proteins and remove the sodium dodecyl sulfate before digestion. The peptide masses obtained from the digests were used to search the SwissProt database or a six-frame translation of the EMBL DNA database using a peptide mass fingerprinting algorithm. A digest can be reanalyzed after deuterium exchange to obtain a second, orthogonal data set to increase the confidence level of protein identification. The digests of the remaining unidentified proteins were used for peptide fragment generation using either post-source decay in a matrix-assisted laser desorption ionization (MALDI) time-of-flight mass spectrometer or collision-induced dissociation (CID) coupled mass specrometry (MS/MS) with triple stage quadrupole or ion trap mass spectrometers. The spectra were used as peptide fragment fingerprints to search the SwissProt and EMBL databases.

Research paper thumbnail of Compact Computer Algebra

Research paper thumbnail of Using insertion and deletion events for improving multiple sequence alignments and building the corresponding evolutionary trees

Research paper thumbnail of Handbook of Algorithms and Data Structures

Research paper thumbnail of Examples of PAT applied to the Oxford English Dictionary

Research paper thumbnail of Analysis of feature influence on Covid-19 Death Rate Per Country Using a Novel Orthogonalization Technique

We have developed a new technique of Feature Importance, a topic of machine learning, to analyze ... more We have developed a new technique of Feature Importance, a topic of machine learning, to analyze the possible causes of the Covid-19 pandemic based on country data. This new approach works well even when there are many more features than countries and is not affected by high correlation of features. It is inspired by the Gram-Schmidt orthogonalization procedure from linear algebra. We study the number of deaths, which is more reliable than the number of cases at the onset of the pandemic, during Apr/May 2020. This is while countries started taking measures, so more light will be shed on the root causes of the pandemic rather than on its handling.The analysis is done against a comprehensive list of roughly 3,200 features. We find that globalization is the main contributing cause, followed by calcium intake, economic factors, environmental factors, preventative measures, and others. This analysis was done for 20 different dates and shows that some factors, like calcium, phase in or ou...

Research paper thumbnail of Less Simple Maple

First Leaves: A Tutorial Introduction to Maple V, 1992

We have seen how to use Maple as a calculator for algebraic and numerical computations, and for g... more We have seen how to use Maple as a calculator for algebraic and numerical computations, and for graphics. In this section, we explore how to use Maple in more sophisticated ways.

Research paper thumbnail of Interactive Use of Maple

First Leaves: A Tutorial Introduction to Maple V, 1992

Maple runs on many types of computer systems. Macintosh, DOS (with or without MS Windows), Unix (... more Maple runs on many types of computer systems. Macintosh, DOS (with or without MS Windows), Unix (with or without the X Window System), SunView, NeXT, IBM CMS, and DEC VMS are some that Maple runs on. Nevertheless, all versions of Maple use essentially the same internal programming to perform the mathematical calculations. This part of Maple is known as the computational engine or algebra engine.

Research paper thumbnail of Overview of the Maple Library

Maple V Language Reference Manual, 1991

The Maple V Library Reference Manual describes all the functions available in the Maple library. ... more The Maple V Library Reference Manual describes all the functions available in the Maple library. The library is where the code for over 95% of Maple’s mathematical knowledge and expertise resides. The library routines are available for your inspection, study, and when appropriate, modification and extension. Each of these routines is written in the Maple programming language. Through the library, the Maple system and the algorithms that it uses can be dynamically extended and customized.

Research paper thumbnail of Packages for Geometry

Maple V Library Reference Manual, 1991

Research paper thumbnail of Statements and Expressions

Maple V Language Reference Manual, 1991

There are eight types of statements in Maple. They will be described informally here. The formal ... more There are eight types of statements in Maple. They will be described informally here. The formal syntax is given in Section 3.3.

Research paper thumbnail of A predicted consensus structure for the N‐Terminal fragment of the heat shock protein HSP90 family

Proteins: Structure, Function, and Genetics, 1997

A secondary structure has been predicted for the heat shock protein HSP90 family from an aligned ... more A secondary structure has been predicted for the heat shock protein HSP90 family from an aligned set of homologous protein sequences by using a transparent method in both manual and automated implementation that extracts conformational information from patterns of variation and conservation within the family. No statistically significant sequence similarity relates this family to any protein with known crystal structure. However, the secondary structure prediction, together with the assignment of active site positions and possible biochemical properties, suggest that the fold is similar to that seen in N-terminal domain of DNA gyrase B (the ATPase fragment).

Research paper thumbnail of The Darwin Manual c

Research paper thumbnail of of Special Issue of Annals of Mathematics and Artificial Intelligence, Vol. 38, No. 1-3, May 2003, Kluwer Academic Publisher, ISSN 1012-2443

Research paper thumbnail of b ma Algonthmlca

Research paper thumbnail of Organizing the Protein-Sequence Data-Base

Research paper thumbnail of On Boyer-Moore Automata

Research paper thumbnail of Testing in large-scale scientific computation: the short circuit method

Research paper thumbnail of Main Routines

Maple V Library Reference Manual, 1991

Research paper thumbnail of Operators

Maple V Language Reference Manual, 1991

Research paper thumbnail of Probing protein function using a combination of gene knockout and proteome analysis by mass spectrometry

Electrophoresis, 1997

Probing protein function using a combination of gene knockout and proteome analysis by mass spect... more Probing protein function using a combination of gene knockout and proteome analysis by mass spectrometry Recently the determination of the genome sequences of three procaryotes (Haemophilus influenzae, Methanococcus ,jannaschii and Mycoplasma genitahum) as well as the first eucaryotic genome (Saccharomyces cerevisiae) were completed. Between 40-60% of the genes were found to code for proteins to which no function could be assigned. We describe an approach which con?bines proteome analysis (mapping of expressed proteins isolated by twodimensional polyacrylamide gel electrophoresis to the genome) with genetic manipulations to study the complex pattern of protein regulation occurring in Escherichia coli in response to sulfate starvation. We have previously described the upregulation of eight spots on two-dimensional (2-D) gels in response to sulfate starvation and the assignment of six of these to entries in the E. coli genome sequence (Quadroni et al., Eur. J. Biochem. 1996, 239, 773-781). Here we describe the identification of the remaining two proteins which are encoded in a sulfate-controlled operon in the 21.5' region of the E. colr genome. Upregulated protein spots were cut from multiple 2-D gels collected and run on a modified funnel gel to concentrate the proteins and remove the sodium dodecyl sulfate before digestion. The peptide masses obtained from the digests were used to search the SwissProt database or a six-frame translation of the EMBL DNA database using a peptide mass fingerprinting algorithm. A digest can be reanalyzed after deuterium exchange to obtain a second, orthogonal data set to increase the confidence level of protein identification. The digests of the remaining unidentified proteins were used for peptide fragment generation using either post-source decay in a matrix-assisted laser desorption ionization (MALDI) time-of-flight mass spectrometer or collision-induced dissociation (CID) coupled mass specrometry (MS/MS) with triple stage quadrupole or ion trap mass spectrometers. The spectra were used as peptide fragment fingerprints to search the SwissProt and EMBL databases.

Research paper thumbnail of Compact Computer Algebra

Research paper thumbnail of Using insertion and deletion events for improving multiple sequence alignments and building the corresponding evolutionary trees

Research paper thumbnail of Handbook of Algorithms and Data Structures

Research paper thumbnail of Examples of PAT applied to the Oxford English Dictionary

Research paper thumbnail of Analysis of feature influence on Covid-19 Death Rate Per Country Using a Novel Orthogonalization Technique

We have developed a new technique of Feature Importance, a topic of machine learning, to analyze ... more We have developed a new technique of Feature Importance, a topic of machine learning, to analyze the possible causes of the Covid-19 pandemic based on country data. This new approach works well even when there are many more features than countries and is not affected by high correlation of features. It is inspired by the Gram-Schmidt orthogonalization procedure from linear algebra. We study the number of deaths, which is more reliable than the number of cases at the onset of the pandemic, during Apr/May 2020. This is while countries started taking measures, so more light will be shed on the root causes of the pandemic rather than on its handling.The analysis is done against a comprehensive list of roughly 3,200 features. We find that globalization is the main contributing cause, followed by calcium intake, economic factors, environmental factors, preventative measures, and others. This analysis was done for 20 different dates and shows that some factors, like calcium, phase in or ou...

Research paper thumbnail of Less Simple Maple

First Leaves: A Tutorial Introduction to Maple V, 1992

We have seen how to use Maple as a calculator for algebraic and numerical computations, and for g... more We have seen how to use Maple as a calculator for algebraic and numerical computations, and for graphics. In this section, we explore how to use Maple in more sophisticated ways.

Research paper thumbnail of Interactive Use of Maple

First Leaves: A Tutorial Introduction to Maple V, 1992

Maple runs on many types of computer systems. Macintosh, DOS (with or without MS Windows), Unix (... more Maple runs on many types of computer systems. Macintosh, DOS (with or without MS Windows), Unix (with or without the X Window System), SunView, NeXT, IBM CMS, and DEC VMS are some that Maple runs on. Nevertheless, all versions of Maple use essentially the same internal programming to perform the mathematical calculations. This part of Maple is known as the computational engine or algebra engine.

Research paper thumbnail of Overview of the Maple Library

Maple V Language Reference Manual, 1991

The Maple V Library Reference Manual describes all the functions available in the Maple library. ... more The Maple V Library Reference Manual describes all the functions available in the Maple library. The library is where the code for over 95% of Maple’s mathematical knowledge and expertise resides. The library routines are available for your inspection, study, and when appropriate, modification and extension. Each of these routines is written in the Maple programming language. Through the library, the Maple system and the algorithms that it uses can be dynamically extended and customized.

Research paper thumbnail of Packages for Geometry

Maple V Library Reference Manual, 1991

Research paper thumbnail of Statements and Expressions

Maple V Language Reference Manual, 1991

There are eight types of statements in Maple. They will be described informally here. The formal ... more There are eight types of statements in Maple. They will be described informally here. The formal syntax is given in Section 3.3.

Research paper thumbnail of A predicted consensus structure for the N‐Terminal fragment of the heat shock protein HSP90 family

Proteins: Structure, Function, and Genetics, 1997

A secondary structure has been predicted for the heat shock protein HSP90 family from an aligned ... more A secondary structure has been predicted for the heat shock protein HSP90 family from an aligned set of homologous protein sequences by using a transparent method in both manual and automated implementation that extracts conformational information from patterns of variation and conservation within the family. No statistically significant sequence similarity relates this family to any protein with known crystal structure. However, the secondary structure prediction, together with the assignment of active site positions and possible biochemical properties, suggest that the fold is similar to that seen in N-terminal domain of DNA gyrase B (the ATPase fragment).