H. Bigelow - Academia.edu (original) (raw)
Papers by H. Bigelow
Genetics, 2010
Whole-genome sequencing (WGS) of organisms displaying a specific mutant phenotype is a powerful a... more Whole-genome sequencing (WGS) of organisms displaying a specific mutant phenotype is a powerful approach to identify the genetic determinants of a plethora of biological processes. We have previously validated the feasibility of this approach by identifying a point-mutated locus responsible for a specific phenotype, observed in an ethyl methanesulfonate (EMS)-mutagenized Caenorhabditis elegans strain. Here we describe the genome-wide mutational profile of 17 EMS-mutagenized genomes as assessed with a bioinformatic pipeline, called MAQGene. Surprisingly, we find that while outcrossing mutagenized strains does reduce the total number of mutations, a striking mutational load is still observed even in outcrossed strains. Such genetic complexity has to be taken into account when establishing a causative relationship between genotype and phenotype. Even though unintentional, the 17 sequenced strains described here provide a resource of allelic variants in almost 1000 genes, including 62 premature stop codons, which represent candidate knockout alleles that will be of further use for the C. elegans community to study gene function.
Nature methods, 2009
Forward genetic screens for mutants in which specific biological processes are disrupted are a ke... more Forward genetic screens for mutants in which specific biological processes are disrupted are a key strength of model systems like C.elegans or Drosophila. However, the road from isolating a phenotype-causing mutant strain to identifying the molecular nature of the genetic change, most often as little as a single point mutation, is cumbersome, traditionally involving timeconsuming genetic mapping strategies. We have recently shown in a proof-of-principle study that conventional mapping steps can be shortcut through the use of whole genome sequencing (WGS) with massively parallel, deep-sequencing technology 1, 2 (Suppl. . A similar proof-of-principle approach has proven successful for Drosophila mutant identification as well 3 .
BMC bioinformatics, Jan 12, 2004
All known genomes code for a large number of transcription factors. It is important to develop me... more All known genomes code for a large number of transcription factors. It is important to develop methods that will reveal how these transcription factors act on a genome wide level, that is, through what target genes they exert their function. We describe here a program pipeline aimed at identifying transcription factor target genes in whole genomes. Starting from a consensus binding site, represented as a weight matrix, potential sites in a pre-filtered genome are identified and then further filtered by assessing conservation of the putative site in the genome of a related species, a process called phylogenetic footprinting. CisOrtho has been successfully used to identify targets for two homeodomain transcription factors in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. CisOrtho will identify targets of other nematode transcription factors whose DNA binding specificity is known and can be easily adapted to search other genomes for transcription facto...
Methods in Molecular Biology, 2009
We identify and describe a set of tools readily available for integral membrane protein predictio... more We identify and describe a set of tools readily available for integral membrane protein prediction. These tools address two problems: finding potential transmembrane proteins in a pool of new sequences, and identifying their transmembrane regions. All methods involve comparing the query protein against one or more target models. In the simplest of these, the target "model" is another protein sequence, while the more elaborate methods group together the entire set of t ansmembrane helical or transmembrane beta-barrel proteins. In general, prediction accuracy either in identifying new integral membrane proteins or transmembrane regions of known integral membrane proteins depends strongly on how closely the query fits the model. Because of this, the best approach is an opportunistic one: submit the protein of interest to all methods and choose the results with the highest confidence scores.
Handbook of Chemoinformatics, 2003
... 5.1 Prediction of Protein Structure Through Evolution Burkhard Rost, Jinfeng Liu, Dariusz Prz... more ... 5.1 Prediction of Protein Structure Through Evolution Burkhard Rost, Jinfeng Liu, Dariusz Przybylski, Rajesh Nair, Kazirnierz 0. Wrzeszczynski, Henry Bigelow, and Yanay Ofan 5.1.1 Introduction Proteins are the machinery of life. ...
Nucleic Acids Research, 2006
PROFtmb predicts transmembrane beta-barrel (TMB) proteins in Gram-negative bacteria. For each que... more PROFtmb predicts transmembrane beta-barrel (TMB) proteins in Gram-negative bacteria. For each query protein, PROFtmb provides both a Z-value indicating that the protein actually contains a membrane barrel, and a four-state per-residue labeling of upward-and downward-facing strands, periplasmic hairpins and extracellular loops. While most users submit individual proteins known to contain TMBs, some groups submit entire proteomes to screen for potential TMBs. Response time is about 4 min for a 500-residue protein. PROFtmb is a profile-based Hidden Markov Model (HMM) with an architecture mirroring the structure of TMBs. The per-residue accuracy on the 8-fold cross-validated testing set is 86% while whole-protein discrimination accuracy was 70 at 60% coverage. The PROFtmb web server includes all source code, training data and whole-proteome predictions from 78 Gram-negative bacterial genomes and is available freely and without registration at http://rostlab.org/ services/proftmb.
Methods, 2007
We survey computational approaches that tackle membrane protein structure and function prediction... more We survey computational approaches that tackle membrane protein structure and function prediction. While describing the main ideas that have led to the development of the most relevant and novel methods, we also discuss pitfalls, provide practical hints and highlight the challenges that remain. The methods covered include: sequence alignment, motif search, functional residue identification, transmembrane segment and protein topology predictions, homology and ab initio modeling. Overall, predictions of functional and structural features of membrane proteins are improving, although progress is hampered by the limited amount of high-resolution experimental information available. While predictions of transmembrane segments and protein topology rank among the most accurate methods in computational biology, more attention and effort will be required in the future to ameliorate database search, homology and ab initio modeling.
ICES Journal of Marine Science, 1930
... WHOTS-4 2007 Mooring Turnaround Cruise Report by Sean P. Whelan, Al Plueddemann, Roger Lukas,... more ... WHOTS-4 2007 Mooring Turnaround Cruise Report by Sean P. Whelan, Al Plueddemann, Roger Lukas, Jeffrey Lord, Paul Lethaby, Jeffrey Snyder, Jason Smith, Frank Bahr, Nan Galbraith and Chris Sabine Woods Hole Oceanographic Institution, Woods Hole, Massachusetts ...
Genetics, 2009
We apply here comparative genome hybridization as a novel tool to identify the molecular lesion i... more We apply here comparative genome hybridization as a novel tool to identify the molecular lesion in two Caenorhabditis elegans mutant strains that affect a neuronal cell fate decision. The phenotype of the mutant strains resembles those of the loss-of-function alleles of the cog-1 homeobox gene, an inducer of the fate of the gustatory neuron ASER. We find that both lesions map to the cis-regulatory control region of cog-1 and affect a phylogenetically conserved binding site for the C2H2 zinc-finger transcription factor CHE-1, a previously known regulator of cog-1 expression in ASER. Identification of this CHE-1-binding site as a critical regulator of cog-1 expression in the ASER in vivo represents one of the rare demonstrations of the in vivo relevance of an experimentally determined or predicted transcription-factor-binding site. Aside from the mutationally defined CHE-1-binding site, cog-1 contains a second, functional CHE-1-binding site, which in isolation is sufficient to drive reporter gene expression in the ASER but in an in vivo context is apparently insufficient for promoting appropriate ASER expression. The cis-regulatory control regions of other ASEexpressed genes also contain ASE motifs that can promote ASE neuron expression when isolated from their genomic context, but appear to depend on multiple ASE motifs in their normal genomic context. The multiplicity of cis-regulatory elements may ensure the robustness of gene expression.
Genetics, 2010
Whole-genome sequencing (WGS) of organisms displaying a specific mutant phenotype is a powerful a... more Whole-genome sequencing (WGS) of organisms displaying a specific mutant phenotype is a powerful approach to identify the genetic determinants of a plethora of biological processes. We have previously validated the feasibility of this approach by identifying a point-mutated locus responsible for a specific phenotype, observed in an ethyl methanesulfonate (EMS)-mutagenized Caenorhabditis elegans strain. Here we describe the genome-wide mutational profile of 17 EMS-mutagenized genomes as assessed with a bioinformatic pipeline, called MAQGene. Surprisingly, we find that while outcrossing mutagenized strains does reduce the total number of mutations, a striking mutational load is still observed even in outcrossed strains. Such genetic complexity has to be taken into account when establishing a causative relationship between genotype and phenotype. Even though unintentional, the 17 sequenced strains described here provide a resource of allelic variants in almost 1000 genes, including 62 premature stop codons, which represent candidate knockout alleles that will be of further use for the C. elegans community to study gene function.
Engineering Structures, 2010
To estimate mechanical properties to be used for numerical analyses of railway bridges, experimen... more To estimate mechanical properties to be used for numerical analyses of railway bridges, experimental tests on railway ballast have been performed within the framework of the European research project DETAILS (Design for optimal life cycle costs of high-speed railway bridges by enhanced monitoring systems), supported by the European RFCS-Fund. German two-track railway bridges often provide two separated bridge decks. However, interaction effects between the two bridge decks take place due to a continuous ballast layer. Not only in view of numerical modelling, the mechanical behaviour of the ballast in the contact area between the separated bridge decks is of great interest, as SLS and even ULS issues are affected by the so far neglected interaction. After a short introduction, experimental tests are described in the first part of the paper. As a first approximation, it is shown that linear elastic springs can be used for taking into account the load transfer between ballast-connected structures. Thus, the springs represent a kind of shear stiffness of the ballast layer. Considering the test results, such an approach is applied for numerical analysis of a filler beam bridge with two separated decks and a continuous ballast layer. The modelling approach and related numerical results are presented in the second part of the paper. As conclusion both experimental and numerical results are discussed with regard to the dynamic design of simply supported and ballasted railway bridges.
... Burkhard Rost 1, 2, 3, * , Jinfeng Liu 1,4 , Dariusz Przybylski 1,5 , Rajesh Nair 1,5 , Kazim... more ... Burkhard Rost 1, 2, 3, * , Jinfeng Liu 1,4 , Dariusz Przybylski 1,5 , Rajesh Nair 1,5 , Kazimierz O. Wrzeszczynski 1 , Henry ... In collaboration with Volker Eyrich (Columbia), Marc Marti-Renom, Andrej Sali (both Rockefeller), Florencio Pazos, and Alfonso Valencia (both CNB Madrid ...
Genetics, 2010
Whole-genome sequencing (WGS) of organisms displaying a specific mutant phenotype is a powerful a... more Whole-genome sequencing (WGS) of organisms displaying a specific mutant phenotype is a powerful approach to identify the genetic determinants of a plethora of biological processes. We have previously validated the feasibility of this approach by identifying a point-mutated locus responsible for a specific phenotype, observed in an ethyl methanesulfonate (EMS)-mutagenized Caenorhabditis elegans strain. Here we describe the genome-wide mutational profile of 17 EMS-mutagenized genomes as assessed with a bioinformatic pipeline, called MAQGene. Surprisingly, we find that while outcrossing mutagenized strains does reduce the total number of mutations, a striking mutational load is still observed even in outcrossed strains. Such genetic complexity has to be taken into account when establishing a causative relationship between genotype and phenotype. Even though unintentional, the 17 sequenced strains described here provide a resource of allelic variants in almost 1000 genes, including 62 premature stop codons, which represent candidate knockout alleles that will be of further use for the C. elegans community to study gene function.
Nature methods, 2009
Forward genetic screens for mutants in which specific biological processes are disrupted are a ke... more Forward genetic screens for mutants in which specific biological processes are disrupted are a key strength of model systems like C.elegans or Drosophila. However, the road from isolating a phenotype-causing mutant strain to identifying the molecular nature of the genetic change, most often as little as a single point mutation, is cumbersome, traditionally involving timeconsuming genetic mapping strategies. We have recently shown in a proof-of-principle study that conventional mapping steps can be shortcut through the use of whole genome sequencing (WGS) with massively parallel, deep-sequencing technology 1, 2 (Suppl. . A similar proof-of-principle approach has proven successful for Drosophila mutant identification as well 3 .
BMC bioinformatics, Jan 12, 2004
All known genomes code for a large number of transcription factors. It is important to develop me... more All known genomes code for a large number of transcription factors. It is important to develop methods that will reveal how these transcription factors act on a genome wide level, that is, through what target genes they exert their function. We describe here a program pipeline aimed at identifying transcription factor target genes in whole genomes. Starting from a consensus binding site, represented as a weight matrix, potential sites in a pre-filtered genome are identified and then further filtered by assessing conservation of the putative site in the genome of a related species, a process called phylogenetic footprinting. CisOrtho has been successfully used to identify targets for two homeodomain transcription factors in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. CisOrtho will identify targets of other nematode transcription factors whose DNA binding specificity is known and can be easily adapted to search other genomes for transcription facto...
Methods in Molecular Biology, 2009
We identify and describe a set of tools readily available for integral membrane protein predictio... more We identify and describe a set of tools readily available for integral membrane protein prediction. These tools address two problems: finding potential transmembrane proteins in a pool of new sequences, and identifying their transmembrane regions. All methods involve comparing the query protein against one or more target models. In the simplest of these, the target "model" is another protein sequence, while the more elaborate methods group together the entire set of t ansmembrane helical or transmembrane beta-barrel proteins. In general, prediction accuracy either in identifying new integral membrane proteins or transmembrane regions of known integral membrane proteins depends strongly on how closely the query fits the model. Because of this, the best approach is an opportunistic one: submit the protein of interest to all methods and choose the results with the highest confidence scores.
Handbook of Chemoinformatics, 2003
... 5.1 Prediction of Protein Structure Through Evolution Burkhard Rost, Jinfeng Liu, Dariusz Prz... more ... 5.1 Prediction of Protein Structure Through Evolution Burkhard Rost, Jinfeng Liu, Dariusz Przybylski, Rajesh Nair, Kazirnierz 0. Wrzeszczynski, Henry Bigelow, and Yanay Ofan 5.1.1 Introduction Proteins are the machinery of life. ...
Nucleic Acids Research, 2006
PROFtmb predicts transmembrane beta-barrel (TMB) proteins in Gram-negative bacteria. For each que... more PROFtmb predicts transmembrane beta-barrel (TMB) proteins in Gram-negative bacteria. For each query protein, PROFtmb provides both a Z-value indicating that the protein actually contains a membrane barrel, and a four-state per-residue labeling of upward-and downward-facing strands, periplasmic hairpins and extracellular loops. While most users submit individual proteins known to contain TMBs, some groups submit entire proteomes to screen for potential TMBs. Response time is about 4 min for a 500-residue protein. PROFtmb is a profile-based Hidden Markov Model (HMM) with an architecture mirroring the structure of TMBs. The per-residue accuracy on the 8-fold cross-validated testing set is 86% while whole-protein discrimination accuracy was 70 at 60% coverage. The PROFtmb web server includes all source code, training data and whole-proteome predictions from 78 Gram-negative bacterial genomes and is available freely and without registration at http://rostlab.org/ services/proftmb.
Methods, 2007
We survey computational approaches that tackle membrane protein structure and function prediction... more We survey computational approaches that tackle membrane protein structure and function prediction. While describing the main ideas that have led to the development of the most relevant and novel methods, we also discuss pitfalls, provide practical hints and highlight the challenges that remain. The methods covered include: sequence alignment, motif search, functional residue identification, transmembrane segment and protein topology predictions, homology and ab initio modeling. Overall, predictions of functional and structural features of membrane proteins are improving, although progress is hampered by the limited amount of high-resolution experimental information available. While predictions of transmembrane segments and protein topology rank among the most accurate methods in computational biology, more attention and effort will be required in the future to ameliorate database search, homology and ab initio modeling.
ICES Journal of Marine Science, 1930
... WHOTS-4 2007 Mooring Turnaround Cruise Report by Sean P. Whelan, Al Plueddemann, Roger Lukas,... more ... WHOTS-4 2007 Mooring Turnaround Cruise Report by Sean P. Whelan, Al Plueddemann, Roger Lukas, Jeffrey Lord, Paul Lethaby, Jeffrey Snyder, Jason Smith, Frank Bahr, Nan Galbraith and Chris Sabine Woods Hole Oceanographic Institution, Woods Hole, Massachusetts ...
Genetics, 2009
We apply here comparative genome hybridization as a novel tool to identify the molecular lesion i... more We apply here comparative genome hybridization as a novel tool to identify the molecular lesion in two Caenorhabditis elegans mutant strains that affect a neuronal cell fate decision. The phenotype of the mutant strains resembles those of the loss-of-function alleles of the cog-1 homeobox gene, an inducer of the fate of the gustatory neuron ASER. We find that both lesions map to the cis-regulatory control region of cog-1 and affect a phylogenetically conserved binding site for the C2H2 zinc-finger transcription factor CHE-1, a previously known regulator of cog-1 expression in ASER. Identification of this CHE-1-binding site as a critical regulator of cog-1 expression in the ASER in vivo represents one of the rare demonstrations of the in vivo relevance of an experimentally determined or predicted transcription-factor-binding site. Aside from the mutationally defined CHE-1-binding site, cog-1 contains a second, functional CHE-1-binding site, which in isolation is sufficient to drive reporter gene expression in the ASER but in an in vivo context is apparently insufficient for promoting appropriate ASER expression. The cis-regulatory control regions of other ASEexpressed genes also contain ASE motifs that can promote ASE neuron expression when isolated from their genomic context, but appear to depend on multiple ASE motifs in their normal genomic context. The multiplicity of cis-regulatory elements may ensure the robustness of gene expression.
Genetics, 2010
Whole-genome sequencing (WGS) of organisms displaying a specific mutant phenotype is a powerful a... more Whole-genome sequencing (WGS) of organisms displaying a specific mutant phenotype is a powerful approach to identify the genetic determinants of a plethora of biological processes. We have previously validated the feasibility of this approach by identifying a point-mutated locus responsible for a specific phenotype, observed in an ethyl methanesulfonate (EMS)-mutagenized Caenorhabditis elegans strain. Here we describe the genome-wide mutational profile of 17 EMS-mutagenized genomes as assessed with a bioinformatic pipeline, called MAQGene. Surprisingly, we find that while outcrossing mutagenized strains does reduce the total number of mutations, a striking mutational load is still observed even in outcrossed strains. Such genetic complexity has to be taken into account when establishing a causative relationship between genotype and phenotype. Even though unintentional, the 17 sequenced strains described here provide a resource of allelic variants in almost 1000 genes, including 62 premature stop codons, which represent candidate knockout alleles that will be of further use for the C. elegans community to study gene function.
Engineering Structures, 2010
To estimate mechanical properties to be used for numerical analyses of railway bridges, experimen... more To estimate mechanical properties to be used for numerical analyses of railway bridges, experimental tests on railway ballast have been performed within the framework of the European research project DETAILS (Design for optimal life cycle costs of high-speed railway bridges by enhanced monitoring systems), supported by the European RFCS-Fund. German two-track railway bridges often provide two separated bridge decks. However, interaction effects between the two bridge decks take place due to a continuous ballast layer. Not only in view of numerical modelling, the mechanical behaviour of the ballast in the contact area between the separated bridge decks is of great interest, as SLS and even ULS issues are affected by the so far neglected interaction. After a short introduction, experimental tests are described in the first part of the paper. As a first approximation, it is shown that linear elastic springs can be used for taking into account the load transfer between ballast-connected structures. Thus, the springs represent a kind of shear stiffness of the ballast layer. Considering the test results, such an approach is applied for numerical analysis of a filler beam bridge with two separated decks and a continuous ballast layer. The modelling approach and related numerical results are presented in the second part of the paper. As conclusion both experimental and numerical results are discussed with regard to the dynamic design of simply supported and ballasted railway bridges.
... Burkhard Rost 1, 2, 3, * , Jinfeng Liu 1,4 , Dariusz Przybylski 1,5 , Rajesh Nair 1,5 , Kazim... more ... Burkhard Rost 1, 2, 3, * , Jinfeng Liu 1,4 , Dariusz Przybylski 1,5 , Rajesh Nair 1,5 , Kazimierz O. Wrzeszczynski 1 , Henry ... In collaboration with Volker Eyrich (Columbia), Marc Marti-Renom, Andrej Sali (both Rockefeller), Florencio Pazos, and Alfonso Valencia (both CNB Madrid ...