A simple, fast, and accurate method of phylogenomic inference (2008)
Abstract The explosive growth of genomic data provides an opportunity to make increased use of protein markers for phylogenetic inference. We have developed an automated pipeline for phylogenomic...
Correction: Comparative Genomics of Emerging Human Ehrlichiosis Agents (2006)
Mingqun Lin, Ramana Madupu, Jonathan Crabtree, Samuel V. Angiuoli, Jonathan A. Eisen, ...
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. (2006)
Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006)
Jonathan A. Eisen, Robert S. Coyne, Martin Wu, Dongying Wu, Mathangi Thiagarajan, Jennifer R. Wortman, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Comparative Genomics of Emerging Human Ehrlichiosis Agents (2006)
Mingqun Lin, Ramana Madupu, Jonathan Crabtree, Samuel V. Angiuoli, Jonathan Eisen, ...
Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006)
Eisen, Jonathan A., Coyne, Robert S., Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R., ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006)
Eisen, Jonathan A., Coyne, Robert S., Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R., ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Martin Wu, Qinghu Ren, A. Scott Durkin, Sean C. Daugherty, Lauren M. Brinkac, Robert J. Dodson, ...
We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are...
Martin Wu, Qinghu Ren, Anthony Scott Durkin, Sean C Daugherty, Lauren M Brinkac, Robert J Dodson, ...
We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are...
Naomi Ward, Øivind Larsen, James Sakwa, Live Bruseth, Hoda Khouri, A. Scott Durkin, ...
Methanotrophs are bacteria that use methane as a sole carbon source. The genome sequence of Methylococcus capsulatus deepens our understanding of methanotroph biology and its relationship to global...
Naomi Ward, Øivind Larsen, James Sakwa, Live Bruseth, Hoda Khouri, A. Scott Durkin, ...
Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular,...
Ward, Naomi, Larsen, Øivind, Sakwa, James, Bruseth, Live, Khouri, Hoda, Durkin, A. Scott, ...
Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular,...
Ward, Naomi, Larsen, Øivind, Sakwa, James, Bruseth, Live, Khouri, Hoda, Durkin, A. Scott, ...
Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular,...
Wu, Martin, Sun, Ling V., Vamathevan, Jessica, Riegler, Markus, Deboy, Robert, Brownlie, Jeremy C., ...
The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a...
Wu, Martin, Sun, Ling V., Vamathevan, Jessica, Riegler, Markus, Deboy, Robert, Brownlie, Jeremy C., ...
The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a...
Wu, Martin, Sun, Ling V., Vamathevan, Jessica, Riegler, Markus, Deboy, Robert, Brownlie, Jeremy C., ...
The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a...
Martin Wu, Ling V. Sun, Jessica Vamathevan, Markus Riegler, Robert Deboy, Jeremy C. Brownlie, ...
The genome sequence of Wolbachia provides insights into the origins of mitochondria, as well as the ecology and evolution of endosymbiosis.
Martin Wu, Ling V. Sun, Jessica Vamathevan, Markus Riegler, Robert Deboy, Jeremy C. Brownlie, ...
The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a...
Wu, Martin, Sun, Ling V., Vamathevan, Jessica, Riegler, Markus, Deboy, Robert, Brownlie, Jeremy C., ...
The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a...
Wu, Martin, Sun, Ling V., Vamathevan, Jessica, Riegler, Markus, Deboy, Robert, Brownlie, Jeremy C., ...
The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a...
Wu, Martin, Sun, Ling V., Vamathevan, Jessica, Riegler, Markus, Deboy, Robert, Brownlie, Jeremy C., ...
The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a...
The role of rigidity in DNA looping-unlooping by AraC
Harmer, Tara, Wu, Martin, Schleif, Robert
We applied two experiments useful in the study of ligand-regulated DNA binding proteins to AraC, the dimeric regulator of the Escherichia coli l-arabinose operon. In the absence of arabinose, AraC...
Mefloquine Is Active In Vitro and In Vivo against Mycobacterium avium Complex
Bermudez, Luiz E., Kolonoski, Peter, Wu, Martin, Aralar, Priscilla A., Inderlied, Clark B., Young, Lowell S.
Despite the development of several agents, new classes of antimicrobials with activity against the Mycobacterium avium complex (MAC) are needed. Based on a broad screening of compounds, we found that...
Bermudez, Luiz E., Inderlied, Clark B., Kolonoski, Peter, Petrofsky, Mary, Aralar, Priscilla, Wu, Martin, ...
Moxifloxacin activity against Mycobacterium avium complex (MAC) was evaluated in vitro against 25 strains. The MIC was determined to range from 0.125 to 2.0 μg/ml. In addition, U937 macrophage...
Bermudez, Luiz E., Inderlied, Clark B., Kolonoski, Peter, Wu, Martin, Aralar, Priscilla, Young, Lowell S.
The activity of telithromycin, a new ketolide, was evaluated in vitro and in vivo against Mycobacterium avium complex (MAC) strains. The MIC of telithromycin for several M. avium isolates obtained...
Eisen, Jonathan A., Nelson, Karen E., Paulsen, Ian T., Heidelberg, John F., Wu, Martin, Dodson, Robert J., ...
The complete genome of the green-sulfur eubacterium Chlorobium tepidum TLS was determined to be a single circular chromosome of 2,154,946 bp. This represents the first genome sequence from the phylum...
Wu, Martin, Sun, Ling V, Vamathevan, Jessica, Riegler, Markus, Deboy, Robert, Brownlie, Jeremy C, ...
The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a...
Bermudez, Luiz E., Kolonoski, Peter, Seitz, Lianne E., Petrofsky, Mary, Reynolds, Robert, Wu, Martin, ...
Treatment of Mycobacterium avium disease remains challenging when macrolide resistance develops. We infected C57 beige mice and treated them with mefloquine, SRI-286, and moxifloxacin. SRI-286 (80...
Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath)
Ward, Naomi, Larsen, Øivind, Sakwa, James, Bruseth, Live, Khouri, Hoda, Durkin, A. Scott, ...
Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular,...
Methé, Barbara A., Nelson, Karen E., Deming, Jody W., Momen, Bahram, Melamud, Eugene, Zhang, Xijun, ...
The completion of the 5,373,180-bp genome sequence of the marine psychrophilic bacterium Colwellia psychrerythraea 34H, a model for the study of life in permanently cold environments, reveals...
Danelishvili, Lia, Wu, Martin, Young, Lowell S., Bermudez, Luiz E.
The emergence of mycobacterial resistance to multiple antimicrobials emphasizes the need for new compounds. The antimycobacterial activity of mefloquine has been recently described. Mycobacterium...
Wu, Martin, Ren, Qinghu, Durkin, A. Scott, Daugherty, Sean C, Brinkac, Lauren M, Dodson, Robert J, ...
We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are...
Mycobacterium avium Genes Associated with the Ability To Form a Biofilm
Yamazaki, Yoshitaka, Danelishvili, Lia, Wu, Martin, MacNab, Molly, Bermudez, Luiz E.
Mycobacterium avium is widely distributed in the environment, and it is chiefly found in water and soil. M. avium, as well as Mycobacterium smegmatis, has been recognized to produce a biofilm or...
Comparative Genomics of Emerging Human Ehrlichiosis Agents
Dunning Hotopp, Julie C., Lin, Mingqun, Madupu, Ramana, Crabtree, Jonathan, Angiuoli, Samuel V, Eisen, Jonathan, ...
Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an...
Wu, Martin, Ren, Qinghu, Durkin, A. Scott, Daugherty, Sean C, Brinkac, Lauren M, Dodson, Robert J, ...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote
Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
The role of rigidity in DNA looping-unlooping by AraC
Harmer, Tara, Wu, Martin, Schleif, Robert
We applied two experiments useful in the study of ligand-regulated DNA binding proteins to AraC, the dimeric regulator of the Escherichia coli l-arabinose operon. In the absence of arabinose, AraC...
Mefloquine Is Active In Vitro and In Vivo against Mycobacterium avium Complex
Bermudez, Luiz E., Kolonoski, Peter, Wu, Martin, Aralar, Priscilla A., Inderlied, Clark B., Young, Lowell S.
Despite the development of several agents, new classes of antimicrobials with activity against the Mycobacterium avium complex (MAC) are needed. Based on a broad screening of compounds, we found that...
Bermudez, Luiz E., Inderlied, Clark B., Kolonoski, Peter, Petrofsky, Mary, Aralar, Priscilla, Wu, Martin, ...
Moxifloxacin activity against Mycobacterium avium complex (MAC) was evaluated in vitro against 25 strains. The MIC was determined to range from 0.125 to 2.0 μg/ml. In addition, U937 macrophage...
Bermudez, Luiz E., Inderlied, Clark B., Kolonoski, Peter, Wu, Martin, Aralar, Priscilla, Young, Lowell S.
The activity of telithromycin, a new ketolide, was evaluated in vitro and in vivo against Mycobacterium avium complex (MAC) strains. The MIC of telithromycin for several M. avium isolates obtained...
Eisen, Jonathan A., Nelson, Karen E., Paulsen, Ian T., Heidelberg, John F., Wu, Martin, Dodson, Robert J., ...
The complete genome of the green-sulfur eubacterium Chlorobium tepidum TLS was determined to be a single circular chromosome of 2,154,946 bp. This represents the first genome sequence from the phylum...
Wu, Martin, Sun, Ling V, Vamathevan, Jessica, Riegler, Markus, Deboy, Robert, Brownlie, Jeremy C, ...
The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a...
Bermudez, Luiz E., Kolonoski, Peter, Seitz, Lianne E., Petrofsky, Mary, Reynolds, Robert, Wu, Martin, ...
Treatment of Mycobacterium avium disease remains challenging when macrolide resistance develops. We infected C57 beige mice and treated them with mefloquine, SRI-286, and moxifloxacin. SRI-286 (80...
Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath)
Ward, Naomi, Larsen, Øivind, Sakwa, James, Bruseth, Live, Khouri, Hoda, Durkin, A. Scott, ...
Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular,...
Methé, Barbara A., Nelson, Karen E., Deming, Jody W., Momen, Bahram, Melamud, Eugene, Zhang, Xijun, ...
The completion of the 5,373,180-bp genome sequence of the marine psychrophilic bacterium Colwellia psychrerythraea 34H, a model for the study of life in permanently cold environments, reveals...
Danelishvili, Lia, Wu, Martin, Young, Lowell S., Bermudez, Luiz E.
The emergence of mycobacterial resistance to multiple antimicrobials emphasizes the need for new compounds. The antimycobacterial activity of mefloquine has been recently described. Mycobacterium...
Wu, Martin, Ren, Qinghu, Durkin, A. Scott, Daugherty, Sean C, Brinkac, Lauren M, Dodson, Robert J, ...
We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are...
Mycobacterium avium Genes Associated with the Ability To Form a Biofilm
Yamazaki, Yoshitaka, Danelishvili, Lia, Wu, Martin, MacNab, Molly, Bermudez, Luiz E.
Mycobacterium avium is widely distributed in the environment, and it is chiefly found in water and soil. M. avium, as well as Mycobacterium smegmatis, has been recognized to produce a biofilm or...
Comparative Genomics of Emerging Human Ehrlichiosis Agents
Dunning Hotopp, Julie C., Lin, Mingqun, Madupu, Ramana, Crabtree, Jonathan, Angiuoli, Samuel V, Eisen, Jonathan, ...
Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an...
Wu, Martin, Ren, Qinghu, Durkin, A. Scott, Daugherty, Sean C, Brinkac, Lauren M, Dodson, Robert J, ...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote
Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Correction: Comparative Genomics of Emerging Human Ehrlichiosis Agents
Dunning Hotopp, Julie C, Lin, Mingqun, Madupu, Ramana, Crabtree, Jonathan, Angiuoli, Samuel V, Eisen, Jonathan A, ...
Genome Sequence of Aeromonas hydrophila ATCC 7966T: Jack of All Trades▿
Seshadri, Rekha, Joseph, Sam W., Chopra, Ashok K., Sha, Jian, Shaw, Jonathan, Graf, Joerg, ...
The complete genome of Aeromonas hydrophila ATCC 7966T was sequenced. Aeromonas, a ubiquitous waterborne bacterium, has been placed by the Environmental Protection Agency on the Contaminant Candidate...
Danelishvili, Lia, Wu, Martin, Stang, Bernadette, Harriff, Melanie, Cirillo, Stuart, Cirillo, Jeffrey, ...
The ability to infect macrophages is a common characteristic shared among many mycobacterial species. Mycobacterium avium, Mycobacterium tuberculosis, and Mycobacterium kansasii enter macrophages,...
Identification of a fourth family of lycopene cyclases in photosynthetic bacteria
Maresca, Julia A., Graham, Joel E., Wu, Martin, Eisen, Jonathan A., Bryant, Donald A.
A fourth and large family of lycopene cyclases was identified in photosynthetic prokaryotes. The first member of this family, encoded by the cruA gene of the green sulfur bacterium Chlorobium...
Harriff, Melanie J., Wu, Martin, Kent, Michael L., Bermudez, Luiz E.
There are many species of environmental mycobacteria (EM) that infect animals that are important to the economy and research and that also have zoonotic potential. The genomes of very few of these...