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Correction: Handling Permutation in Sequence Comparison: Genome-Wide Enhancer Prediction in Vertebrates by a Novel Non-Linear Alignment Scoring Principle.

PloS one

Dolle D, Mateo JL, Eichenlaub MP, Sinn R, Reinhardt R, Höckendorf B, Inoue D, Centanin L, Ettwiller L, Wittbrodt J.
PMID: 26599359
PLoS One. 2015 Nov 23;10(11):e0143989. doi: 10.1371/journal.pone.0143989. eCollection 2015.

[This corrects the article DOI: 10.1371/journal.pone.0141487.].

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Dolle D, Mateo JL, Eichenlaub MP, et al. Correction: Handling Permutation in Sequence Comparison: Genome-Wide Enhancer Prediction in Vertebrates by a Novel Non-Linear Alignment Scoring Principle. PLoS One. 2015;10(11):e0143989doi: 10.1371/journal.pone.0143989.
Dolle, D., Mateo, J. L., Eichenlaub, M. P., Sinn, R., Reinhardt, R., Höckendorf, B., Inoue, D., Centanin, L., Ettwiller, L., & Wittbrodt, J. (2015). Correction: Handling Permutation in Sequence Comparison: Genome-Wide Enhancer Prediction in Vertebrates by a Novel Non-Linear Alignment Scoring Principle. PloS one, 10(11), e0143989. https://doi.org/10.1371/journal.pone.0143989
Dolle, Dirk, et al. "Correction: Handling Permutation in Sequence Comparison: Genome-Wide Enhancer Prediction in Vertebrates by a Novel Non-Linear Alignment Scoring Principle." PloS one vol. 10,11 (2015): e0143989. doi: https://doi.org/10.1371/journal.pone.0143989
Dolle D, Mateo JL, Eichenlaub MP, Sinn R, Reinhardt R, Höckendorf B, Inoue D, Centanin L, Ettwiller L, Wittbrodt J. Correction: Handling Permutation in Sequence Comparison: Genome-Wide Enhancer Prediction in Vertebrates by a Novel Non-Linear Alignment Scoring Principle. PLoS One. 2015 Nov 23;10(11):e0143989. doi: 10.1371/journal.pone.0143989. eCollection 2015. PMID: 26599359; PMCID: PMC4658166.
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Biological treatment in systemic juvenile idiopathic arthritis: achievement of inactive disease or clinical remission on a first, second or third biological agent.

RMD open

Woerner A, Uettwiller F, Melki I, Mouy R, Wouters C, Bader-Meunier B, Quartier P.
PMID: 26509061
RMD Open. 2015 Apr 30;1(1):e000036. doi: 10.1136/rmdopen-2014-000036. eCollection 2015.

OBJECTIVES: To analyse the effect of biological agents (BAs) in terms of achieving inactive disease (ID) or clinical remission (CR) in patients with systemic juvenile idiopathic arthritis (SJIA), to describe effects of switching or discontinuing a BA and to...

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Woerner A, Uettwiller F, Melki I, et al. Biological treatment in systemic juvenile idiopathic arthritis: achievement of inactive disease or clinical remission on a first, second or third biological agent. RMD Open. 2015;1(1):e000036doi: 10.1136/rmdopen-2014-000036.
Woerner, A., Uettwiller, F., Melki, I., Mouy, R., Wouters, C., Bader-Meunier, B., & Quartier, P. (2015). Biological treatment in systemic juvenile idiopathic arthritis: achievement of inactive disease or clinical remission on a first, second or third biological agent. RMD open, 1(1), e000036. https://doi.org/10.1136/rmdopen-2014-000036
Woerner, A, et al. "Biological treatment in systemic juvenile idiopathic arthritis: achievement of inactive disease or clinical remission on a first, second or third biological agent." RMD open vol. 1,1 (2015): e000036. doi: https://doi.org/10.1136/rmdopen-2014-000036
Woerner A, Uettwiller F, Melki I, Mouy R, Wouters C, Bader-Meunier B, Quartier P. Biological treatment in systemic juvenile idiopathic arthritis: achievement of inactive disease or clinical remission on a first, second or third biological agent. RMD Open. 2015 Apr 30;1(1):e000036. doi: 10.1136/rmdopen-2014-000036. eCollection 2015. PMID: 26509061; PMCID: PMC4613174.
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Paraxial imaging and walk-off effects with birefringent media in refracting surfaces, lenses, and slabs.

Applied optics

Dettwiller L.
PMID: 18204732
Appl Opt. 2008 Jan 20;47(3):442-52. doi: 10.1364/ao.47.000442.

The paraxial theory of spherical refracting surfaces, spherical lenses, and slabs with one birefringent medium is investigated analytically: using walk-off effects in the paraxial domain, a number of relations between objects and images are deduced, along with cardinal elements,...

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Dettwiller L. Paraxial imaging and walk-off effects with birefringent media in refracting surfaces, lenses, and slabs. Appl Opt. 2008;47(3):442-52doi: 10.1364/ao.47.000442.
Dettwiller, L. (2008). Paraxial imaging and walk-off effects with birefringent media in refracting surfaces, lenses, and slabs. Applied optics, 47(3), 442-52. https://doi.org/10.1364/ao.47.000442
Dettwiller, Luc. "Paraxial imaging and walk-off effects with birefringent media in refracting surfaces, lenses, and slabs." Applied optics vol. 47,3 (2008): 442-52. doi: https://doi.org/10.1364/ao.47.000442
Dettwiller L. Paraxial imaging and walk-off effects with birefringent media in refracting surfaces, lenses, and slabs. Appl Opt. 2008 Jan 20;47(3):442-52. doi: 10.1364/ao.47.000442. PMID: 18204732.
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Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq.

Genome research

Yan B, Tzertzinis G, Schildkraut I, Ettwiller L.
PMID: 34815308
Genome Res. 2022 Jan;32(1):162-174. doi: 10.1101/gr.275784.121. Epub 2021 Nov 23.

Determination of eukaryotic transcription start sites (TSSs) has been based on methods that require the cap structure at the 5' end of transcripts derived from Pol II RNA polymerase. Consequently, these methods do not reveal TSSs derived from the...

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Yan B, Tzertzinis G, Schildkraut I, et al. Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq. Genome Res. 2021;32(1):162-174doi: 10.1101/gr.275784.121.
Yan, B., Tzertzinis, G., Schildkraut, I., & Ettwiller, L. (2022). Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq. Genome research, 32(1), 162-174. https://doi.org/10.1101/gr.275784.121
Yan, Bo, et al. "Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq." Genome research vol. 32,1 (2022): 162-174. doi: https://doi.org/10.1101/gr.275784.121
Yan B, Tzertzinis G, Schildkraut I, Ettwiller L. Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq. Genome Res. 2022 Jan;32(1):162-174. doi: 10.1101/gr.275784.121. Epub 2021 Nov 23. PMID: 34815308.
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Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq.

Genome research

Yan B, Tzertzinis G, Schildkraut I, Ettwiller L.
PMID: 34815308
Genome Res. 2021 Nov 23; doi: 10.1101/gr.275784.121. Epub 2021 Nov 23.

Determination of eukaryotic transcription start sites (TSSs) has been based on methods that require the cap structure at the 5' end of transcripts derived from Pol II RNA polymerase. Consequently, these methods do not reveal TSSs derived from the...

Cite
Yan B, Tzertzinis G, Schildkraut I, et al. Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq. Genome Res. 2021;doi: 10.1101/gr.275784.121.
Yan, B., Tzertzinis, G., Schildkraut, I., & Ettwiller, L. (2021). Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq. Genome research, . https://doi.org/10.1101/gr.275784.121
Yan, Bo, et al. "Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq." Genome research vol. (2021). doi: https://doi.org/10.1101/gr.275784.121
Yan B, Tzertzinis G, Schildkraut I, Ettwiller L. Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq. Genome Res. 2021 Nov 23; doi: 10.1101/gr.275784.121. Epub 2021 Nov 23. PMID: 34815308.
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A Genome-Phenome Association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA.

eLife

Yang W, Lin YC, Johnson W, Dai N, Vaisvila R, Weigele P, Lee YJ, Corrêa IR, Schildkraut I, Ettwiller L.
PMID: 34747693
Elife. 2021 Nov 08;10. doi: 10.7554/eLife.70021. Epub 2021 Nov 08.

Shotgun metagenomic sequencing is a powerful approach to study microbiomes in an unbiased manner and of increasing relevance for identifying novel enzymatic functions. However, the potential of metagenomics to relate from microbiome composition to function has thus far been...

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Yang W, Lin YC, Johnson W, et al. A Genome-Phenome Association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA. Elife. 2021;10doi: 10.7554/eLife.70021.
Yang, W., Lin, Y. C., Johnson, W., Dai, N., Vaisvila, R., Weigele, P., Lee, Y. J., Corrêa, I. R., Schildkraut, I., & Ettwiller, L. (2021). A Genome-Phenome Association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA. eLife, 10. https://doi.org/10.7554/eLife.70021
Yang, Weiwei, et al. "A Genome-Phenome Association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA." eLife vol. 10 (2021). doi: https://doi.org/10.7554/eLife.70021
Yang W, Lin YC, Johnson W, Dai N, Vaisvila R, Weigele P, Lee YJ, Corrêa IR, Schildkraut I, Ettwiller L. A Genome-Phenome Association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA. Elife. 2021 Nov 08;10. doi: 10.7554/eLife.70021. Epub 2021 Nov 08. PMID: 34747693.
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Corrigendum: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.

Genome research

Mateo JL, van den Berg DL, Haeussler M, Drechsel D, Gaber ZB, Castro DS, Robson P, Lu QR, Crawford GE, Flicek P, Ettwiller L, Wittbrodt J, Guillemot F, Martynoga B.
PMID: 27803196
Genome Res. 2016 Nov;26(11):1626. doi: 10.1101/gr.216044.116.

No abstract available.

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Mateo JL, van den Berg DL, Haeussler M, et al. Corrigendum: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal. Genome Res. 2016;26(11):1626doi: 10.1101/gr.216044.116.
Mateo, J. L., van den Berg, D. L., Haeussler, M., Drechsel, D., Gaber, Z. B., Castro, D. S., Robson, P., Lu, Q. R., Crawford, G. E., Flicek, P., Ettwiller, L., Wittbrodt, J., Guillemot, F., & Martynoga, B. (2016). Corrigendum: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal. Genome research, 26(11), 1626. https://doi.org/10.1101/gr.216044.116
Mateo, Juan L, et al. "Corrigendum: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal." Genome research vol. 26,11 (2016): 1626. doi: https://doi.org/10.1101/gr.216044.116
Mateo JL, van den Berg DL, Haeussler M, Drechsel D, Gaber ZB, Castro DS, Robson P, Lu QR, Crawford GE, Flicek P, Ettwiller L, Wittbrodt J, Guillemot F, Martynoga B. Corrigendum: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal. Genome Res. 2016 Nov;26(11):1626. doi: 10.1101/gr.216044.116. PMID: 27803196; PMCID: PMC5088603.
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Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis.

Cell reports

Raposo AASF, Vasconcelos FF, Drechsel D, Marie C, Johnston C, Dolle D, Bithell A, Gillotin S, van den Berg DLC, Ettwiller L, Flicek P, Crawford GE, Parras CM, Berninger B, Buckley NJ, Guillemot F, Castro DS.
PMID: 25753420
Cell Rep. 2015 Mar 10;10(9):1544-1556. doi: 10.1016/j.celrep.2015.02.025. Epub 2015 Mar 05.

The proneural transcription factor Ascl1 coordinates gene expression in both proliferating and differentiating progenitors along the neuronal lineage. Here, we used a cellular model of neurogenesis to investigate how Ascl1 interacts with the chromatin landscape to regulate gene expression...

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Raposo AASF, Vasconcelos FF, Drechsel D, et al. Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis. Cell Rep. 2015;10(9):1544-1556doi: 10.1016/j.celrep.2015.02.025.
Raposo, A. A. S. F., Vasconcelos, F. F., Drechsel, D., Marie, C., Johnston, C., Dolle, D., Bithell, A., Gillotin, S., van den Berg, D. L. C., Ettwiller, L., Flicek, P., Crawford, G. E., Parras, C. M., Berninger, B., Buckley, N. J., Guillemot, F., & Castro, D. S. (2015). Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis. Cell reports, 10(9), 1544-1556. https://doi.org/10.1016/j.celrep.2015.02.025
Raposo, Alexandre A S F, et al. "Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis." Cell reports vol. 10,9 (2015): 1544-1556. doi: https://doi.org/10.1016/j.celrep.2015.02.025
Raposo AASF, Vasconcelos FF, Drechsel D, Marie C, Johnston C, Dolle D, Bithell A, Gillotin S, van den Berg DLC, Ettwiller L, Flicek P, Crawford GE, Parras CM, Berninger B, Buckley NJ, Guillemot F, Castro DS. Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis. Cell Rep. 2015 Mar 10;10(9):1544-1556. doi: 10.1016/j.celrep.2015.02.025. Epub 2015 Mar 05. PMID: 25753420; PMCID: PMC5383937.
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ADA2 deficiency: case report of a new phenotype and novel mutation in two sisters.

RMD open

Uettwiller F, Sarrabay G, Rodero MP, Rice GI, Lagrue E, Marot Y, Deiva K, Touitou I, Crow YJ, Quartier P.
PMID: 27252897
RMD Open. 2016 May 16;2(1):e000236. doi: 10.1136/rmdopen-2015-000236. eCollection 2016.

The objective of this paper is to: describe the phenotype compound heterozygote for mutations in CECR1 in two children. We describe the clinical and immunological phenotype, including the assessment of ADA2 activity, cytokine expression, interferon-stimulated and neutrophil-stimulated gene signatures,...

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Uettwiller F, Sarrabay G, Rodero MP, et al. ADA2 deficiency: case report of a new phenotype and novel mutation in two sisters. RMD Open. 2016;2(1):e000236doi: 10.1136/rmdopen-2015-000236.
Uettwiller, F., Sarrabay, G., Rodero, M. P., Rice, G. I., Lagrue, E., Marot, Y., Deiva, K., Touitou, I., Crow, Y. J., & Quartier, P. (2016). ADA2 deficiency: case report of a new phenotype and novel mutation in two sisters. RMD open, 2(1), e000236. https://doi.org/10.1136/rmdopen-2015-000236
Uettwiller, F, et al. "ADA2 deficiency: case report of a new phenotype and novel mutation in two sisters." RMD open vol. 2,1 (2016): e000236. doi: https://doi.org/10.1136/rmdopen-2015-000236
Uettwiller F, Sarrabay G, Rodero MP, Rice GI, Lagrue E, Marot Y, Deiva K, Touitou I, Crow YJ, Quartier P. ADA2 deficiency: case report of a new phenotype and novel mutation in two sisters. RMD Open. 2016 May 16;2(1):e000236. doi: 10.1136/rmdopen-2015-000236. eCollection 2016. PMID: 27252897; PMCID: PMC4879337.
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Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq.

Genome research

Yan B, Tzertzinis G, Schildkraut I, Ettwiller L.
PMID: 34815308
Genome Res. 2021 Nov 23; doi: 10.1101/gr.275784.121. Epub 2021 Nov 23.

Determination of eukaryotic Transcription Start Sites (TSS) has been based on methods that require the cap structure at the 5-prime end of transcripts derived from Pol-II RNA polymerase. Consequently, these methods do not reveal TSS derived from the other...

Cite
Yan B, Tzertzinis G, Schildkraut I, et al. Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq. Genome Res. 2021;doi: 10.1101/gr.275784.121.
Yan, B., Tzertzinis, G., Schildkraut, I., & Ettwiller, L. (2021). Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq. Genome research, . https://doi.org/10.1101/gr.275784.121
Yan, Bo, et al. "Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq." Genome research vol. (2021). doi: https://doi.org/10.1101/gr.275784.121
Yan B, Tzertzinis G, Schildkraut I, Ettwiller L. Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq. Genome Res. 2021 Nov 23; doi: 10.1101/gr.275784.121. Epub 2021 Nov 23. PMID: 34815308.
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Rapid identification of methylase specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes.

Nucleic acids research

Baum C, Lin YC, Fomenkov A, Anton BP, Chen L, Yan B, Evans TC, Roberts RJ, Tolonen AC, Ettwiller L.
PMID: 34417598
Nucleic Acids Res. 2021 Nov 08;49(19):e113. doi: 10.1093/nar/gkab705.

DNA methylation is widespread amongst eukaryotes and prokaryotes to modulate gene expression and confer viral resistance. 5-Methylcytosine (m5C) methylation has been described in genomes of a large fraction of bacterial species as part of restriction-modification systems, each composed of...

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Baum C, Lin YC, Fomenkov A, et al. Rapid identification of methylase specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes. Nucleic Acids Res. 2021;49(19):e113doi: 10.1093/nar/gkab705.
Baum, C., Lin, Y. C., Fomenkov, A., Anton, B. P., Chen, L., Yan, B., Evans, T. C., Roberts, R. J., Tolonen, A. C., & Ettwiller, L. (2021). Rapid identification of methylase specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes. Nucleic acids research, 49(19), e113. https://doi.org/10.1093/nar/gkab705
Baum, Chloé, et al. "Rapid identification of methylase specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes." Nucleic acids research vol. 49,19 (2021): e113. doi: https://doi.org/10.1093/nar/gkab705
Baum C, Lin YC, Fomenkov A, Anton BP, Chen L, Yan B, Evans TC, Roberts RJ, Tolonen AC, Ettwiller L. Rapid identification of methylase specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes. Nucleic Acids Res. 2021 Nov 08;49(19):e113. doi: 10.1093/nar/gkab705. PMID: 34417598; PMCID: PMC8565308.
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A genome-phenome association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA.

eLife

Yang W, Lin YC, Johnson W, Dai N, Vaisvila R, Weigele P, Lee YJ, Corrêa IR, Schildkraut I, Ettwiller L.
PMID: 34747693
Elife. 2021 Nov 08;10. doi: 10.7554/eLife.70021.

Shotgun metagenomic sequencing is a powerful approach to study microbiomes in an unbiased manner and of increasing relevance for identifying novel enzymatic functions. However, the potential of metagenomics to relate from microbiome composition to function has thus far been...

Cite
Yang W, Lin YC, Johnson W, et al. A genome-phenome association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA. Elife. 2021;10doi: 10.7554/eLife.70021.
Yang, W., Lin, Y. C., Johnson, W., Dai, N., Vaisvila, R., Weigele, P., Lee, Y. J., Corrêa, I. R., Schildkraut, I., & Ettwiller, L. (2021). A genome-phenome association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA. eLife, 10. https://doi.org/10.7554/eLife.70021
Yang, Weiwei, et al. "A genome-phenome association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA." eLife vol. 10 (2021). doi: https://doi.org/10.7554/eLife.70021
Yang W, Lin YC, Johnson W, Dai N, Vaisvila R, Weigele P, Lee YJ, Corrêa IR, Schildkraut I, Ettwiller L. A genome-phenome association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA. Elife. 2021 Nov 08;10. doi: 10.7554/eLife.70021. PMID: 34747693.
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Showing 1 to 12 of 31 entries