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Phandango: an interactive viewer for bacterial population genomics.

Bioinformatics (Oxford, England)

Hadfield J, Croucher NJ, Goater RJ, Abudahab K, Aanensen DM, Harris SR.
PMID: 29028899
Bioinformatics. 2018 Jan 15;34(2):292-293. doi: 10.1093/bioinformatics/btx610.

SUMMARY: Fully exploiting the wealth of data in current bacterial population genomics datasets requires synthesizing and integrating different types of analysis across millions of base pairs in hundreds or thousands of isolates. Current approaches often use static representations of...

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Hadfield J, Croucher NJ, Goater RJ, et al. Phandango: an interactive viewer for bacterial population genomics. Bioinformatics. 2018;34(2):292-293doi: 10.1093/bioinformatics/btx610.
Hadfield, J., Croucher, N. J., Goater, R. J., Abudahab, K., Aanensen, D. M., & Harris, S. R. (2018). Phandango: an interactive viewer for bacterial population genomics. Bioinformatics (Oxford, England), 34(2), 292-293. https://doi.org/10.1093/bioinformatics/btx610
Hadfield, James, et al. "Phandango: an interactive viewer for bacterial population genomics." Bioinformatics (Oxford, England) vol. 34,2 (2018): 292-293. doi: https://doi.org/10.1093/bioinformatics/btx610
Hadfield J, Croucher NJ, Goater RJ, Abudahab K, Aanensen DM, Harris SR. Phandango: an interactive viewer for bacterial population genomics. Bioinformatics. 2018 Jan 15;34(2):292-293. doi: 10.1093/bioinformatics/btx610. PMID: 29028899; PMCID: PMC5860215.
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A cornucopia of candidates for deafness.

Cell

Lewis MA, Steel KP.
PMID: 22939617
Cell. 2012 Aug 31;150(5):879-81. doi: 10.1016/j.cell.2012.08.007.

Many genes involved in deafness are yet to be discovered. Here, Senthilan et al. focus on the Drosophila Johnston's organ to uncover a wide variety of genes, including several unexpected candidates as well as those already known to underlie...

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Lewis MA, Steel KP. A cornucopia of candidates for deafness. Cell. 2012;150(5):879-81doi: 10.1016/j.cell.2012.08.007.
Lewis, M. A., & Steel, K. P. (2012). A cornucopia of candidates for deafness. Cell, 150(5), 879-81. https://doi.org/10.1016/j.cell.2012.08.007
Lewis, Morag A, and Steel, Karen P. "A cornucopia of candidates for deafness." Cell vol. 150,5 (2012): 879-81. doi: https://doi.org/10.1016/j.cell.2012.08.007
Lewis MA, Steel KP. A cornucopia of candidates for deafness. Cell. 2012 Aug 31;150(5):879-81. doi: 10.1016/j.cell.2012.08.007. PMID: 22939617.
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A computational lens for sexual-stage transmission, reproduction, fitness and kinetics in Plasmodium falciparum.

Malaria journal

Lawniczak MK, Eckhoff PA.
PMID: 27653663
Malar J. 2016 Sep 21;15(1):487. doi: 10.1186/s12936-016-1538-5.

BACKGROUND: The burden of falciparum malaria remains unacceptably high in much of sub-Saharan Africa and massive efforts are underway to eliminate the parasite. While symptoms of malaria are caused by asexual reproduction of the parasite, transmission to new human...

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Lawniczak MK, Eckhoff PA. A computational lens for sexual-stage transmission, reproduction, fitness and kinetics in Plasmodium falciparum. Malar J. 2016;15(1):487doi: 10.1186/s12936-016-1538-5.
Lawniczak, M. K., & Eckhoff, P. A. (2016). A computational lens for sexual-stage transmission, reproduction, fitness and kinetics in Plasmodium falciparum. Malaria journal, 15(1), 487. https://doi.org/10.1186/s12936-016-1538-5
Lawniczak, Mara K N, and Eckhoff, Philip A. "A computational lens for sexual-stage transmission, reproduction, fitness and kinetics in Plasmodium falciparum." Malaria journal vol. 15,1 (2016): 487. doi: https://doi.org/10.1186/s12936-016-1538-5
Lawniczak MK, Eckhoff PA. A computational lens for sexual-stage transmission, reproduction, fitness and kinetics in Plasmodium falciparum. Malar J. 2016 Sep 21;15(1):487. doi: 10.1186/s12936-016-1538-5. PMID: 27653663; PMCID: PMC5031309.
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Two microbiota subtypes identified in irritable bowel syndrome with distinct responses to the low FODMAP diet.

Gut

Vervier K, Moss S, Kumar N, Adoum A, Barne M, Browne H, Kaser A, Kiely CJ, Neville BA, Powell N, Raine T, Stares MD, Zhu A, De La Revilla Negro J, Lawley TD, Parkes M.
PMID: 34810234
Gut. 2021 Nov 22; doi: 10.1136/gutjnl-2021-325177. Epub 2021 Nov 22.

OBJECTIVE: Reducing FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides and polyols) can be clinically beneficial in IBS but the mechanism is incompletely understood. We aimed to detect microbial signatures that might predict response to the low FODMAP diet and assess whether...

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Vervier K, Moss S, Kumar N, et al. Two microbiota subtypes identified in irritable bowel syndrome with distinct responses to the low FODMAP diet. Gut. 2021;doi: 10.1136/gutjnl-2021-325177.
Vervier, K., Moss, S., Kumar, N., Adoum, A., Barne, M., Browne, H., Kaser, A., Kiely, C. J., Neville, B. A., Powell, N., Raine, T., Stares, M. D., Zhu, A., De La Revilla Negro, J., Lawley, T. D., & Parkes, M. (2021). Two microbiota subtypes identified in irritable bowel syndrome with distinct responses to the low FODMAP diet. Gut, . https://doi.org/10.1136/gutjnl-2021-325177
Vervier, Kevin, et al. "Two microbiota subtypes identified in irritable bowel syndrome with distinct responses to the low FODMAP diet." Gut vol. (2021). doi: https://doi.org/10.1136/gutjnl-2021-325177
Vervier K, Moss S, Kumar N, Adoum A, Barne M, Browne H, Kaser A, Kiely CJ, Neville BA, Powell N, Raine T, Stares MD, Zhu A, De La Revilla Negro J, Lawley TD, Parkes M. Two microbiota subtypes identified in irritable bowel syndrome with distinct responses to the low FODMAP diet. Gut. 2021 Nov 22; doi: 10.1136/gutjnl-2021-325177. Epub 2021 Nov 22. PMID: 34810234.
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An Orphan CpG Island Drives Expression of a .

Epigenomes

Koerner MV, Chhatbar K, Webb S, Cholewa-Waclaw J, Selfridge J, De Sousa D, Skarnes B, Rosen B, Thomas M, Bottomley J, Ramires-Solis R, Lelliott C, Adams DJ, Bird A.
PMID: 31354981
Epigenomes. 2019 Mar;3(1):7. doi: 10.3390/epigenomes3010007. Epub 2019 Mar 13.

Most human genes are associated with promoters embedded in non-methylated, G + C-rich CpG islands (CGIs). Not all CGIs are found at annotated promoters, however, raising the possibility that many serve as promoters for transcripts that do not code...

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Koerner MV, Chhatbar K, Webb S, et al. An Orphan CpG Island Drives Expression of a . Epigenomes. 2019;3(1):7doi: 10.3390/epigenomes3010007.
Koerner, M. V., Chhatbar, K., Webb, S., Cholewa-Waclaw, J., Selfridge, J., De Sousa, D., Skarnes, B., Rosen, B., Thomas, M., Bottomley, J., Ramires-Solis, R., Lelliott, C., Adams, D. J., & Bird, A. (2019). An Orphan CpG Island Drives Expression of a . Epigenomes, 3(1), 7. https://doi.org/10.3390/epigenomes3010007
Koerner, Martha V, et al. "An Orphan CpG Island Drives Expression of a ." Epigenomes vol. 3,1 (2019): 7. doi: https://doi.org/10.3390/epigenomes3010007
Koerner MV, Chhatbar K, Webb S, Cholewa-Waclaw J, Selfridge J, De Sousa D, Skarnes B, Rosen B, Thomas M, Bottomley J, Ramires-Solis R, Lelliott C, Adams DJ, Bird A. An Orphan CpG Island Drives Expression of a . Epigenomes. 2019 Mar;3(1):7. doi: 10.3390/epigenomes3010007. Epub 2019 Mar 13. PMID: 31354981; PMCID: PMC6660310.
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Complete genome for .

Microbial genomics

Bossé JT, Li Y, Cohen LM, Stegger M, Angen Ø, Lacouture S, Gottschalk M, Lei L, Koene M, Kuhnert P, Bandara AB, Inzana TJ, Holden MTG, Harris D, Oshota O, Maskell DJ, Tucker AW, Wren BW, Rycroft AN, Langford PR, On Behalf Of The BRaDP T Consortium.
PMID: 34818145
Microb Genom. 2021 Nov;7(11). doi: 10.1099/mgen.0.000687.

We report here the complete genome sequence of the widely studied

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Bossé JT, Li Y, Cohen LM, et al. Complete genome for . Microb Genom. 2021;7(11)doi: 10.1099/mgen.0.000687.
Bossé, J. T., Li, Y., Cohen, L. M., Stegger, M., Angen, �. �., Lacouture, S., Gottschalk, M., Lei, L., Koene, M., Kuhnert, P., Bandara, A. B., Inzana, T. J., Holden, M. T. G., Harris, D., Oshota, O., Maskell, D. J., Tucker, A. W., Wren, B. W., Rycroft, A. N., Langford, P. R., & On Behalf Of The BRaDP T Consortium. (2021). Complete genome for . Microbial genomics, 7(11), . https://doi.org/10.1099/mgen.0.000687
Bossé, Janine T, et al. "Complete genome for ." Microbial genomics vol. 7,11 (2021). doi: https://doi.org/10.1099/mgen.0.000687
Bossé JT, Li Y, Cohen LM, Stegger M, Angen Ø, Lacouture S, Gottschalk M, Lei L, Koene M, Kuhnert P, Bandara AB, Inzana TJ, Holden MTG, Harris D, Oshota O, Maskell DJ, Tucker AW, Wren BW, Rycroft AN, Langford PR, On Behalf Of The BRaDP T Consortium. Complete genome for . Microb Genom. 2021 Nov;7(11). doi: 10.1099/mgen.0.000687. PMID: 34818145.
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Sibling rivalry among paralogs promotes evolution of the human brain.

Cell

Tyler-Smith C, Xue Y.
PMID: 22579279
Cell. 2012 May 11;149(4):737-9. doi: 10.1016/j.cell.2012.04.020.

Geneticists have long sought to identify the genetic changes that made us human, but pinpointing the functionally relevant changes has been challenging. Two papers in this issue suggest that partial duplication of SRGAP2, producing an incomplete protein that antagonizes...

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Tyler-Smith C, Xue Y. Sibling rivalry among paralogs promotes evolution of the human brain. Cell. 2012;149(4):737-9doi: 10.1016/j.cell.2012.04.020.
Tyler-Smith, C., & Xue, Y. (2012). Sibling rivalry among paralogs promotes evolution of the human brain. Cell, 149(4), 737-9. https://doi.org/10.1016/j.cell.2012.04.020
Tyler-Smith, Chris, and Xue, Yali. "Sibling rivalry among paralogs promotes evolution of the human brain." Cell vol. 149,4 (2012): 737-9. doi: https://doi.org/10.1016/j.cell.2012.04.020
Tyler-Smith C, Xue Y. Sibling rivalry among paralogs promotes evolution of the human brain. Cell. 2012 May 11;149(4):737-9. doi: 10.1016/j.cell.2012.04.020. PMID: 22579279; PMCID: PMC3477634.
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Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders.

Nature genetics

Eijsbouts C, Zheng T, Kennedy NA, Bonfiglio F, Anderson CA, Moutsianas L, Holliday J, Shi J, Shringarpure S, Voda AI, Farrugia G, Franke A, Hübenthal M, Abecasis G, Zawistowski M, Skogholt AH, Ness-Jensen E, Hveem K, Esko T, Teder-Laving M, Zhernakova A, Camilleri M, Boeckxstaens G, Whorwell PJ, Spiller R, McVean G, D'Amato M, Jostins L, Parkes M.
PMID: 34741163
Nat Genet. 2021 Nov;53(11):1543-1552. doi: 10.1038/s41588-021-00950-8. Epub 2021 Nov 05.

Irritable bowel syndrome (IBS) results from disordered brain-gut interactions. Identifying susceptibility genes could highlight the underlying pathophysiological mechanisms. We designed a digestive health questionnaire for UK Biobank and combined identified cases with IBS with independent cohorts. We conducted a...

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Eijsbouts C, Zheng T, Kennedy NA, et al. Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders. Nat Genet. 2021;53(11):1543-1552doi: 10.1038/s41588-021-00950-8.
Eijsbouts, C., Zheng, T., Kennedy, N. A., Bonfiglio, F., Anderson, C. A., Moutsianas, L., Holliday, J., Shi, J., Shringarpure, S., Voda, A. I., Farrugia, G., Franke, A., Hübenthal, M., Abecasis, G., Zawistowski, M., Skogholt, A. H., Ness-Jensen, E., Hveem, K., Esko, T., Teder-Laving, M., Zhernakova, A., Camilleri, M., Boeckxstaens, G., Whorwell, P. J., Spiller, R., McVean, G., D'Amato, M., Jostins, L., & Parkes, M. (2021). Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders. Nature genetics, 53(11), 1543-1552. https://doi.org/10.1038/s41588-021-00950-8
Eijsbouts, Chris, et al. "Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders." Nature genetics vol. 53,11 (2021): 1543-1552. doi: https://doi.org/10.1038/s41588-021-00950-8
Eijsbouts C, Zheng T, Kennedy NA, Bonfiglio F, Anderson CA, Moutsianas L, Holliday J, Shi J, Shringarpure S, Voda AI, Farrugia G, Franke A, Hübenthal M, Abecasis G, Zawistowski M, Skogholt AH, Ness-Jensen E, Hveem K, Esko T, Teder-Laving M, Zhernakova A, Camilleri M, Boeckxstaens G, Whorwell PJ, Spiller R, McVean G, D'Amato M, Jostins L, Parkes M. Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders. Nat Genet. 2021 Nov;53(11):1543-1552. doi: 10.1038/s41588-021-00950-8. Epub 2021 Nov 05. PMID: 34741163; PMCID: PMC8571093.
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Relative Suffix Trees.

The computer journal

Farruggia A, Gagie T, Navarro G, Puglisi SJ, Sirén J.
PMID: 29795706
Comput J. 2018 May;61(5):773-788. doi: 10.1093/comjnl/bxx108. Epub 2017 Nov 21.

Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put...

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Farruggia A, Gagie T, Navarro G, et al. Relative Suffix Trees. Comput J. 2017;61(5):773-788doi: 10.1093/comjnl/bxx108.
Farruggia, A., Gagie, T., Navarro, G., Puglisi, S. J., & Sirén, J. (2018). Relative Suffix Trees. The computer journal, 61(5), 773-788. https://doi.org/10.1093/comjnl/bxx108
Farruggia, Andrea, et al. "Relative Suffix Trees." The computer journal vol. 61,5 (2018): 773-788. doi: https://doi.org/10.1093/comjnl/bxx108
Farruggia A, Gagie T, Navarro G, Puglisi SJ, Sirén J. Relative Suffix Trees. Comput J. 2018 May;61(5):773-788. doi: 10.1093/comjnl/bxx108. Epub 2017 Nov 21. PMID: 29795706; PMCID: PMC5956352.
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PhenoPlasm: a database of disruption phenotypes for malaria parasite genes.

Wellcome open research

Sanderson T, Rayner JC.
PMID: 28748223
Wellcome Open Res. 2017 Jul 24;2:45. doi: 10.12688/wellcomeopenres.11896.2. eCollection 2017.

Two decades after the first

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Sanderson T, Rayner JC. PhenoPlasm: a database of disruption phenotypes for malaria parasite genes. Wellcome Open Res. 2017;2:45doi: 10.12688/wellcomeopenres.11896.2.
Sanderson, T., & Rayner, J. C. (2017). PhenoPlasm: a database of disruption phenotypes for malaria parasite genes. Wellcome open research, 245. https://doi.org/10.12688/wellcomeopenres.11896.2
Sanderson, Theo, and Rayner, Julian C. "PhenoPlasm: a database of disruption phenotypes for malaria parasite genes." Wellcome open research vol. 2 (2017): 45. doi: https://doi.org/10.12688/wellcomeopenres.11896.2
Sanderson T, Rayner JC. PhenoPlasm: a database of disruption phenotypes for malaria parasite genes. Wellcome Open Res. 2017 Jul 24;2:45. doi: 10.12688/wellcomeopenres.11896.2. eCollection 2017. PMID: 28748223; PMCID: PMC5500895.
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Returning genome sequences to research participants: Policy and practice.

Wellcome open research

Wright CF, Middleton A, Barrett JC, Firth HV, FitzPatrick DR, Hurles ME, Parker M.
PMID: 28317033
Wellcome Open Res. 2017 Feb 24;2:15. doi: 10.12688/wellcomeopenres.10942.1.

Despite advances in genomic science stimulating an explosion of literature around returning health-related findings, the possibility of returning entire genome sequences to individual research participants has not been widely considered. Through direct involvement in large-scale translational genomics studies, we...

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Wright CF, Middleton A, Barrett JC, et al. Returning genome sequences to research participants: Policy and practice. Wellcome Open Res. 2017;2:15doi: 10.12688/wellcomeopenres.10942.1.
Wright, C. F., Middleton, A., Barrett, J. C., Firth, H. V., FitzPatrick, D. R., Hurles, M. E., & Parker, M. (2017). Returning genome sequences to research participants: Policy and practice. Wellcome open research, 215. https://doi.org/10.12688/wellcomeopenres.10942.1
Wright, Caroline F, et al. "Returning genome sequences to research participants: Policy and practice." Wellcome open research vol. 2 (2017): 15. doi: https://doi.org/10.12688/wellcomeopenres.10942.1
Wright CF, Middleton A, Barrett JC, Firth HV, FitzPatrick DR, Hurles ME, Parker M. Returning genome sequences to research participants: Policy and practice. Wellcome Open Res. 2017 Feb 24;2:15. doi: 10.12688/wellcomeopenres.10942.1. PMID: 28317033; PMCID: PMC5351846.
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Complete Genome Sequence of MIDG2331, a Genetically Tractable Serovar 8 Clinical Isolate of Actinobacillus pleuropneumoniae.

Genome announcements

Bossé JT, Chaudhuri RR, Li Y, Leanse LG, Fernandez Crespo R, Coupland P, Holden MT, Bazzolli DM, Maskell DJ, Tucker AW, Wren BW, Rycroft AN, Langford PR.
PMID: 26823596
Genome Announc. 2016 Jan 28;4(1). doi: 10.1128/genomeA.01667-15.

We report here the complete annotated genome sequence of a clinical serovar 8 isolate Actinobacillus pleuropneumoniae MIDG2331. Unlike the serovar 8 reference strain 405, MIDG2331 is amenable to genetic manipulation via natural transformation as well as conjugation, making it...

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Bossé JT, Chaudhuri RR, Li Y, et al. Complete Genome Sequence of MIDG2331, a Genetically Tractable Serovar 8 Clinical Isolate of Actinobacillus pleuropneumoniae. Genome Announc. 2016;4(1)doi: 10.1128/genomeA.01667-15.
Bossé, J. T., Chaudhuri, R. R., Li, Y., Leanse, L. G., Fernandez Crespo, R., Coupland, P., Holden, M. T., Bazzolli, D. M., Maskell, D. J., Tucker, A. W., Wren, B. W., Rycroft, A. N., & Langford, P. R. (2016). Complete Genome Sequence of MIDG2331, a Genetically Tractable Serovar 8 Clinical Isolate of Actinobacillus pleuropneumoniae. Genome announcements, 4(1), . https://doi.org/10.1128/genomeA.01667-15
Bossé, Janine T, et al. "Complete Genome Sequence of MIDG2331, a Genetically Tractable Serovar 8 Clinical Isolate of Actinobacillus pleuropneumoniae." Genome announcements vol. 4,1 (2016). doi: https://doi.org/10.1128/genomeA.01667-15
Bossé JT, Chaudhuri RR, Li Y, Leanse LG, Fernandez Crespo R, Coupland P, Holden MT, Bazzolli DM, Maskell DJ, Tucker AW, Wren BW, Rycroft AN, Langford PR. Complete Genome Sequence of MIDG2331, a Genetically Tractable Serovar 8 Clinical Isolate of Actinobacillus pleuropneumoniae. Genome Announc. 2016 Jan 28;4(1). doi: 10.1128/genomeA.01667-15. PMID: 26823596; PMCID: PMC4732349.
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Showing 1 to 12 of 41 entries