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Method: Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing
- Ole Skovgaard,
- Mads Bak,
- Anders Løbner-Olesen,
- and Niels Tommerup
Genome Res. August 2011 21: 1388-1393; Published in Advance May 9, 2011, doi:10.1101/gr.117416.110
.... 2007. An evaluation of Comparative Genome Sequencing (CGS) by comparing two previously-sequenced bacterial s. BMC Genomics 8: 274. doi: 10.1186/1471-2164-8-274. Hill CW, Harnish BW. 1981. Inversions between ribosomal RNA genes of Escherichia coli. Proc Natl Acad Sci 78: 70697072. Kaguni JM. 2006. Dna ...
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Research: Microevolution of extensively drug-resistant tuberculosis in Russia
- Nicola Casali,
- Vladyslav Nikolayevskyy,
- Yanina Balabanova,
- Olga Ignatyeva,
- Irina Kontsevaya,
- Simon R. Harris,
- Stephen D. Bentley,
- Julian Parkhill,
- Sergey Nejentsev,
- Sven E. Hoffner,
- Rolf D. Horstmann,
- Timothy Brown,
- and Francis Drobniewski
Genome Res. April 2012 22: 735-745; Published in Advance January 31, 2012, doi:10.1101/gr.128678.111
...the biology of Mycobacterium tuberculosis from the complete sequence. Nature 393: 537544. Collins CH, Grange JM, Yates MD. 1997. Drug susceptibility testing. In Tuberculosis bacteriology: Organization and practice, pp. 98109. Butterworth-Heinemann, Oxford, UK. Drobniewski F, Balabanova Y, Nikolayevsky V ...
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Research: Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent
- Joseph E. Powell,
- Anjali K. Henders,
- Allan F. McRae,
- Margaret J. Wright,
- Nicholas G. Martin,
- Emmanouil T. Dermitzakis,
- Grant W. Montgomery,
- and Peter M. Visscher
Genome Res. March 2012 22: 456-466; Published in Advance December 19, 2011, doi:10.1101/gr.126540.111
...transcript values for individual i in MZpair j,m represents themeannormalized transcript levels across all individuals, Gj is the random effect of MZ pair j, Sk is the fixed effect of sex, and eijk is the residual. For each of the 9555 genes, Equation 2 was applied to the normalized transcript values from ...
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Research: Genetic and environmental exposures constrain epigenetic drift over the human life course
- Sonia Shah,
- Allan F. McRae,
- Riccardo E. Marioni,
- Sarah E. Harris,
- Jude Gibson,
- Anjali K. Henders,
- Paul Redmond,
- Simon R. Cox,
- Alison Pattie,
- Janie Corley,
- Lee Murphy,
- Nicholas G. Martin,
- Grant W. Montgomery,
- John M. Starr,
- Naomi R. Wray,
- Ian J. Deary,
- and Peter M. Visscher
Genome Res. November 2014 24: 1725-1733; Published in Advance September 23, 2014, doi:10.1101/gr.176933.114
...Harris Harris Naomi R, Wray Henders, AK RiccardoE Marioni Cox, Simon R A Henders Sonia Shah NG Martin S Shah JM Starr Deary, I Allan F, McRae McRae, A.F Montgomery Grant W. SE Harris McRae, A Starr Grant W, Montgomery Peter Martin Nicholas G. Martin, N Pattie, A Janie, Corley Murphy Lee Harris, S Wray, N ...
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Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
- David C.H. Metzger,
- Imogen Porter,
- Brendan Mobley,
- Benjamin A. Sandkam,
- Lydia J.M. Fong,
- Andrew P. Anderson,
- and Judith E. Mank
Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
...David C.H. Metzger1, Imogen Porter1, Brendan Mobley2, Benjamin A. Sandkam3, Lydia J.M. Fong1, Andrew P. Anderson2 and Judith E. Mank1 1Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada; 2Biology Department, Reed ...
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Method: Incorporating valuable prior knowledge to improve deep learning prediction of genetic perturbation responses
- Xiuhao Fu,
- Chao Yang,
- Chunyan Cui,
- Aoyun Geng,
- Yidi Sun,
- Chao Zha,
- Feifei Cui,
- Leyi Wei,
- Quan Zou,
- Xin Gao,
- and Zilong Zhang
Genome Res. March 26, 2026 gr.281523.125; Published in Advance March 26, 2026, doi:10.1101/gr.281523.125
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Research: The spring-loaded genome: Nucleosome redistributions are widespread, transient, and DNA-directed
- Brittany S. Sexton,
- Denis Avey,
- Brooke R. Druliner,
- Justin A. Fincher,
- Daniel L. Vera,
- Daniel J. Grau,
- Mark L. Borowsky,
- Shobhit Gupta,
- Senthil B. Girimurugan,
- Eric Chicken,
- Jinfeng Zhang,
- William S. Noble,
- Fanxiu Zhu,
- Robert E. Kingston,
- and Jonathan H. Dennis
Genome Res. February 2014 24: 251-259; Published in Advance December 5, 2013, doi:10.1101/gr.160150.113
.... 2003. Chromatin remodeling in vivo: Evidence for a nucleosome sliding mechanism. Mol Cell 12: 13331340. Fincher J, Dennis JH. 2011. DNA sequence determinates of nucleosome position. In Epigenetics: A reference manual (ed. Craig JM, Wong NC), pp. 133142. Caister Academic Press, Norfolk, UK. Fincher JA ...
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Perspective: Can I be sued for that? Liability risk and the disclosure of clinically significant genetic research findings
- Amy L. McGuire,
- Bartha Maria Knoppers,
- Ma’n H. Zawati,
- and Ellen Wright Clayton
Genome Res. May 2014 24: 719-723; Published in Advance March 27, 2014, doi:10.1101/gr.170514.113
...for International Organizations of Medical Sciences (CIOMS). 2002. International ethical guidelines for biomedical research involving human subjects. http://www.cioms.ch/publications/ layout_guide2002.pdf. Dressler LG, Smolek S, Ponsaran R, Markey JM, Starks H, Gerson N, Lewis S, Press N, Juengst E, Wiesner GL ...
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ARTICLE: A second-generation linkage map of the bovine genome.
- S M Kappes,
- J W Keele,
- R T Stone,
- R A McGraw,
- T S Sonstegard,
- T P Smith,
- N L Lopez-Corrales,
- and C W Beattie
Genome Res. March 1997 7: 235-249; doi:10.1101/gr.7.3.235
....G. , Ede, A.J. , Pierson, C.A. , Montgomery, G.W. , Garmonsway, H.G. , Beattie, A.E. , Davies, K. , Maddox, J.F. , Kappes, S.M. , Stone, R.T. , Nguyen, T.C. , Penty, J.M. , Lord, E.A. , Broom, J.E. , Buitkamp, J. , Schwaiger, W. , Epplen, J.T. , Matthew, P. , Matthews, M.E. , Hulme, D.J. , Beh, K.J. , Mc ...
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ARTICLE: Approach to genotyping errors caused by nontemplated nucleotide addition by Taq DNA polymerase.
- J R Smith,
- J D Carpten,
- M J Brownstein,
- S Ghosh,
- V L Magnuson,
- D A Gilbert,
- J M Trent,
- and F S Collins
Genome Res. October 1995 5: 312-317; doi:10.1101/gr.5.3.312
...Trent, J.M M J J.D. Carpten J R DA Gilbert F Collins F S Collins Collins F S J.M. Trent D A M J Brownstein Smith, J.R Carpten Trent, JM Smith, J Collins, FS J M Trent J M J R Smith F S J D JM Trent Brownstein, M.J J D Carpten F.S. Collins Trent Carpten, J D V L Magnuson Collins, F F S, Collins J Carpten ...

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