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Perspective: The path to routine use of genomic biomarkers in the cancer clinic
- Paul C. Boutros
Genome Res. October 2015 25: 1508-1513; doi:10.1101/gr.191114.115
...are clonal and carry a high mutation burden. J Pathol 236: 201209. Baca SC, Prandi D, Lawrence MS, Mosquera JM, Romanel A, Drier Y, Park K, Kitabayashi N, MacDonald TY, Ghandi M, et al. 2013. Punctuated evolution of prostate cancer s. Cell 153: 666677. Bachtiary B, Boutros PC, Pintilie M, Shi W ...
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INSIGHT/OUTLOOK: Looking at Old Tools in New Ways: Using Knockouts as Congenics to Study QTLs
- Jeremy Peirce
Genome Res. September 1, 2001 11: 1469-1471; doi:10.1101/gr.206201
...R. , Yip P. , Kelley J. , Little D.P. , Strausberg R. , Koester H. , Cantor C.R. , et al. ( 2001 ) Proc. Natl. Acad. Sci. 98 : 581 584 . Caldarone B. , Saavedra C. , Tartaglia K. , Wehner J.M. , Dudek B.C. , Flaherty L. ( 1997 ) Nat. Genet. 17 : 335 337 . Darvasi A. , Soller M. ( 1995 ...
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Method: HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies
- Xian Fan,
- Mark Chaisson,
- Luay Nakhleh,
- and Ken Chen
Genome Res. May 2017 27: 793-800; Published in Advance January 19, 2017, doi:10.1101/gr.214767.116
.... Improving PacBio long read accuracy by short read alignment. PLoS One 7: e46679. Berlin K, Koren S, Chin CS, Drake JP, Landolin JM, Phillippy AM. 2015. Assembling large s with single-molecule sequencing and locality-sensitive hashing. Nat Biotechnol 33: 623630. Butler J, MacCallum I, Kleber M, Shlyakhter ...
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Research: Sumoylation of Rap1 mediates the recruitment of TFIID to promote transcription of ribosomal protein genes
- Pierre Chymkowitch,
- Aurélie Nguéa P,
- Håvard Aanes,
- Christian J. Koehler,
- Bernd Thiede,
- Susanne Lorenz,
- Leonardo A. Meza-Zepeda,
- Arne Klungland,
- and Jorrit M. Enserink
Genome Res. June 2015 25: 897-906; Published in Advance March 23, 2015, doi:10.1101/gr.185793.114
...in Saccharomyces cerevisiae replication and recombination defective mutants. Nat Genet 23: 8185. Chen X, Ding B, LeJeune D, Ruggiero C, Li S. 2009. Rpb1 sumoylation in response to UV radiation or transcriptional impairment in yeast. PLoS One 4: e5267. Chymkowitch P, Eldholm V, Lorenz S, Zimmermann C, Lindvall JM ...
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Method: Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates
- Christopher Faulk
Genome Res. June 2023 33: 948-956; Published in Advance July 13, 2023, doi:10.1101/gr.277743.123
....11.2365 Bewick AJ, Hofmeister BT, Lee K, Zhang X, Hall DW, Schmitz RJ. 2016. FASTmC: a suite of predictive models for nonreference-based estimations of DNA methylation. G3 (Bethesda) 6: 447452. doi:10.1534/g3.115.025668 Breton CV, Marsit CJ, Faustman E, Nadeau K, Goodrich JM, Dolinoy DC, Herbstman J, Holland N ...
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Method: Analytical validation of germline small variant detection using long-read HiFi genome sequencing
- Nathan Hammond,
- Linda Liao,
- Pun Wai Tong,
- Zena Ng,
- Thuy-Mi P. Nguyen,
- Chandler Ho,
- Yao Yang,
- and Stuart A. Scott
Genome Res. June 2025 35: 1391-1399; Published in Advance April 11, 2025, doi:10.1101/gr.278836.123
...Hon T, Mars K, Young G, Tsai YC, Karalius JW, Landolin JM, Maurer N, Kudrna D, Hardigan MA, Steiner CC, et al. 2020. Highly accurate long-read HiFi sequencing data for five complex s. Sci Data 7: 399. doi:10.1038/s41597-020-00743-4 Jennings L, Van Deerlin VM, Gulley ML, College of American ...
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Research: Identification of copy number variants in horses
- Ryan Doan,
- Noah Cohen,
- Jessica Harrington,
- Kylee Veazy,
- Rytis Juras,
- Gus Cothran,
- Molly E. McCue,
- Loren Skow,
- and Scott V. Dindot
Genome Res. May 2012 22: 899-907; Published in Advance March 1, 2012, doi:10.1101/gr.128991.111
...the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37: 113. Huang D-W, Sherman BT, Lempicki RA Huang D-W, Sherman BT, Lempicki RA. 2009b. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 4457. Kidd JM, Cooper GM, Donahue WF ...
ARTICLE: PCR with degenerate primers containing deoxyinosine fails with Pfu DNA polymerase.
- T Knittel and
- D Picard
Genome Res. May 1993 2: 346-347; doi:10.1101/gr.2.4.346
..... Batzer, M.A., , Carlton, J.E. , Deiniger. P.L. Batzer, M.A., Carlton, J.E. and Deiniger. P.L. 1991 . Enhanced evolutionary PCR using oligonucleotides with inosine at the 3 terminus. Nucleic Acids Res. 19 : 5081 . 5.. Lundberg, K.S., , Shoemaker, D.D. , Adams, M.W.W. , Short, J.M. , Sorge, J.A. , Mathur ...
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ARTICLES: Detection of mutation delta F508 in the cystic fibrosis gene using allele-specific PCR primers and time-resolved fluorometry.
- A Iitiä,
- E Høgdall,
- P Dahlen,
- P Hurskainen,
- J Vuust,
- and H Siitari
Genome Res. November 1992 2: 157-162; doi:10.1101/gr.2.2.157
....R., Elliott, R.B. and Smith. P.A. 1979 . Dried blood spot screening for cystic fibrosis in the newborn. Lancet i : 472 474 . 3.. Rommens, J.M., , Iannuzzi, M.C. , Kerem, B-S. , Drumm, M.L. , Melmer, G. , Dean, M. , Rozmahel, R. , Cole, J.L. , Kennedy, D. , Hidaka, N. , Zsiga, M. , Buchwald, M. , Riordan, J ...
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Resource: Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis
- Chirag Nepal,
- Yavor Hadzhiev,
- Christopher Previti,
- Vanja Haberle,
- Nan Li,
- Hazuki Takahashi,
- Ana Maria M. Suzuki,
- Ying Sheng,
- Rehab F. Abdelhamid,
- Santosh Anand,
- Jochen Gehrig,
- Altuna Akalin,
- Christel E.M. Kockx,
- Antoine A.J. van der Sloot,
- Wilfred F.J. van IJcken,
- Olivier Armant,
- Sepand Rastegar,
- Craig Watson,
- Uwe Strähle,
- Elia Stupka,
- Piero Carninci,
- Boris Lenhard,
- and Ferenc Müller
Genome Res. November 2013 23: 1938-1950; Published in Advance September 3, 2013, doi:10.1101/gr.153692.112

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