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Method: Quantitative insertion-site sequencing (QIseq) for high throughput phenotyping of transposon mutants
- Iraad F. Bronner,
- Thomas D. Otto,
- Min Zhang,
- Kenneth Udenze,
- Chengqi Wang,
- Michael A. Quail,
- Rays H.Y. Jiang,
- John H. Adams,
- and Julian C. Rayner
Genome Res. July 2016 26: 980-989; Published in Advance May 10, 2016, doi:10.1101/gr.200279.115
..., Langlois AC, Khim N, Kim S, Duru V, Bouchier C, Ma L, et al. 2014. A molecular marker of artemisinin-resistant Plasmodium falciparum malaria. Nature 505: 5055. Ashley EA, Dhorda M, Fairhurst RM, Amaratunga C, Lim P, Suon S, Sreng S, Anderson JM,Mao S, Sam B, et al. 2014. Spread of artemisinin resistance ...
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Method: Integrative subcellular proteomic analysis allows accurate prediction of human disease-causing genes
- Li Zhao,
- Yiyun Chen,
- Amol Onkar Bajaj,
- Aiden Eblimit,
- Mingchu Xu,
- Zachry T. Soens,
- Feng Wang,
- Zhongqi Ge,
- Sung Yun Jung,
- Feng He,
- Yumei Li,
- Theodore G. Wensel,
- Jun Qin,
- and Rui Chen
Genome Res. May 2016 26: 660-669; Published in Advance February 24, 2016, doi:10.1101/gr.198911.115
..., and clinical applications. Am Soc Clin Oncol Educ Book: e504e510. Jones KA, Kim PD, Patel BB, Kelsen SG, Braverman A, Swinton DJ, Gafken PR, Jones LA, LaneWS, Neveu JM, et al. 2013. Immunodepletion plasma proteomics by tripleTOF 5600 and Orbitrap elite/LTQ-Orbitrap Velos/Q exactive mass spectrometers. J ...
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Research: Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia
- Sanchita Bhattacharya,
- Jian Li,
- Alexandra Sockell,
- Matthew J. Kan,
- Felice A. Bava,
- Shann-Ching Chen,
- María C. Ávila-Arcos,
- Xuhuai Ji,
- Emery Smith,
- Narges B. Asadi,
- Ralph S. Lachman,
- Hugo Y.K. Lam,
- Carlos D. Bustamante,
- Atul J. Butte,
- and Garry P. Nolan
Genome Res. April 2018 28: 423-431; Published in Advance March 22, 2018, doi:10.1101/gr.223693.117
..., Sikora M, Rasmussen M, Gravel S, Guilln S, Nekhrizov G, et al. 2013. Pulling out the 1%: whole- capture for the targeted enrichment of ancient DNA sequencing libraries. Am J Hum Genet 93: 852864. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP ...
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Research: Fitness benefits of loss of heterozygosity in Saccharomyces hybrids
- Samuel M. Lancaster,
- Celia Payen,
- Caiti Smukowski Heil,
- and Maitreya J. Dunham
Genome Res. October 2019 29: 1685-1692; Published in Advance September 23, 2019, doi:10.1101/gr.245605.118
.... 2002. Functional profiling of the Saccharomyces cerevisiae . Nature 418: 387391. doi:10.1038/nature00935 Gittelman RM, Schraiber JG, Vernot B, Mikacenic C, Wurfel MM, Akey JM. 2016. Archaic hominin admixture facilitated adaptation to out-of-Africa environments. Curr Biol 26: 33753382. doi:10.1016/j ...
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Research: Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program
- Vishnu Dileep,
- Ferhat Ay,
- Jiao Sima,
- Daniel L. Vera,
- William S. Noble,
- and David M. Gilbert
Genome Res. August 2015 25: 1104-1113; Published in Advance May 20, 2015, doi:10.1101/gr.183699.114
..., Babled A, Lapasset L, Milhavet O, Parrinello H, Dantec C, Marin J-M, Lemaitre J-M. 2012. Unraveling cell type-specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs. Nat Struct Mol Biol 19: 837844. Bridger JM, Boyle S, Kill IR, Bickmore WA. 2000 ...
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Method: Ancestry-agnostic estimation of DNA sample contamination from sequence reads
- Fan Zhang,
- Matthew Flickinger,
- Sarah A. Gagliano Taliun,
- InPSYght Psychiatric Genetics Consortium,
- Gonçalo R. Abecasis,
- Laura J. Scott,
- Steven A. McCaroll,
- Carlos N. Pato,
- Michael Boehnke,
- and Hyun Min Kang
Genome Res. February 2020 30: 185-194; Published in Advance January 24, 2020, doi:10.1101/gr.246934.118
..., Hetrick KN, Romm JM, Doheny KF, Abecasis GR, Boehnke M, Kang HM. 2012. Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data. Am J Hum Genet 91: 839848. doi:10.1016/j.ajhg.2012.09.004 Jun G, Wing MK, Abecasis GR, Kang HM. 2015. An efficient and scalable ...
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Research: Crosstalk between alternative polyadenylation and miRNAs in the regulation of protein translational efficiency
- Yonggui Fu,
- Liutao Chen,
- Chengyong Chen,
- Yutong Ge,
- Mingjing Kang,
- Zili Song,
- Jingwen Li,
- Yuchao Feng,
- Zhanfeng Huo,
- Guopei He,
- Mengmeng Hou,
- Shangwu Chen,
- and Anlong Xu
Genome Res. November 2018 28: 1656-1663; Published in Advance September 18, 2018, doi:10.1101/gr.231506.117
..., Rohl CA, Johnson JM, Babak T. 2012. A quantitative atlas of polyadenylation in five mammals. Genome Res 22: 11731183. Di Giammartino DC, Nishida K, Manley JL. 2011. Mechanisms and consequences of alternative polyadenylation. Mol Cell 43: 853866. Elkon R, Ugalde AP, Agami R. 2013. Alternative ...
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Method: Targeted genotyping of variable number tandem repeats with adVNTR
- Mehrdad Bakhtiari,
- Sharona Shleizer-Burko,
- Melissa Gymrek,
- Vikas Bansal,
- and Vineet Bafna
Genome Res. November 2018 28: 1709-1719; Published in Advance October 23, 2018, doi:10.1101/gr.235119.118
...445: 184187. 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. Brookes K. 2013. The VNTR in complex disorders: the forgotten polymorphisms? A functional way forward ...
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Method: Contamination detection in sequencing studies using the mitochondrial phylogeny
- Hansi Weissensteiner,
- Lukas Forer,
- Liane Fendt,
- Azin Kheirkhah,
- Antonio Salas,
- Florian Kronenberg,
- and Sebastian Schoenherr
Genome Res. February 2021 31: 309-316; Published in Advance January 15, 2021, doi:10.1101/gr.256545.119
...service and methods. Nat Genet 48: 12841287. doi:10.1038/ng.3656 Dayama G, Emery SB, Kidd JM, Mills RE. 2014. The genomic landscape of polymorphic human nuclear mitochondrial insertions. Nucleic Acids Res 42: 1264012649. doi:10.1093/nar/gku1038 Dickins B, Rebolledo-Jaramillo B, Su MS-W, Paul IM ...
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Method: Global quantification exposes abundant low-level off-target activity by base editors
- Ilana Buchumenski,
- Shalom Hillel Roth,
- Eli Kopel,
- Efrat Katsman,
- Ariel Feiglin,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. December 2021 31: 2354-2361; Published in Advance October 19, 2021, doi:10.1101/gr.275770.121
...-bio.GN]. Gehrke JM, Cervantes O, Clement MK, Wu Y, Zeng J, Bauer DE, Pinello L, Joung JK. 2018. An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities. Nat Biotechnol 36: 977982. doi:10.1038/nbt.4199 Gout J-F, Thomas WK, Smith Z, Okamoto K, Lynch M. 2013. Large-scale detection ...

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