Johnson, J.G., Spurbeck, R.R., Sandhu, S.K. and Matson, J.S. (2014a). Genome Sequence of Klebsiella pneumoniae Respiratory Isolate IA565. Genome Announcements, [online] 2(5). Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4161749/ [Accessed 13 Nov. 2019].
Johnson, J.G., Spurbeck, R.R., Sandhu, S.K. and Matson, J.S. (2014b). Genome Sequence of Klebsiella pneumoniae Urinary Tract Isolate Top52. Genome Announcements, [online] 2(4). Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4082006/ [Accessed 13 Nov. 2019].
Bennett, C.W., Berchem, G., Kim, Y.J. and El-Khoury, V. (2016). Cell-free DNA and next-generation sequencing in the service of personalized medicine for lung cancer. Oncotarget, [online] 7(43). Available at: http://www.oncotarget.com/index.php?journal=oncotarget&page=article&op=view&path%5b%5d=11717 [Accessed 13 Nov. 2019].
Bolognesi, C., Forcato, C., Buson, G., Fontana, F., Mangano, C., Doffini, A., Sero, V., Lanzellotto, R., Signorini, G., Calanca, A., Sergio, M., Romano, R., Gianni, S., Medoro, G., Giorgini, G., Morreau, H., Barberis, M., Corver, W.E. and Manaresi, N. (2016). Digital Sorting of Pure Cell Populations Enables Unambiguous Genetic Analysis of Heterogeneous Formalin-Fixed Paraffin-Embedded Tumors by Next Generation Sequencing. Scientific Reports, [online] 6(1). Available at: https://www.nature.com/articles/srep20944 [Accessed 13 Nov. 2019].
Girotti, M.R., Gremel, G., Lee, R., Galvani, E., Rothwell, D., Viros, A., Mandal, A.K., Lim, K.H.J., Saturno, G., Furney, S.J., Baenke, F., Pedersen, M., Rogan, J., Swan, J., Smith, M., Fusi, A., Oudit, D., Dhomen, N., Brady, G., Lorigan, P., Dive, C. and Marais, R. (2016). Application of Sequencing, Liquid Biopsies, and Patient-Derived Xenografts for Personalized Medicine in Melanoma. Cancer discovery, [online] 6(3), pp.286–99. Available at: https://www.ncbi.nlm.nih.gov/pubmed/26715644 [Accessed 13 Nov. 2019].
Gremel, G., Lee, R.J., Girotti, M.R., Mandal, A.K., Valpione, S., Garner, G., Ayub, M., Wood, S., Rothwell, D.G., Fusi, A., Wallace, A., Brady, G., Dive, C., Dhomen, N., Lorigan, P. and Marais, R. (2016). Distinct subclonal tumour responses to therapy revealed by circulating cell-free DNA. Annals of Oncology, [online] 27(10), pp.1959–1965. Available at: https://academic.oup.com/annonc/article/27/10/1959/2389057 [Accessed 13 Nov. 2019].
Ricci, D.P., Melfi, M.D., Lasker, K., Dill, D.L., McAdams, H.H. and Shapiro, L. (2016). Cell cycle progression inCaulobacterrequires a nucleoid-associated protein with high AT sequence recognition. Proceedings of the National Academy of Sciences, [online] 113(40), pp.E5952–E5961. Available at: http://www.pnas.org/content/113/40/E5952.abstract [Accessed 13 Nov. 2019].
Sundaram, A.Y.M., Hughes, T., Biondi, S., Bolduc, N., Bowman, S.K., Camilli, A., Chew, Y.C., Couture, C., Farmer, A., Jerome, J.P., Lazinski, D.W., McUsic, A., Peng, X., Shazand, K., Xu, F., Lyle, R. and Gilfillan, G.D. (2016). A comparative study of ChIP-seq sequencing library preparation methods. BMC Genomics, [online] 17(1). Available at: https://bit.ly/34Vv61F [Accessed 13 Nov. 2019].
Williamson, S.C., Metcalf, R.L., Trapani, F., Mohan, S., Antonello, J., Abbott, B., Leong, H.S., Chester, C.P.E., Simms, N., Polanski, R., Nonaka, D., Priest, L., Fusi, A., Carlsson, F., Carlsson, A., Hendrix, M.J.C., Seftor, R.E.B., Seftor, E.A., Rothwell, D.G., Hughes, A., Hicks, J., Miller, C., Kuhn, P., Brady, G., Simpson, K.L., Blackhall, F.H. and Dive, C. (2016). Vasculogenic mimicry in small cell lung cancer. Nature Communications, [online] 7(1). Available at: https://www.nature.com/articles/ncomms13322 [Accessed 13 Nov. 2019].
Baranzoni, G.M., Fratamico, P.M., Kim, G.-H., Reichenberger, E.R., Funk, J.A., Manning, S.D. and Bosilevac, J.M. (2017). Genome Sequences of 34 Shiga Toxin-Producing Escherichia coli Isolates from Swine and Other Sources. Genome Announcements, [online] 5(44). Available at: http://genomea.asm.org/content/5/44/e01214-17.full.pdf+html [Accessed 13 Nov. 2019].
Dong, X., Zhang, L., Milholland, B., Lee, M., Maslov, A.Y., Wang, T. and Vijg, J. (2017). Accurate identification of single-nucleotide variants in whole-genome-amplified single cells. Nature Methods, [online] 14(5), pp.491–493. Available at: https://www.nature.com/articles/nmeth.4227 [Accessed 13 Nov. 2019].
Metsky, H.C., Matranga, C.B., Wohl, S., Schaffner, S.F., Freije, C.A., Winnicki, S.M., West, K., Qu, J., Baniecki, M.L., Gladden-Young, A., Lin, A.E., Tomkins-Tinch, C.H., Ye, S.H., Park, D.J., Luo, C.Y., Barnes, K.G., Shah, R.R., Chak, B., Barbosa-Lima, G., Delatorre, E., Vieira, Y.R., Paul, L.M., Tan, A.L., Barcellona, C.M., Porcelli, M.C., Vasquez, C., Cannons, A.C., Cone, M.R., Hogan, K.N., Kopp, E.W., Anzinger, J.J., Garcia, K.F., Parham, L.A., Ramírez, R.M.G., Montoya, M.C.M., Rojas, D.P., Brown, C.M., Hennigan, S., Sabina, B., Scotland, S., Gangavarapu, K., Grubaugh, N.D., Oliveira, G., Robles-Sikisaka, R., Rambaut, A., Gehrke, L., Smole, S., Halloran, M.E., Villar, L., Mattar, S., Lorenzana, I., Cerbino-Neto, J., Valim, C., Degrave, W., Bozza, P.T., Gnirke, A., Andersen, K.G., Isern, S., Michael, S.F., Bozza, F.A., Souza, T.M.L., Bosch, I., Yozwiak, N.L., MacInnis, B.L. and Sabeti, P.C. (2017). Zika virus evolution and spread in the Americas. Nature, [online] 546(7658), pp.411–415. Available at: https://www.nature.com/articles/nature22402.pdf [Accessed 13 Nov. 2019].
Milholland, B., Dong, X., Zhang, L., Hao, X., Suh, Y. and Vijg, J. (2017). Differences between germline and somatic mutation rates in humans and mice. Nature Communications, [online] 8(1). Available at: https://www.nature.com/articles/ncomms15183.pdf [Accessed 13 Nov. 2019].
Cavalcanti, G.S., Shukla, P., Morris, M., Ribeiro, B., Foley, M., Doane, M.P., Thompson, C.C., Edwards, M.S., Dinsdale, E.A. and Thompson, F.L. (2018). Rhodoliths holobionts in a changing ocean: host-microbes interactions mediate coralline algae resilience under ocean acidification. BMC Genomics, [online] 19(1). Available at: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5064-4 [Accessed 13 Nov. 2019].
Gan, H., Serra-Cardona, A., Hua, X., Zhou, H., Labib, K., Yu, C. and Zhang, Z. (2018). The Mcm2-Ctf4-Polα Axis Facilitates Parental Histone H3-H4 Transfer to Lagging Strands. Molecular Cell, [online] 72(1), pp.140-151.e3. Available at: https://www.sciencedirect.com/science/article/pii/S1097276518307408 [Accessed 13 Nov. 2019].
Khanshour, A.M., Kou, I., Fan, Y., Einarsdottir, E., Makki, N., Kidane, Y.H., Kere, J., Grauers, A., Johnson, T.A., Paria, N., Patel, C., Singhania, R., Kamiya, N., Takeda, K., Otomo, N., Watanabe, K., Luk, K.D.K., Cheung, K.M.C., Herring, J.A., Rios, J.J., Ahituv, N., Gerdhem, P., Gurnett, C.A., Song, Y.-Q., Ikegawa, S. and Wise, C.A. (2018). Genome-wide meta-analysis and replication studies in multiple ethnicities identify novel adolescent idiopathic scoliosis susceptibility loci. Human Molecular Genetics, [online] 27(22), pp.3986–3998. Available at: https://academic.oup.com/hmg/advance-article-abstract/doi/10.1093/hmg/ddy306/5079034?redirectedFrom=fulltext [Accessed 13 Nov. 2019].
Ma, S., Hsieh, Y.-P., Ma, J. and Lu, C. (2018). Low-input and multiplexed microfluidic assay reveals epigenomic variation across cerebellum and prefrontal cortex. Science Advances, [online] 4(4), p.eaar8187. Available at: http://advances.sciencemag.org/content/4/4/eaar8187 [Accessed 13 Nov. 2019].
Parker, H., Carr, L., Syeda, S., Bryant, D. and Strefford, J.C. (2018). Characterization of Somatically-Acquired Copy Number Alterations in Chronic Lymphocytic Leukaemia Using Shallow Whole Genome Sequencing. Methods in Molecular Biology, [online] pp.327–353. Available at: https://link.springer.com/protocol/10.1007/978-1-4939-8876-1_23#citeas [Accessed 13 Nov. 2019].
Scheper, W., Kelderman, S., Fanchi, L.F., Linnemann, C., Bendle, G., de Rooij, M.A.J., Hirt, C., Mezzadra, R., Slagter, M., Dijkstra, K., Kluin, R.J.C., Snaebjornsson, P., Milne, K., Nelson, B.H., Zijlmans, H., Kenter, G., Voest, E.E., Haanen, J.B.A.G. and Schumacher, T.N. (2018). Low and variable tumor reactivity of the intratumoral TCR repertoire in human cancers. Nature Medicine, [online] 25(1), pp.89–94. Available at: https://www.nature.com/articles/s41591-018-0266-5 [Accessed 13 Nov. 2019].
Seehawer, M., Heinzmann, F., D’Artista, L., Harbig, J., Roux, P.-F., Hoenicke, L., Dang, H., Klotz, S., Robinson, L., Doré, G., Rozenblum, N., Kang, T.-W., Chawla, R., Buch, T., Vucur, M., Roth, M., Zuber, J., Luedde, T., Sipos, B., Longerich, T., Heikenwälder, M., Wang, X.W., Bischof, O. and Zender, L. (2018). Necroptosis microenvironment directs lineage commitment in liver cancer. Nature, [online] 562(7725), pp.69–75. Available at: https://www.nature.com/articles/s41586-018-0519-y [Accessed 13 Nov. 2019].
Wylie, K.M., Wylie, T.N., Buller, R., Herter, B., Cannella, M.T. and Storch, G.A. (2018). Detection of Viruses in Clinical Samples by Use of Metagenomic Sequencing and Targeted Sequence Capture. Journal of Clinical Microbiology, [online] 56(12). Available at: https://jcm.asm.org/content/early/2018/09/14/JCM.01123-18 [Accessed 13 Nov. 2019].
Xing, J. (2018). Epigenetic Profiling of Active Enhancers in Mouse Retinal Ganglion Cells. [online] OpenCommons@UConn. Available at: https://opencommons.uconn.edu/gs_theses/1268/ [Accessed 13 Nov. 2019].
Ciucci, T., Vacchio, M.S., Gao, Y., Tomassoni Ardori, F., Candia, J., Mehta, M., Zhao, Y., Tran, B., Pepper, M., Tessarollo, L., McGavern, D.B. and Bosselut, R. (2019). The Emergence and Functional Fitness of Memory CD4+ T Cells Require the Transcription Factor Thpok. Immunity, [online] 50(1), pp.91-105.e4. Available at: https://www.sciencedirect.com/science/article/abs/pii/S1074761318305673 [Accessed 13 Nov. 2019].
Genga, R.M.J., Kernfeld, E.M., Parsi, K.M., Parsons, T.J., Ziller, M.J. and Maehr, R. (2019). Single-Cell RNA-Sequencing-Based CRISPRi Screening Resolves Molecular Drivers of Early Human Endoderm Development. Cell Reports, [online] 27(3), pp.708-718.e10. Available at: https://www.sciencedirect.com/science/article/pii/S2211124719304061 [Accessed 13 Nov. 2019].
Grace, H.E., Galdun, P., Lesnefsky, E.J., West, F.D. and Iyer, S. (2019). mRNA Reprogramming of T8993G Leigh’s Syndrome Fibroblast Cells to Create Induced Pluripotent Stem Cell Models for Mitochondrial Disorders. Stem Cells and Development, [online] 28(13), pp.846–859. Available at: https://www.liebertpub.com/doi/abs/10.1089/scd.2019.0045 [Accessed 13 Nov. 2019].
Guo, Y.E., Manteiga, J.C., Henninger, J.E., Sabari, B.R., Dall’Agnese, A., Hannett, N.M., Spille, J.-H., Afeyan, L.K., Zamudio, A.V., Shrinivas, K., Abraham, B.J., Boija, A., Decker, T.-M., Rimel, J.K., Fant, C.B., Lee, T.I., Cisse, I.I., Sharp, P.A., Taatjes, D.J. and Young, R.A. (2019). Pol II phosphorylation regulates a switch between transcriptional and splicing condensates. Nature, [online] 572(7770), pp.543–548. Available at: https://www.nature.com/articles/s41586-019-1464-0 [Accessed 13 Nov. 2019].
Jenkins, M.M., Almli, L.M., Pangilinan, F., Chong, J.X., Blue, E.E., Shapira, S.K., White, J., McGoldrick, D., Smith, J.D., Mullikin, J.C., Bean, C.J., Nembhard, W.N., Lou, X.-Y., Shaw, G.M., Romitti, P.A., Keppler-Noreuil, K., Yazdy, M.M., Kay, D.M., Carter, T.C., Olshan, A.F., Moore, K.J., Nascone-Yoder, N., Finnell, R.H., Lupo, P.J., Feldkamp, M.L., NISC Comparative Sequencing Program, University of Washington Center for Mendelian Genomics, Nickerson, D.A., Bamshad, M.J., Brody, L.C., Reefhuis, J. and National Birth Defects Prevention Study (2019). Exome sequencing of family trios from the National Birth Defects Prevention Study: Tapping into a rich resource of genetic and environmental data. Birth defects research, [online] p.10.1002/bdr2.1554. Available at: https://www.ncbi.nlm.nih.gov/pubmed/31328417 [Accessed 13 Nov. 2019].
Jiang, Q., Isquith, J., Zipeto, M.A., Diep, R.H., Pham, J., Delos Santos, N., Reynoso, E., Chau, J., Leu, H., Lazzari, E., Melese, E., Ma, W., Fang, R., Minden, M., Morris, S., Ren, B., Pineda, G., Holm, F. and Jamieson, C. (2019). Hyper-Editing of Cell-Cycle Regulatory and Tumor Suppressor RNA Promotes Malignant Progenitor Propagation. Cancer Cell, [online] 35(1), pp.81-94.e7. Available at: https://www.sciencedirect.com/science/article/abs/pii/S1535610818305385 [Accessed 13 Nov. 2019].
Kang, M., Cho, E., Jang, J., Lee, J., Jeon, Y., Jeong, B.C., Seo, S.I., Jeon, S.S., Lee, H.M., Choi, H.Y. and Jeon, H.G. (2019). Genomic analysis of Korean patients with advanced prostate cancer by use of a comprehensive next-generation sequencing panel and low-coverage, whole-genome sequencing. Investigative and Clinical Urology, [online] 60(4), p.227. Available at: https://synapse.koreamed.org/DOIx.php?id=10.4111/icu.2019.60.4.227 [Accessed 13 Nov. 2019].
Parry, M.A., Srivastava, S., Ali, A., Cannistraci, A., Antonello, J., Barros-Silva, J.D., Ubertini, V., Ramani, V., Lau, M., Shanks, J., Nonaka, D., Oliveira, P., Hambrock, T., Leong, H.S., Dhomen, N., Miller, C., Brady, G., Dive, C., Clarke, N.W., Marais, R. and Baena, E. (2019). Genomic Evaluation of Multiparametric Magnetic Resonance Imaging-visible and -nonvisible Lesions in Clinically Localised Prostate Cancer. European Urology Oncology, [online] 2(1), pp.1–11. Available at: https://www.sciencedirect.com/science/article/pii/S258893111830124X [Accessed 13 Nov. 2019].
Pastore, A., Gaiti, F., Lu, S.X., Brand, R.M., Kulm, S., Chaligne, R., Gu, H., Huang, K.Y., Stamenova, E.K., Béguelin, W., Jiang, Y., Schulman, R.C., Kim, K.-T., Alonso, A., Allan, J.N., Furman, R.R., Gnirke, A., Wu, C.J., Melnick, A.M., Meissner, A., Bernstein, B.E., Abdel-Wahab, O. and Landau, D.A. (2019). Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL. Nature Communications, [online] 10(1). Available at: https://www.nature.com/articles/s41467-019-09645-5 [Accessed 13 Nov. 2019].
Pérez Castro, S., Cleland, E.E., Wagner, R., Sawad, R.A. and Lipson, D.A. (2019). Soil microbial responses to drought and exotic plants shift carbon metabolism. The ISME Journal, [online] 13(7), pp.1776–1787. Available at: https://www.nature.com/articles/s41396-019-0389-9 [Accessed 13 Nov. 2019].
Rothwell, D.G., Ayub, M., Cook, N., Thistlethwaite, F., Carter, L., Dean, E., Smith, N., Villa, S., Dransfield, J., Clipson, A., White, D., Nessa, K., Ferdous, S., Howell, M., Gupta, A., Kilerci, B., Mohan, S., Frese, K., Gulati, S., Miller, C., Jordan, A., Eaton, H., Hickson, N., O’Brien, C., Graham, D., Kelly, C., Aruketty, S., Metcalf, R., Chiramel, J., Tinsley, N., Vickers, A.J., Kurup, R., Frost, H., Stevenson, J., Southam, S., Landers, D., Wallace, A., Marais, R., Hughes, A.M., Brady, G., Dive, C. and Krebs, M.G. (2019). Utility of ctDNA to support patient selection for early phase clinical trials: the TARGET study. Nature Medicine, [online] 25(5), pp.738–743. Available at: https://swiftbiosci.com/wp-content/uploads/2019/08/s41591-019-0380-z.pdf [Accessed 13 Nov. 2019].
Song, Y., van den Berg, P.R., Markoulaki, S., Soldner, F., Dall’Agnese, A., Henninger, J.E., Drotar, J., Rosenau, N., Cohen, M.A., Young, R.A., Semrau, S., Stelzer, Y. and Jaenisch, R. (2019). Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs. Molecular Cell, [online] 75(5), pp.905-920.e6. Available at: https://www.sciencedirect.com/science/article/abs/pii/S1097276519305027 [Accessed 13 Nov. 2019].
Zhang, R., Qi, C., Hu, Y., Shan, Y., Hsieh, Y.-P., Xu, F., Lu, G., Dai, J., Gupta, M., Cui, M., Peng, L., Yang, J., Xue, Q., Chen-Liang, R., Chen, K., Zhang, Y., Fung-Leung, W.-P., Mora, J.R., Li, L., Morse, H.C., Ozato, K., Heeger, P.S. and Xiong, H. (2019a). T follicular helper cells restricted by IRF8 contribute to T cell-mediated inflammation. Journal of Autoimmunity, [online] 96, pp.113–122. Available at: https://www.sciencedirect.com/science/article/pii/S0896841118302877?via%3Dihub [Accessed 13 Nov. 2019].
Zhang, Y., Li, T., Preissl, S., Amaral, M.L., Grinstein, J.D., Farah, E.N., Destici, E., Qiu, Y., Hu, R., Lee, A.Y., Chee, S., Ma, K., Ye, Z., Zhu, Q., Huang, H., Fang, R., Yu, L., Izpisua Belmonte, J.C., Wu, J., Evans, S.M., Chi, N.C. and Ren, B. (2019b). Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells. Nature Genetics, [online] 51(9), pp.1380–1388. Available at: https://www.nature.com/articles/s41588-019-0479-7 [Accessed 13 Nov. 2019].