Items where Subject is "next generation sequencing"

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Amin, M. R., Skiena, S., Schatz, M. C. (October 2016) NanoBLASTer: Fast alignment and characterization of Oxford Nanopore single molecule sequencing reads. 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS).

Anaparthy, N., Ho, Y. J., Martelotto, L., Hammell, M., Hicks, J. (January 2019) Single-Cell Applications of Next-Generation Sequencing. Cold Spring Harb Perspect Med, 9 (10). ISSN 2157-1422

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Baslan, T., Hicks, J. (July 2014) Single cell sequencing approaches for complex biological systems. Curr Opin Genet Dev, 26c. pp. 59-65. ISSN 0959-437x

Baslan, T., Kendall, J., Rodgers, L., Cox, H., Riggs, M., Stepansky, A., Troge, J., Ravi, K., Esposito, D., Lakshmi, B., Wigler, M., Navin, N., Hicks, J. (March 2016) Corrigendum: Genome-wide copy number analysis of single cells. Nat Protoc, 11 (3). p. 616. ISSN 1750-2799

Baslan, T., Kendall, J., Ward, B., Cox, H., Leotta, A., Rodgers, L., Riggs, M., D'Italia, S., Sun, G., Yong, M., Miskimen, K., Gilmore, H., Saborowski, M., Dimitrova, N., Krasnitz, A., Harris, L., Wigler, M., Hicks, J. (May 2015) Optimizing sparse sequencing of single cells for highly multiplex copy number profiling. Genome Research, 25 (5). pp. 714-724. ISSN 1088-9051

Batut, P., Gingeras, T. R. (2013) RAMPAGE: Promoter activity profiling by paired-end sequencing of 5'-complete cDNAs. Current Protocols in Molecular Biology (SUPPL). Unit25B. ISSN 19343639 (ISSN)

Blood, P. D., Marcus, S., Schatz, M. C. (July 2014) Large-scale sequencing and assembly of cereal genomes using blacklight. Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment. Article number 20.

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Chen, X., Sun, Y. C., Church, G. M., Lee, J. H., Zador, A. M. (February 2018) Efficient in situ barcode sequencing using padlock probe-based BaristaSeq. Nucleic Acids Res, 46 (4). e22. ISSN 0305-1048

Chipman, A. D., Ferrier, D. E. K., Brena, C., Qu, J., Hughes, D. S. T., Schröder, R., Torres-Oliva, M., Znassi, N., Jiang, H., Almeida, F. C., Alonso, C. R., Apostolou, Z., Aqrawi, P., Arthur, W., Barna, J. C. J., Blankenburg, K. P., Brites, D., Capella-Gutiérrez, S., Coyle, M., Dearden, P. K., Du Pasquier, L., Duncan, E. J., Ebert, D., Eibner, C., Erikson, G., Evans, P. D., Extavour, C. G., Francisco, L., Gabaldón, T., Gillis, W. J., Goodwin-Horn, E. A., Green, J. E., Griffiths-Jones, S., Grimmelikhuijzen, C. J. P., Gubbala, S., Guigó, R., Han, Y., Hauser, F., Havlak, P., Hayden, L., Helbing, S., Holder, M., Hui, J. H. L., Hunn, J. P., Hunnekuhl, V. S., Jackson, L. R., Javaid, M., Jhangiani, S. N., Jiggins, F. M., Jones, T. E., Kaiser, T. S., Kalra, D., Kenny, N. J., Korchina, V., Kovar, C. L., Kraus, F. B., Lapraz, F., Lee, S. L., Lv, J., Mandapat, C., Manning, G., Mariotti, M., Mata, R., Mathew, T., Neumann, T., Newsham, I., Ngo, D. N., Ninova, M., Okwuonu, G., Ongeri, F., Palmer, W. J., Patil, S., Patraquim, P., Pham, C., Pu, L. L., Putman, N. H., Rabouille, C., Ramos, O. M., Rhodes, A. C., Robertson, H. E., Robertson, H. M., Ronshaugen, M., Rozas, J., Saada, N., Sánchez-Gracia, A., Scherer, S. E., Schurko, A. M., Siggens, K. W., Simmons, D. N., Stief, A., Stolle, E., Telford, M. J., Tessmar-Raible, K., Thornton, R., van der Zee, M., von Haeseler, A., Williams, J. M., Willis, J. H., Wu, Y., Zou, X. (2014) The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima. PLoS Biology, 12 (11).

Cho, May T, Gholami, Sepideh, Gui, Dorina, Tejaswi, Sooraj L, Fananapazir, Ghaneh, Abi-Jaoudeh, Nadine, Jutric, Zeljka, Samarasena, Jason B, Li, Xiaodong, Valerin, Jennifer B, Mercer, Jacob, Dayyani, Farshid (January 2022) Optimizing the Diagnosis and Biomarker Testing for Patients with Intrahepatic Cholangiocarcinoma: A Multidisciplinary Approach. Cancers, 14 (2). p. 392. ISSN 2072-6694

Consortium, 1000 Genomes Project (September 2015) A global reference for human genetic variation. Nature, 526 (7571). pp. 68-74. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Couger, M. B., Pipes, L., Squina, F., Prade, R., Siepel, A., Palermo, R., Katze, M. G., Mason, C. E., Blood, P. D. (September 2014) Enabling large-scale next-generation sequence assembly with Blacklight. Concurrency and computation : practice & experience, 26 (13). pp. 2157-2166. ISSN 1532-0626 (Print)1532-0626

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Erlich, Yaniv, Gordon, Assaf, Brand, Michael, Hannon, Gregory J, Mitra, Partha P (September 2009) Compressed Genotyping. IEEE Transactions on Information Theory. (Submitted)

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Fang, H., Bergmann, E. A., Arora, K., Vacic, V., Zody, M. C., Iossifov, I., O'Rawe, J. A., Wu, Y., Jimenez Barron, L. T., Rosenbaum, J., Ronemus, M., Lee, Y. H., Wang, Z., Dikoglu, E., Jobanputra, V., Lyon, G. J., Wigler, M., Schatz, M. C., Narzisi, G. (December 2016) Indel variant analysis of short-read sequencing data with Scalpel. Nat Protoc, 11 (12). pp. 2529-2548. ISSN 1750-2799 (Electronic)1750-2799 (Linking)

Fang, Han (July 2013) Whole Genome Sequencing in support of Wellness and Health Maintenance. Journal Club. (Unpublished)

Freedman, A. H., Schweizer, R. M., Ortega-Del Vecchyo, D., Han, E., Davis, B. W., Gronau, I., Silva, P. M., Galaverni, M., Fan, Z., Marx, P., Lorente-Galdos, B., Ramirez, O., Hormozdiari, F., Alkan, C., Vila, C., Squire, K., Geffen, E., Kusak, J., Boyko, A. R., Parker, H. G., Lee, C., Tadigotla, V., Siepel, A., Bustamante, C. D., Harkins, T. T., Nelson, S. F., Marques-Bonet, T., Ostrander, E. A., Wayne, R. K., Novembre, J. (March 2016) Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs. PLoS Genet, 12 (3). e1005851. ISSN 1553-7390

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Ganapathy, G., Howard, J. T., Ward, J. M., Li, J., Li, B., Li, Y., Xiong, Y., Zhang, Y., Zhou, S., Schwartz, D. C., Schatz, M., Aboukhalil, R., Fedrigo, O., Bukovnik, L., Wang, T., Wray, G., Rasolonjatovo, I., Winer, R., Knight, J. R., Koren, S., Warren, W. C., Zhang, G., Phillippy, A. M., Jarvis, E. D. (July 2014) High-coverage sequencing and annotated assemblies of the budgerigar genome. Gigascience, 3. p. 11. ISSN 2047-217x

Goodwin, S., Gade, A. M., Byrom, M., Herrera, B., Spears, C., Anslyn, E. V., Ellington, A. D. (March 2015) Next-Generation Sequencing as Input for Chemometrics in Differential Sensing Routines. Angew Chem Int Ed Engl, 54 (21). pp. 6339-6342. ISSN 1433-7851

Goodwin, S., Gurtowski, J., Ethe-Sayers, S., Deshpande, P., Schatz, M. C., McCombie, W. R. (November 2015) Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res, 25 (11). pp. 1750-1756. ISSN 1088-9051

Goodwin, S., McPherson, J. D., McCombie, W. R. (May 2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet, 17 (6). pp. 333-51. ISSN 1471-0064 (Electronic)1471-0056 (Linking)

Goodwin, S., Wappel, R., McCombie, W. R. (July 2017) 1D Genome Sequencing on the Oxford Nanopore MinION. Curr Protoc Hum Genet, 94. 18.11.1-18.11.14. ISSN 1934-8258

Grativol, C., Regulski, M., Bertalan, M., McCombie, W. R., da Silva, F. R., Zerlotini Neto, A., Vicentini, R., Farinelli, L., Hemerly, A. S., Martienssen, R. A., Ferreira, P. C. G. (July 2014) Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum. Plant Journal, 79 (1). pp. 162-172. ISSN 09607412

Guo, Y., Ding, X., Shen, Y., Lyon, G. J., Wang, K. (September 2015) SeqMule: automated pipeline for analysis of human exome/genome sequencing data. Sci Rep, 5. p. 14283. ISSN 2045-2322 (Electronic)2045-2322 (Linking)

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Hicks, J. B. (November 2012) Talk from Jim Hicks at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

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Ip, C. L., Loose, M., Tyson, J. R., de Cesare, M., Brown, B. L., Jain, M., Leggett, R. M., Eccles, D. A., Zalunin, V., Urban, J. M., Piazza, P., Bowden, R. J., Paten, B., Mwaigwisya, S., Batty, E. M., Simpson, J. T., Snutch, T. P., Birney, E., Buck, D., Goodwin, S., Jansen, H. J., O'Grady, J., Olsen, H. E. (October 2015) MinION Analysis and Reference Consortium: Phase 1 data release and analysis. F1000Res, 4. p. 1075. ISSN 2046-1402 (Electronic)2046-1402 (Linking)

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Jansen, S., van der Werf, I. M., Innes, A. M., Afenjar, A., Agrawal, P. B., Anderson, I. J., Atwal, P. S., van Binsbergen, E., van den Boogaard, M. J., Castiglia, L., Coban-Akdemir, Z. H., van Dijck, A., Doummar, D., van Eerde, A. M., van Essen, A. J., van Gassen, K. L., Guillen Sacoto, M. J., van Haelst, M. M., Iossifov, I., Jackson, J. L., Judd, E., Kaiwar, C., Keren, B., Klee, E. W., Klein Wassink-Ruiter, J. S., Meuwissen, M. E., Monaghan, K. G., de Munnik, S. A., Nava, C., Ockeloen, C. W., Pettinato, R., Racher, H., Rinne, T., Romano, C., Sanders, V. R., Schnur, R. E., Smeets, E. J., Stegmann, A. P. A., Stray-Pedersen, A., Sweetser, D. A., Terhal, P. A., Tveten, K., VanNoy, G. E., de Vries, P. F., Waxler, J. L., Willing, M., Pfundt, R., Veltman, J. A., Kooy, R. F., Vissers, Lelm, de Vries, B. B. A. (January 2019) De novo variants in FBXO11 cause a syndromic form of intellectual disability with behavioral problems and dysmorphisms. Eur J Hum Genet, 27 (5). pp. 738-746. ISSN 1018-4813

Jiao, Y., Lee, Y. K., Gladman, N., Chopra, R., Christensen, S. A., Regulski, M., Burow, G., Hayes, C., Burke, J., Ware, D., Xin, Z. (February 2018) MSD1 regulates pedicellate spikelet fertility in sorghum through the jasmonic acid pathway. Nat Commun, 9 (1). p. 822. ISSN 2041-1723

Jiao, Y. P., Burow, G., Gladman, N., Acosta-Martinez, V., Chen, J. P., Burke, J., Ware, D., Xin, Z. G. (January 2018) Efficient Identification of Causal Mutations through Sequencing of Bulked F-2 from Two Allelic Bloomless Mutants of Sorghum bicolor. Frontiers in Plant Science, 8. p. 2267. ISSN 1664-462X

Judge, Sean J, Cho, May, Gholami, Sepideh (November 2022) Genomic Predictors of Recurrence Patterns After Complete Resection of Colorectal Liver Metastases and Adjuvant Hepatic Artery Infusion Chemotherapy by Narayan et al. Annals of Surgical Oncology, 29 (12). pp. 7246-7247. ISSN 1068-9265

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Kamalakaran, Sitharthan, Varadan, Vinay, Janevski, Angel, Banerjee, Nilanjana, Tuck, David, McCombie, Richard, Dimitrova, Nevenka, Harris, Lyndsay N. (August 2013) Translating Next Generation Sequencing to practice: opportunities and necessary steps. Molecular Oncology, 7 (4). pp. 743-755. ISSN 1574-7891

Kebschull, J. M., Zador, A. M. (December 2015) Sources of PCR-induced distortions in high-throughput sequencing data sets. Nucleic Acids Res, 43 (21). e143. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

Kinney, J. B. (November 2011) Talk from Justin Kinney at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Kumar, V., Rosenbaum, J., Wang, Z., Forcier, T., Ronemus, M., Wigler, M., Levy, D. (January 2018) Partial bisulfite conversion for unique template sequencing. Nucleic Acids Res, 46 (2). e10. ISSN 0305-1048

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Liu, Lei, Chen, Richelle, Fugina, Christopher John, Siegel, Ben, Jackson, David (April 2021) High-Throughput and Low-Cost Genotyping Method for Plant Genome Editing. Curr Protoc, 1 (4). e100. ISSN 2691-1299

Loman, N., Goodwin, S., Jansen, H., Loose, M. (October 2015) A disruptive sequencer meets disruptive publishing. F1000Res, 4. p. 1074. ISSN 2046-1402 (Electronic)2046-1402 (Linking)

Luo, M. C., Gu, Y. Q., You, F. M., Deal, K. R., Ma, Y., Hu, Y., Huo, N., Wang, Y., Wang, J., Chen, S., Jorgensen, C. M., Zhang, Y., McGuire, P. E., Pasternak, S., Stein, J. C., Ware, D., Kramer, M., McCombie, W. R., Kianian, S. F., Martis, M. M., Mayer, K. F. X., Sehgal, S. K., Li, W., Gill, B. S., Bevan, M. W., Šimková, H., Doležel, J., Weining, S., Lazo, G. R., Anderson, O. D., Dvorak, J. (May 2013) A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proceedings of the National Academy of Sciences of the United States of America, 110 (19). pp. 7940-7945. ISSN 00278424

Lyon, G. J. (May 2015) Using next generation sequencing to discover new human genetic syndromes and reveal new biology. In: GTCbio: 5th Next Generation Sequencing Conference, Boston, MA. (Unpublished)

Lyon, Gholson J. (October 2013) Amino-terminal acetylation of proteins: role in human disease and biology. In: Stony Brook University Department of Pharmacology Seminar Series, Oct 29th 2013, Stony Brook, NY. (Unpublished)

Lyon, Gholson J. (November 2013) Cambridge HealthTech Institute Clinical Genomics Podcast: Highlights from the Upcoming Clinical Exome Sequencing Conference. [Audio]

Lyon, Gholson J. (September 2013) Childhood-­onset Neuropsychiatric Disorders. In: FarGen Summit (Faroe Genome Project), Sept 19th-20th 2013, Tórshavn, The Faroe Islands. (Unpublished)

Lyon, Gholson J. (January 2014) Clinical Genomics of Neuropsychiatric Illnesses. In: Stony Brook University Division of Child and Adolescent Psychiatry, Seminar, Invited Speaker, January 2014, Stony Brook, NY. (Unpublished)

Lyon, Gholson J. (January 2014) Deep Brain Stimulation, Psychiatric Genetics, and iPS cell models of disease. In: CSHL In-House Seminar Series, Jan 24th 2014, Cold Spring Harbor Laboratory . (Unpublished)

Lyon, Gholson J. (December 2013) FDA Crackdown on 23andMe Delays a Revolution in Medicine. [Audio] (Unpublished)

Lyon, Gholson J. (December 2013) Increasing Accuracy for Exome and Whole Genome Sequencing. In: Bio-IT World and Cambridge Healthtech Institute's Inaugural- Clinical Exome Sequencing, December 4-5th 2013, Lisbon, Portugal. (Unpublished)

Lyon, Gholson J. (September 2015) Optimized sequencing leading to new human genetic syndromes involving transcription, translation, and protein degradation. In: The 24th KOGO Annual Conference 2015 & The 10th Asian Epigenomics Meeting, The Korea Science and Technology Center, Seoul, Korea. (Unpublished)

Lyon, Gholson J. (September 2015) Optimized sequencing leading to new human genetic syndromes involving transcription, translation, and protein degradation. In: Seminar, Pohang University of Science and Technology (POSTECH), Pohang, South Korea. (Unpublished)

Lyon, Gholson J. (November 2012) Talk from Gholson Lyon at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Lyon, Gholson J. (June 2013) Toward more accurate variant calling for personal genomes. In: The Clinical Genome Conference, June 25th-26th 2013, San Francisco, CA. (Unpublished)

Lyon, Gholson J. (September 2015) Variants in TAF1 are associated with a new syndrome with severe intellectual disability and characteristic dysmorphic features. In: 17th International Fragile X and Other Early-Onset Cognitive Disorders Workshop, Strasbourg, France. (Unpublished)

Lyon, Gholson J. (October 2015) Variants in TAF1 are associated with a new syndrome with severe intellectual disability and characteristic dysmorphic features. In: he American Society of Human Genetics (ASHG) 2015, Baltimore, MD. (Unpublished)

Lyon, Gholson J. (July 2013) Whole genome sequencing, clinical interpretation, and deep brain stimulation in a severely mentally ill person. In: Gordon Research Conference, Human Genetics and Genomics, July 7th-12th 2013, Bryant University, Smithfield, RI . (Unpublished)

Lyon, Gholson J. (July 2013) Whole genome sequencing, clinical interpretation, and deep brain stimulation in a severely mentally ill person. In: Wiring the Brain - Cold Spring Harbor Laboratory, July 18th-22nd 2013, Cold Spring Harbor, New York. (Unpublished)

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Martin, L., Cook, C., Matasci, N., Williams, J., Bastow, R. (2015) Data mining with iPlant: A meeting report from the 2013 GARNet workshop, Data mining with iPlant. Journal of Experimental Botany, 66 (1). pp. 1-6. ISSN 0022-0957

McCarthy, S. E., McCombie, W. R., Corvin, A. (March 2014) Unlocking the Treasure Trove: From Genes to Schizophrenia Biology. Schizophrenia Bulletin, 40 (3). pp. 492-496. ISSN 0586-7614

McCombie, W. R. (1994) Large-scale automated sequencing human chromosomal regions. In: Automated DNA Sequencing and Analysis. Academic Press, pp. 159-166. ISBN 9780127170107

McCombie, W. R. (1994) The use of automated DNA sequencing in the analysis of cDNAs of model organisms. In: Automated DNA Sequencing and Analysis. Academic Press, pp. 77-80. ISBN 9780127170107

McCombie, W. R., Mardis, E. (2012) DNA Sequencing. In: Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, pp. 736-892. ISBN 9781936113422

McCombie, W. R., McPherson, J. D. (November 2018) Future Promises and Concerns of Ubiquitous Next-Generation Sequencing. Cold Spring Harb Perspect Med, 9 (9). ISSN 2157-1422

McCombie, W. R., McPherson, J. D., Mardis, E. R. (November 2018) Next-Generation Sequencing Technologies. Cold Spring Harb Perspect Med, 9 (11). ISSN 2157-1422

McGinn, J., Czech, B. (2014) Small RNA library construction for high-throughput sequencing. Methods in Molecular Biology, 1093. pp. 195-208. ISSN 10643745 (ISSN); 9781627036931 (ISBN)

Miller, J. R., Zhou, P., Mudge, J., Gurtowski, J., Lee, H., Ramaraj, T., Walenz, B. P., Liu, J., Stupar, R. M., Denny, R., Song, L., Singh, N., Maron, L. G., McCouch, S. R., McCombie, W. R., Schatz, M. C., Tiffin, P., Young, N. D., Silverstein, K. A. T. (July 2017) Hybrid assembly with long and short reads improves discovery of gene family expansions. BMC Genomics, 18 (1). p. 541. ISSN 1471-2164

Ming, R., VanBuren, R., Liu, Y. L., Yang, M., Han, Y. P., Li, L. T., Zhang, Q., Kim, M. J., Schatz, M. C., Campbell, M., Li, J. P., Bowers, J. E., Tang, H. B., Lyons, E., Ferguson, A. A., Narzisi, G., Nelson, D. R., Blaby-Haas, C. E., Gschwend, A. R., Jiao, Y. N., Der, J. P., Zeng, F. C., Han, J., Min, X. J., Hudson, K. A., Singh, R., Grennan, A. K., Karpowicz, S. J., Watling, J. R., Ito, K., Robinson, S. A., Hudson, M. E., Yu, Q. Y., Mockler, T. C., Carroll, A., Zheng, Y., Sunkar, R., Jia, R. Z., Chen, N., Arro, J., Wai, C. M., Wafula, E., Spence, A., Han, Y. N., Xu, L. M., Zhang, J. S., Peery, R., Haus, M. J., Xiong, W. W., Walsh, J. A., Wu, J., Wang, M. L., Zhu, Y. J., Paull, R. E., Britt, A. B., Du, C. G., Downie, S. R., Schuler, M. A., Michael, T. P., Long, S. P., Ort, D. R., Schopf, J. W., Gang, D. R., Jiang, N., Yandell, M., dePamphilis, C. W., Merchant, S. S., Paterson, A. H., Buchanan, B. B., Li, S. H., Shen-Miller, J. (2013) Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology, 14 (5). ISSN 1465-6906

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Narzisi, G., Schatz, M. C. (2015) The challenge of small-scale repeats for indel discovery. Front Bioeng Biotechnol, 3. p. 8. ISSN 2296-4185

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O'Rawe, J. A., Ferson, S., Lyon, G. J. (January 2015) Accounting for uncertainty in DNA sequencing data. Trends Genet, 31 (2). pp. 61-68. ISSN 0168-9525

O'Rawe, Jason, Fang, Han, Rynearson, Shawn, Robison, Reid J., Kiruluta, Edward S., Higgins, Gerald, Eilbeck, Karen, Reese, Martin G., Lyon, Gholson J. (August 2013) Supplemental figure 1 for "Integrating precision medicine in the study and clinical treatment of a severely mentally ill person.". [Image] (Unpublished)

O'Rawe, Jason, Fang, Han, Rynearson, Shawn, Robison, Reid J., Kiruluta, Edward S., Higgins, Gerald, Eilbeck, Karen, Reese, Martin G., Lyon, Gholson J. (August 2013) Supplemental figure 2 for "Integrating precision medicine in the study and clinical treatment of a severely mentally ill person.". [Image] (Unpublished)

O'Rawe, Jason, Fang, Han, Rynearson, Shawn, Robison, Reid J., Kiruluta, Edward S., Higgins, Gerald, Eilbeck, Karen, Reese, Martin G., Lyon, Gholson J. (August 2013) Supplemental file 12 for "Integrating precision medicine in the study and clinical treatment of a severely mentally ill person.". [Dataset] (Unpublished)

O'Rawe, Jason, Lyon, Gholson J. (November 2014) Large pedigrees in human sequencing studies: toward a more resolved and accurate picture of genetic disease. In: Cold Spring Harbor Laboratory Personal Genomes Meeting, November 2014, Cold Spring Harbor, NY. (Unpublished)

O'Rawe, Jason, Wu, Yiyang, Rope, Alan, Jimenez Barron, Laura, Swensen, Jeffrey J., Fang, Han, Mittelman, David, Highnam, Gareth, Robison, Reid J., Yang, Edward, Wang, Kai, Lyon, Gholson (2015) A variant in TAF1 is associated with a new syndrome with severe intellectual disability and characteristic dysmorphic features. bioRxiv. (Unpublished)

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Pendleton, M., Sebra, R., Pang, A. W., Ummat, A., Franzen, O., Rausch, T., Stutz, A. M., Stedman, W., Anantharaman, T., Hastie, A., Dai, H., Fritz, M. H., Cao, H., Cohain, A., Deikus, G., Durrett, R. E., Blanchard, S. C., Altman, R., Chin, C. S., Guo, Y., Paxinos, E. E., Korbel, J. O., Darnell, R. B., McCombie, W. R., Kwok, P. Y., Mason, C. E., Schadt, E. E., Bashir, A. (August 2015) Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat Methods, 12 (8). pp. 780-786. ISSN 1548-7105 (Electronic)1548-7091 (Linking)

Pirooznia, M., Kramer, M., Parla, J., Goes, F. S., Potash, J. B., McCombie, W. R., Zandi, P. P. (July 2014) Validation and assessment of variant calling pipelines for next-generation sequencing. Human Genomics, 8. ISSN 1473-95421479-7364 eISSN

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Roberts, R. J., Carneiro, M. O., Schatz, M. C. (2013) The advantages of SMRT sequencing. Genome Biology, 14 (7). p. 4. ISSN 1465-6906

Rosenfeld, J. A., Reeves, D., Brugler, M. R., Narechania, A., Simon, S., Durrett, R., Foox, J., Shianna, K., Schatz, M. C., Gandara, J., Afshinnekoo, E., Lam, E. T., Hastie, A. R., Chan, S., Cao, H., Saghbini, M., Kentsis, A., Planet, P. J., Kholodovych, V., Tessler, M., Baker, R., DeSalle, R., Sorkin, L. N., Kolokotronis, S. O., Siddall, M. E., Amato, G., Mason, C. E. (February 2016) Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius. Nat Commun, 7. p. 10164. ISSN 2041-1723 (Electronic)2041-1723 (Linking)

Ryan, N. M., Lihm, J., Kramer, M., McCarthy, S., Morris, S. W., Arnau-Soler, A., Davies, G., Duff, B., Ghiban, E., Hayward, C., Deary, I. J., Blackwood, D. H. R., Lawrie, S. M., McIntosh, A. M., Evans, K. L., Porteous, D. J., McCombie, W. R., Thomson, P. A. (June 2018) DNA sequence-level analyses reveal potential phenotypic modifiers in a large family with psychiatric disorders. Mol Psychiatry, 23 (12). pp. 2254-2285. ISSN 1359-4184

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Saw, J. H. W., Schatz, M., Brown, M. V., Kunkel, D. D., Foster, J. S., Shick, H., Christensen, S., Hou, S., Wan, X., Donachie, S. P. (October 2013) Cultivation and Complete Genome Sequencing of Gloeobacter kilaueensis sp. nov., from a Lava Cave in Kīlauea Caldera, Hawai'i. PLoS ONE, 8 (10). ISSN 19326203 (ISSN)

Schatz, M. C. (March 2017) Nanopore sequencing meets epigenetics. Nat Methods, 14 (4). pp. 347-348. ISSN 1548-7091

Schatz, M. C. (November 2012) Talk from Mike Schatz at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Schatz, M. C., Maron, L. G., Stein, J. C., Hernandez Wences, A., Gurtowski, J., Biggers, E., Lee, H., Kramer, M., Antoniou, E., Ghiban, E., Wright, M. H., Chia, J. M., Ware, D., McCouch, S. R., McCombie, W. R. (December 2014) Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol, 15 (11). p. 506. ISSN 1465-6906

Seaver, S. M., Gerdes, S., Frelin, O., Lerma-Ortiz, C., Bradbury, L. M., Zallot, R., Hasnain, G., Niehaus, T. D., El Yacoubi, B., Pasternak, S., Olson, R., Pusch, G., Overbeek, R., Stevens, R., de Crecy-Lagard, V., Ware, D., Hanson, A. D., Henry, C. S. (June 2014) High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. Proceedings of the National Academy of Sciences of the United States of America, 111 (26). pp. 9645-9650. ISSN 0027-8424

Sedlazeck, F. J., Lee, H., Darby, C. A., Schatz, M. C. (June 2018) Piercing the dark matter: bioinformatics of long-range sequencing and mapping. Nat Rev Genet, 19 (6). pp. 329-346. ISSN 1471-0056

Shi, L., Guo, Y., Dong, C., Huddleston, J., Yang, H., Han, X., Fu, A., Li, Q., Li, N., Gong, S., Lintner, K. E., Ding, Q., Wang, Z., Hu, J., Wang, D., Wang, F., Wang, L., Lyon, G. J., Guan, Y., Shen, Y., Evgrafov, O. V., Knowles, J. A., Thibaud-Nissen, F., Schneider, V., Yu, C. Y., Zhou, L., Eichler, E. E., So, K. F., Wang, K. (June 2016) Long-read sequencing and de novo assembly of a Chinese genome. Nat Commun, 7. p. 12065. ISSN 2041-1723 (Electronic)2041-1723 (Linking)

Smolka, M., Rescheneder, P., Schatz, M. C., von Haeseler, A., Sedlazeck, F. J. (October 2015) Teaser: Individualized benchmarking and optimization of read mapping results for NGS data. Genome Biol, 16 (1). p. 235. ISSN 1474-760X (Electronic)1474-7596 (Linking)

Streppel, M. M., Lata, S., Delabastide, M., Montgomery, E. A., Wang, J. S., Canto, M. I., Macgregor-Das, A. M., Pai, S., Morsink, F. H., Offerhaus, G. J., Antoniou, E., Maitra, A., McCombie, W. R. (January 2014) Next-generation sequencing of endoscopic biopsies identifies ARID1A as a tumor-suppressor gene in Barrett's esophagus. Oncogene, 33 (3). pp. 347-57. ISSN 0950-9232

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Thomas, C. G., Wang, W., Jovelin, R., Ghosh, R., Lomasko, T., Trinh, Q., Kruglyak, L., Stein, L. D., Cutter, A. D. (May 2015) Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis. Genome Research, 25 (5). pp. 667-678. ISSN 1088-9051

Thomson, P. A., Parla, J. S., McRae, A. F., Kramer, M., Ramakrishnan, K., Yao, J., Soares, D. C., McCarthy, S., Morris, S. W., Cardone, L., Cass, S., Ghiban, E., Hennah, W., Evans, K. L., Rebolini, D., Millar, J. K., Harris, S. E., Starr, J. M., MacIntyre, D. J., McIntosh, A. M., Watson, J. D., Deary, I. J., Visscher, P. M., Blackwood, D. H., McCombie, W. R., Porteous, D. J. (June 2014) 708 Common and 2010 rare DISC1 locus variants identified in 1542 subjects: Analysis for association with psychiatric disorder and cognitive traits. Molecular Psychiatry, 19 (6). pp. 668-675. ISSN 14765578

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Vembar, S. S., Seetin, M., Lambert, C., Nattestad, M., Schatz, M. C., Baybayan, P., Scherf, A., Smith, M. L. (August 2016) Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing. DNA Res, 23 (4). pp. 339-351. ISSN 1756-1663 (Electronic)1340-2838 (Linking)

Vidal, E. A., Moyano, T. C., Krouk, G., Katari, M. S., Tanurdzic, M., McCombie, W. R., Coruzzi, G. M., Gutierrez, R. A. (October 2013) Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots. BMC Genomics, 14. p. 701. ISSN 1471-2164

Vij, S., Kuhl, H., Kuznetsova, I. S., Komissarov, A., Yurchenko, A. A., Van Heusden, P., Singh, S., Thevasagayam, N. M., Prakki, S. R., Purushothaman, K., Saju, J. M., Jiang, J., Mbandi, S. K., Jonas, M., Hin Yan Tong, A., Mwangi, S., Lau, D., Ngoh, S. Y., Liew, W. C., Shen, X., Hon, L. S., Drake, J. P., Boitano, M., Hall, R., Chin, C. S., Lachumanan, R., Korlach, J., Trifonov, V., Kabilov, M., Tupikin, A., Green, D., Moxon, S., Garvin, T., Sedlazeck, F. J., Vurture, G. W., Gopalapillai, G., Kumar Katneni, V., Noble, T. H., Scaria, V., Sivasubbu, S., Jerry, D. R., O'Brien, S. J., Schatz, M. C., Dalmay, T., Turner, S. W., Lok, S., Christoffels, A., Orban, L. (April 2016) Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet, 12 (4). e1005954. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

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Wang, B., Tseng, E., Regulski, M., Clark, T. A., Hon, T., Jiao, Y., Lu, Z., Olson, A., Stein, J. C., Ware, D. (June 2016) Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing. Nat Commun, 7. p. 11708. ISSN 2041-1723 (Electronic)2041-1723 (Linking)

Wang, K., Kim, C., Bradfield, J., Guo, Y. F., Toskala, E., Otieno, F. G., Hou, C. P., Thomas, K., Cardinale, C., Lyon, G. J., Golhar, R., Hakonarson, H. (July 2013) Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease with neuromuscular and cardiac involvement. Genome Medicine, 5. ISSN 1756-994X

Wang, X., Yu, X., Zhu, W., McCombie, W. R., Antoniou, E., Powers, R. S., Davidson, N. O., Li, E., Williams, J. (June 2015) A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing. Bioinformatics, 31 (12). pp. 2040-2042. ISSN 1367-4803

Wiggs, J. L., Howell, G. R., Linkroum, K., Abdrabou, W., Hodges, E., Braine, C. E., Pasquale, L. R., Hannon, G. J., Haines, J. L., John, S. W. M. (April 2013) Variations in COL15A1 and COL18A1 influence age of onset of primary open angle glaucoma. Clinical Genetics, 84 (2). p. 167. ISSN 00099163

Wu, Yiyang (March 2013) The evolution of MIP technology. Journal Club. (Unpublished)

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Xu, X., Zhang, Y., Williams, J., Antoniou, E., McCombie, W. R., Wu, S., Zhu, W., Davidson, N. O., Denoya, P., Li, E. (June 2013) Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets. BMC Bioinformatics, 14 Sup. S1. ISSN 1471-2105 (Electronic)1471-2105 (Linking)

Xu, M., Ergin, I., Beyaz, S. (April 2020) Advances in Diagnostic Procedures and Their Applications in the Era of Cancer Immunotherapy. In: Immunotherapy. Springer, pp. 37-50.

Y

Yao, J., Zhang, K. X., Kramer, M., Pellegrini, M., McCombie, W. R. (January 2014) FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies. Bioinformatics. ISSN 1367-4803

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Zwickl, D. J., Stein, J. C., Wing, R. A., Ware, D., Sanderson, M. J. (September 2014) Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3. Systematic Biology, 63 (5). pp. 645-659. ISSN 1076836X (ISSN)