Items where Subject is "assays"

A

Abel, Haley J, Larson, David E, Regier, Allison A, Chiang, Colby, Das, Indraniel, Kanchi, Krishna L, Layer, Ryan M, Neale, Benjamin M, Salerno, William J, Reeves, Catherine, Buyske, Steven, NHGRI Centers for Common Disease Genomics, Matise, Tara C, Muzny, Donna M, Zody, Michael C, Lander, Eric S, Dutcher, Susan K, Stitziel, Nathan O, Hall, Ira M (July 2020) Mapping and characterization of structural variation in 17,795 human genomes. Nature, 583 (7814). pp. 83-89. ISSN 0028-0836

Aganezov, S., Goodwin, S., Sherman, R. M., Sedlazeck, F. J., Arun, G., Bhatia, S., Lee, I., Kirsche, M., Wappel, R., Kramer, M., Kostroff, K., Spector, D. L., Timp, W., McCombie, W. R., Schatz, M. C. (September 2020) Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing. Genome Res, 30 (9). pp. 1258-1273. ISSN 1088-9051 (Print)1088-9051

Aganezov, Sergey, Yan, Stephanie M, Soto, Daniela C, Kirsche, Melanie, Zarate, Samantha, Avdeyev, Pavel, Taylor, Dylan J, Shafin, Kishwar, Shumate, Alaina, Xiao, Chunlin, Wagner, Justin, McDaniel, Jennifer, Olson, Nathan D, Sauria, Michael EG, Vollger, Mitchell R, Rhie, Arang, Meredith, Melissa, Martin, Skylar, Lee, Joyce, Koren, Sergey, Rosenfeld, Jeffrey A, Paten, Benedict, Layer, Ryan, Chin, Chen-Shan, Sedlazeck, Fritz J, Hansen, Nancy F, Miller, Danny E, Phillippy, Adam M, Miga, Karen H, McCoy, Rajiv C, Dennis, Megan Y, Zook, Justin M, Schatz, Michael C (April 2022) A complete reference genome improves analysis of human genetic variation. Science, 376 (6588). eabl3533. ISSN 0036-8075

Aguzzoli Heberle, Bernardo, Brandon, J Anthony, Page, Madeline L, Nations, Kayla A, Dikobe, Ketsile I, White, Brendan J, Gordon, Lacey A, Fox, Grant A, Wadsworth, Mark E, Doyle, Patricia H, Williams, Brittney A, Fox, Edward J, Shantaraman, Anantharaman, Ryten, Mina, Goodwin, Sara, Ghiban, Elena, Wappel, Robert, Mavruk-Eskipehlivan, Senem, Miller, Justin B, Seyfried, Nicholas T, Nelson, Peter T, Fryer, John D, Ebbert, Mark TW (May 2024) Mapping medically relevant RNA isoform diversity in the aged human frontal cortex with deep long-read RNA-seq. Nature Biotechnology. ISSN 1087-0156 (Public Dataset)

Ahmed, Waheed-Ul-Rahman, Kleeman, Sam, Ng, Michael, Wang, Wei, Auton, Adam, 23andMe Research Team, Lee, Regent, Handa, Ashok, Zondervan, Krina T, Wiberg, Akira, Furniss, Dominic (June 2022) Genome-wide association analysis and replication in 810,625 individuals with varicose veins. Nature Communications, 13 (1). p. 3065. ISSN 2041-1723

Alexander, J., Kendall, J., McIndoo, J., Rodgers, L., Aboukhalil, R., Levy, D., Stepansky, A., Sun, G., Chobadjiev, L., Riggs, M., Cox, H., Hakker, I., Nowak, D. G., Laze, J., Llukani, E., Srivastava, A., Gruschow, S., Yadav, S. S., Robinson, B. D., Atwal, G., Trotman, L. C., Lepor, H., Hicks, J. B., Wigler, M., Krasnitz, A. (January 2018) Utility of single cell genomics in diagnostic evaluation of prostate cancer. Cancer Res, 78 (2). pp. 348-358. ISSN 0008-5472

Alonge, M., Soyk, S., Ramakrishnan, S., Wang, X., Goodwin, S., Sedlazeck, F. J., Lippman, Z. B., Schatz, M. C. (October 2019) RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol, 20 (1). p. 224. ISSN 1474-7596 (Public Dataset)

Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Jenike, Katie, Ou, Shujun, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary B, Schatz, Michael C, Soyk, Sebastian (December 2022) Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biology, 23 (1). p. 258. ISSN 1474-7596

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

Anttila, V., Bulik-Sullivan, B., Finucane, H. K., Walters, R. K., Bras, J., Duncan, L., Escott-Price, V., Falcone, G. J., Gormley, P., Malik, R., Patsopoulos, N. A., Ripke, S., Wei, Z., Yu, D., Lee, P. H., Turley, P., Grenier-Boley, B., Chouraki, V., Kamatani, Y., Berr, C., Letenneur, L., Hannequin, D., Amouyel, P., Boland, A., Deleuze, J. F., Duron, E., Vardarajan, B. N., Reitz, C., Goate, A. M., Huentelman, M. J., Kamboh, M. I., Larson, E. B., Rogaeva, E., St George-Hyslop, P., Hakonarson, H., Kukull, W. A., Farrer, L. A., Barnes, L. L., Beach, T. G., Demirci, F. Y., Head, E., Hulette, C. M., Jicha, G. A., Kauwe, J. S. K., Kaye, J. A., Leverenz, J. B., Levey, A. I., Lieberman, A. P., Pankratz, V. S., Poon, W. W., Quinn, J. F., Saykin, A. J., Schneider, L. S., Smith, A. G., Sonnen, J. A., Stern, R. A., Van Deerlin, V. M., Van Eldik, L. J., Harold, D., Russo, G., Rubinsztein, D. C., Bayer, A., Tsolaki, M., Proitsi, P., Fox, N. C., Hampel, H., Owen, M. J., Mead, S., Passmore, P., Morgan, K., Nothen, M. M., Rossor, M., Lupton, M. K., Hoffmann, P., Kornhuber, J., Lawlor, B., McQuillin, A., Al-Chalabi, A., Bis, J. C., Ruiz, A., Boada, M., Seshadri, S., Beiser, A., Rice, K., van der Lee, S. J., De Jager, P. L., Geschwind, D. H., Riemenschneider, M., Riedel-Heller, S., Rotter, J. I., Ransmayr, G., Hyman, B. T., Cruchaga, C., Alegret, M., Winsvold, B., Palta, P., Farh, K. H., Cuenca-Leon, E., Furlotte, N., Kurth, T. (June 2018) Analysis of shared heritability in common disorders of the brain. Science, 360 (6395). ISSN 0036-8075

Arakawa, S., Gocayne, J. D., McCombie, W. R., Urquhart, D. A., Hall, L. M., Fraser, C. M., Venter, J. C. (1990) Cloning, localization, and permanent expression of a Drosophila octopamine receptor. Neuron, 4 (3). pp. 343-354. ISSN 08966273 (ISSN)

Asiimwe, Rebecca, Alexander, Dobin (February 2024) STAR+WASP reduces reference bias in the allele-specific mapping of RNA-seq reads. bioRxiv. (Submitted)

Asp, M., Giacomello, S., Larsson, L., Wu, C., Furth, D., Qian, X., Wardell, E., Custodio, J., Reimegard, J., Salmen, F., Osterholm, C., Stahl, P. L., Sundstrom, E., Akesson, E., Bergmann, O., Bienko, M., Mansson-Broberg, A., Nilsson, M., Sylven, C., Lundeberg, J. (December 2019) A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart. Cell, 179 (7). 1647-1660.e19. ISSN 0092-8674

B

Ballouz, S., Dobin, A., Gingeras, T. R., Gillis, J. (May 2018) The fractured landscape of RNA-seq alignment: the default in our STARs. Nucleic Acids Res. ISSN 0305-1048

Ballouz, Sara, Mangala, Melissa M, Perry, Matthew D, Heitmann, Stewart, Gillis, Jesse A, Hill, Adam P, Vandenberg, Jamie I (October 2020) Co-expression of calcium and hERG potassium channels reduces the incidence of proarrhythmic events. Cardiovascular Research. ISSN 0008-6363

Baslan, T., Kendall, J., Volyanskyy, K., McNamara, K., Cox, H., D'Italia, S., Ambrosio, F., Riggs, M., Rodgers, L., Leotta, A., Song, J., Mao, Y., Wu, J., Shah, R., Gularte-Merida, R., Chadalavada, K., Nanjangud, G., Varadan, V., Gordon, A., Curtis, C., Krasnitz, A., Dimitrova, N., Harris, L., Wigler, M., Hicks, J. (May 2020) Novel Insights Into Breast Cancer Copy Number Genetic Heterogeneity Revealed by Single-Cell Genome Sequencing. Elife, 9. e51480. ISSN 2050-084X

Baumbusch, L. O., Aaroe, J., Johansen, F. E., Hicks, J. B., Sun, H., Bruhn, L., Gunderson, K., Naume, B., Kristensen, V. N., Liestol, K., Borresen-Dale, A. L., Lingjaerde, O. C. (August 2008) Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors. BMC Genomics, 9. p. 379.

Bell, C. C., Fennell, K. A., Chan, Y. C., Rambow, F., Yeung, M. M., Vassiliadis, D., Lara, L., Yeh, P., Martelotto, L. G., Rogiers, A., Kremer, B. E., Barbash, O., Mohammad, H. P., Johanson, T. M., Burr, M. L., Dhar, A., Karpinich, N., Tian, L., Tyler, D. S., MacPherson, L., Shi, J., Pinnawala, N., Yew Fong, C., Papenfuss, A. T., Grimmond, S. M., Dawson, S. J., Allan, R. S., Kruger, R. G., Vakoc, C. R., Goode, D. L., Naik, S. H., Gilan, O., Lam, E. Y. N., Marine, J. C., Prinjha, R. K., Dawson, M. A. (June 2019) Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia. Nat Commun, 10 (1). p. 2723. ISSN 2041-1723

Bhaloo, Shirin, Gazzo, Andrea, Paula, Arnaud Da Cruz, da Silva, Edaise M, Selenica, Pier, Zhu, Yingjie, Blanco-Heredia, Juan, Pei, Xin, Patel, Juber, Wen, Hannah, Riaz, Nadeem, Powell, Simon, Chandarlapaty, Sarat, Norton, Larry, Brown, David, Weigelt, Britta, Pareja, Fresia, Reis-Filho, Jorge (2023) Whole-genome Sequencing Analysis of Metaplastic Breast Cancers Shows Infrequent Homologous Recombination Deficiency. In: 112th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology (USCAP), MAR 11-16, 2023, Mexico.

Biederstedt, E., Oliver, J. C., Hansen, N. F., Jajoo, A., Dunn, N., Olson, A., Busby, B., Dilthey, A. T. (September 2018) NovoGraph: Human genome graph construction from multiple long-read de novo assemblies. F1000Res, 7. p. 1391. ISSN 2046-1402

Bignon, Christophe, Gruet, Antoine, Longhi, Sonia (October 2022) Split-GFP Reassembly Assay: Strengths and Caveats from a Multiparametric Analysis. International Journal of Molecular Sciences, 23 (21). p. 13167. ISSN 1422-0067

Biton, M., Haber, A. L., Rogel, N., Burgin, G., Beyaz, S., Schnell, A., Ashenberg, O., Su, C. W., Smillie, C., Shekhar, K., Chen, Z., Wu, C., Ordovas-Montanes, J., Alvarez, D., Herbst, R. H., Zhang, M., Tirosh, I., Dionne, D., Nguyen, L. T., Xifaras, M. E., Shalek, A. K., von Andrian, U. H., Graham, D. B., Rozenblatt-Rosen, O., Shi, H. N., Kuchroo, V., Yilmaz, O. H., Regev, A., Xavier, R. J. (October 2018) T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation. Cell, 175 (5). pp. 1307-1320. ISSN 0092-8674

Blumberg, Amit, Zhao, Yixin, Huang, Yi-Fei, Dukler, Noah, Rice, Edward J, Chivu, Alexandra G, Krumholz, Katie, Danko, Charles G, Siepel, Adam (February 2021) Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data. BMC Biology, 19 (1). p. 30. ISSN 1741-7007

Breuss, M. W., Antaki, D., George, R. D., Kleiber, M., James, K. N., Ball, L. L., Hong, O., Mitra, I., Yang, X., Wirth, S. A., Gu, J., Garcia, C. A. B., Gujral, M., Brandler, W. M., Musaev, D., Nguyen, A., McEvoy-Venneri, J., Knox, R., Sticca, E., Botello, M. C. C., Uribe Fenner, J., Perez, M. C., Arranz, M., Moffitt, A. B., Wang, Z., Hervas, A., Devinsky, O., Gymrek, M., Sebat, J., Gleeson, J. G. (December 2019) Autism risk in offspring can be assessed through quantification of male sperm mosaicism. Nat Med, 26 (1). pp. 143-150. ISSN 1078-8956

Brown, Anna-Leigh, Wilkins, Oscar G, Keuss, Matthew J, Hill, Sarah E, Zanovello, Matteo, Lee, Weaverly Colleen, Bampton, Alexander, Lee, Flora CY, Masino, Laura, Qi, Yue A, Bryce-Smith, Sam, Gatt, Ariana, Hallegger, Martina, Fagegaltier, Delphine, Phatnani, Hemali, NYGC ALS Consortium, Newcombe, Jia, Gustavsson, Emil K, Seddighi, Sahba, Reyes, Joel F, Coon, Steven L, Ramos, Daniel, Schiavo, Giampietro, Fisher, Elizabeth MC, Raj, Towfique, Secrier, Maria, Lashley, Tammaryn, Ule, Jernej, Buratti, Emanuele, Humphrey, Jack, Ward, Michael E, Fratta, Pietro (February 2022) TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A. Nature, 603 (7899). pp. 131-137. ISSN 0028-0836

Bukowski, R., Guo, X., Lu, Y., Zou, C., He, B., Rong, Z., Wang, B., Xu, D., Yang, B., Xie, C., Fan, L., Gao, S., Xu, X., Zhang, G., Li, Y., Jiao, Y., Doebley, J. F., Ross-Ibarra, J., Lorant, A., Buffalo, V., Romay, M. C., Buckler, E. S., Ware, D., Lai, J., Sun, Q., Xu, Y. (April 2018) Construction of the third generation Zea mays haplotype map. Gigascience, 7 (4). pp. 1-12. ISSN 2047-217x

C

Carillo, P., Feil, R., Gibon, Y., Satoh-Nagasawa, N., Jackson, D., Blasing, O. E., Stitt, M., Lunn, J. E. (June 2013) A fluorometric assay for trehalose in the picomole range. Plant methods, 9 (1). p. 21. ISSN 1746-4811

Carter, J. A., Preall, J. B., Atwal, G. S. (October 2019) Bayesian Inference of Allelic Inclusion Rates in the Human T Cell Receptor Repertoire. Cell Syst, 9 (5). pp. 475-482. ISSN 2405-4712 (Public Dataset)

Chan-Seng-Yue, M., Kim, J. C., Wilson, G. W., Ng, K., Figueroa, E. F., O'Kane, G. M., Connor, A. A., Denroche, R. E., Grant, R. C., McLeod, J., Wilson, J. M., Jang, G. H., Zhang, A., Liang, S. B., Borgida, A., Chadwick, D., Kalimuthu, S., Lungu, I., Bartlett, J. M. S., Krzyzanowski, P. M., Sandhu, V., Tiriac, H., Froeling, F. E. M., Karasinska, J. M., Topham, J. T., Renouf, D. J., Schaeffer, D. F., Jones, S. J. M., Marra, M. A., Laskin, J., Chetty, R., Stein, L. D., Zogopoulos, G., Haibe-Kains, B., Campbell, P. J., Tuveson, D. A., Knox, J. J., Fischer, S. E., Gallinger, S., Notta, F. (January 2020) Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution. Nat Genet. ISSN 1061-4036 (Public Dataset)

Chatterjee, Deeptiman, Deng, Wu-Min (2023) Standardization of Single-Cell RNA-Sequencing Analysis Workflow to Study Drosophila Ovary. Methods in Molecular Biology, 2677. pp. 151-171. ISSN 1064-3745

Chatterjee, Deeptiman, Costa, Caique Almeida Machado, Wang, Xian-Feng, Jevitt, Allison, Huang, Yi-Chun, Deng, Wu-Min (November 2022) Single-cell transcriptomics identifies Keap1-Nrf2 regulated collective invasion in a Drosophila tumor model. eLife, 11. e80956. ISSN 2050-084X

Chen, S., Krusche, P., Dolzhenko, E., Sherman, R. M., Petrovski, R., Schlesinger, F., Kirsche, M., Bentley, D. R., Schatz, M. C., Sedlazeck, F. J., Eberle, M. A. (December 2019) Paragraph: A graph-based structural variant genotyper for short-read sequence data. Genome Biology, 20 (1). Article 291. ISSN 14747596 (ISSN)

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

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

Chougule, K. M., Wang, L., Stein, J. C., Wang, X., Devisetty, U. K., Klein, R. R., Ware, D. (August 2018) Improved RNA-seq Workflows Using CyVerse Cyberinfrastructure. Curr Protoc Bioinformatics. e53. ISSN 1934-3396

Cifani, Paolo (2022) Automated Multidimensional Nanoscale Chromatography for Ultrasensitive Targeted Mass Spectrometry. Methods in Molecular Biology, 1 . Humana Press, New York, New York.

Concia, L., Brooks, A. M., Wheeler, E., Zynda, G. J., Wear, E. E., LeBlanc, C., Song, J., Lee, T. J., Pascuzzi, P. E., Martienssen, R. A., Vaughn, M. W., Thompson, W. F., Hanley-Bowdoin, L. (March 2018) Genome-Wide Analysis of the Arabidopsis Replication Timing Program. Plant Physiol, 176 (3). pp. 2166-2185. ISSN 0032-0889

Creason, Allison, Haan, David, Dang, Kristen, Chiotti, Kami E, Inkman, Matthew, Lamb, Andrew, Yu, Thomas, Hu, Yin, Norman, Thea C, Buchanan, Alex, van Baren, Marijke J, Spangler, Ryan, Rollins, M Rick, Spellman, Paul T, Rozanov, Dmitri, Zhang, Jin, Maher, Christopher A, Caloian, Cristian, Watson, John D, Uhrig, Sebastian, Haas, Brian J, Jain, Miten, Akeson, Mark, Ahsen, Mehmet Eren, SMC-RNA Challenge Participants, Stolovitzky, Gustavo, Guinney, Justin, Boutros, Paul C, Stuart, Joshua M, Ellrott, Kyle (August 2021) A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery. Cell Systems, 12 (8). 827-838.e5. ISSN 2405-4712

Croft, A. P., Campos, J., Jansen, K., Turner, J. D., Marshall, J., Attar, M., Savary, L., Wehmeyer, C., Naylor, A. J., Kemble, S., Begum, J., Durholz, K., Perlman, H., Barone, F., McGettrick, H. M., Fearon, D. T., Wei, K., Raychaudhuri, S., Korsunsky, I., Brenner, M. B., Coles, M., Sansom, S. N., Filer, A., Buckley, C. D. (May 2019) Distinct fibroblast subsets drive inflammation and damage in arthritis. Nature, 570 (7760). pp. 246-251. ISSN 0028-0836

Crow, M., Denk, F. (July 2019) RNA-seq data in pain research-an illustrated guide. Pain, 160 (7). pp. 1502-1504. ISSN 0304-3959

Crow, M., Gillis, J. (August 2018) Co-expression in Single-Cell Analysis: Saving Grace or Original Sin? Trends Genet, 34 (11). pp. 823-831. ISSN 0168-9525 (Print)0168-9525

Crow, M., Gillis, J. (June 2019) Single cell RNA-sequencing: replicability of cell types. Current Opinion in Neurobiology, 56. pp. 69-77. ISSN 09594388 (ISSN)

Crow, M., Paul, A., Ballouz, S., Huang, Z. J., Gillis, J. (February 2018) Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor. Nat Commun, 9 (1). p. 884. ISSN 2041-1723

D

Das, Arun, Schatz, Michael C (October 2022) Sketching and sampling approaches for fast and accurate long read classification. BMC Bioinformatics, 23 (1). p. 452. ISSN 1471-2105

Dennenmoser, S., Sedlazeck, F. J., Schatz, M. C., Altmuller, J., Zytnicki, M., Nolte, A. W. (December 2018) Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish. Mol Ecol, 28 (6). pp. 1491-1505. ISSN 0962-1083

Dewan, R, Chia, R, Ding, J, Hickman, RA, Stein, TD, Abramzon, Y, Ahmed, S, Sabir, MS, Portley, MK, Tucci, A, Ibáñez, K, Shankaracharya, FNU, Keagle, P, Rossi, G, Caroppo, P, Tagliavini, F, Waldo, ML, Johansson, PM, Nilsson, CF, Adeleye, A, Alba, C, Bacikova, D, Hupalo, DN, Martinez, EMG, Pollard, HB, Sukumar, G, Soltis, AR, Tuck, M, Zhang, X, Wilkerson, MD, Smith, BN, Ticozzi, N, Fallini, C, Gkazi, AS, Topp, SD, Kost, J, Scotter, EL, Kenna, KP, Miller, JW, Tiloca, C, Vance, C, Danielson, EW, Troakes, C, Colombrita, C, Al-Sarraj, S, Lewis, EA, King, A, Calini, D, Pensato, V, Castellotti, B, de Belleroche, J, Baas, F, ten Asbroek, ALMA, Sapp, PC, McKenna-Yasek, D, McLaughlin, RL, Polak, M, Asress, S, Esteban-Pérez, J, Muñoz-Blanco, JL, Stevic, Z, D'Alfonso, S, Mazzini, L, Comi, GP, Del Bo, R, Ceroni, M, Gagliardi, S, Querin, G, Bertolin, C, van Rheenen, W, Diekstra, FP, Rademakers, R, van Blitterswijk, M, Boylan, KB, Lauria, G, Duga, S, Corti, S, Cereda, C, Corrado, L, Sorarù, G, Williams, KL, Nicholson, GA, Blair, IP, Leblond-Manry, C, Rouleau, GA, Hardiman, O, Morrison, KE, Veldink, JH, van den Berg, LH, Al-Chalabi, A, Pall, H, Shaw, PJ, Turner, MR, Talbot, K, Taroni, F, García-Redondo, A, Wu, Z, Gellera, C, Ratti, A, Brown, RH (February 2021) Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis. Neuron, 109 (3). 448-460.e4. ISSN 0896-6273

Dhabaria, Avantika, Cifani, Paolo, Reed, Casie, Steen, Hanno, Kentsis, Alex (August 2015) A High-Efficiency Cellular Extraction System for Biological Proteomics. Journal of Proteome Research, 14 (8). pp. 3403-3408. ISSN 1535-3893

Du, Yanfang, Lunde, China, Li, Yunfu, Jackson, David, Hake, Sarah, Zhang, Zuxin (February 2021) Gene duplication at the Fascicled ear1 locus controls the fate of inflorescence meristem cells in maize. Proceedings of the National Academy of Sciences of USA, 118 (7). e2019218118-e2019218118. ISSN 0027-8424

Ducommun, B., Beach, D. (May 1990) A versatile microtiter assay for the universal cdc2 cell cycle regulator. Anal Biochem, 187 (1). pp. 94-7. ISSN 0003-2697 (Print)0003-2697 (Linking)

Dyson, N., Duffy, L. A., Harlow, E. (1989) In-Vitro Assays to Detect the Interaction of DNA Tumor Virus Transforming Proteins with the Retinoblastoma Protein. In: Molecular diagnostics of human cancer. Cancer cells Cold Spring Harbor, 7 (ED.). Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, pp. 235-240. ISBN 087969324X

E

Einson, Jonah, Glinos, Dafni, Boerwinkle, Eric, Castaldi, Peter, Darbar, Dawood, de Andrade, Mariza, Ellinor, Patrick, Fornage, Myriam, Gabriel, Stacey, Germer, Soren, Gibbs, Richard, Hersh, Craig P, Johnsen, Jill, Kaplan, Robert, Konkle, Barbara A, Kooperberg, Charles, Nassir, Rami, Loos, Ruth JF, Meyers, Deborah A, Mitchell, Braxton D, Psaty, Bruce, Vasan, Ramachandran S, Rich, Stephen S, Rienstra, Michael, Rotter, Jerome I, Saferali, Aabida, Shoemaker, M Benjamin, Silverman, Edwin, Smith, Albert Vernon, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Mohammadi, Pejman, Castel, Stephane E, Iossifov, Ivan, Lappalainen, Tuuli (January 2023) Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants. bioRxiv. (Submitted)

Elyada, E., Bolisetty, M., Laise, P., Flynn, W. F., Courtois, E. T., Burkhart, R. A., Teinor, J. A., Belleau, P., Biffi, G., Lucito, M. S., Sivajothi, S., Armstrong, T. D., Engle, D. D., Yu, K. H., Hao, Y., Wolfgang, C. L., Park, Y., Preall, J., Jaffee, E. M., Califano, A., Robson, P., Tuveson, D. A. (June 2019) Cross-species single-cell analysis of pancreatic ductal adenocarcinoma reveals antigen-presenting cancer-associated fibroblasts. Cancer Discov, 9 (8). pp. 1102-1123. ISSN 2159-8274

F

Fahy, E., Barringer, K. J., Kwoh, D. Y., Prodanovich, P., Gingeras, T. R. (1996) The self-sustained sequence replication (3SR) reaction and its application to the detection of mutations associated with Zidovudine resistance in HIV-1. In: PCR Protocols and Applications: Laboratory Manual. Academic Press, New York. ISBN 9780080886718

Fairfield, H., Gilbert, G. J., Barter, M., Corrigan, R. R., Curtain, M., Ding, Y. M., D'Ascenzo, M., Gerhardt, D. J., He, C., Huang, W. H., Richmond, T., Rowe, L., Probst, F. J., Bergstrom, D. E., Murray, S. A., Bult, C., Richardson, J., Kile, B. T., Gut, I., Hager, J., Sigurdsson, S., Mauceli, E., Di Palma, F., Lindblad-Toh, K., Cunningham, M. L., Cox, T. C., Justice, M. J., Spector, M. S., Lowe, S. W., Albert, T., Donahue, L. R., Jeddeloh, J., Shendure, J., Reinholdt, L. G. (2011) Mutation discovery in mice by whole exome sequencing. Genome Biology, 12 (9). ISSN 1474-7596

Fasano, O., Birnbaum, D., Edlund, L., Fogh, J., Wigler, M. H. (September 1984) New human transforming genes detected by a tumorigenicity assay. Molecular & Cellular Biology, 4 (9). pp. 1695-1705.

Ferrero-Serrano, Ángel, Sylvia, Megan M, Forstmeier, Peter C, Olson, Andrew J, Ware, Doreen, Bevilacqua, Philip C, Assmann, Sarah M (April 2022) Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis. Genome Biology, 23 (1). p. 101. ISSN 1474-7596

Fleischer, J. G., Schulte, R., Tsai, H. H., Tyagi, S., Ibarra, A., Shokhirev, M. N., Huang, L., Hetzer, M. W., Navlakha, S. (December 2018) Predicting age from the transcriptome of human dermal fibroblasts. Genome Biol, 19 (1). p. 221. ISSN 1474-7596 (Public Dataset)

Fraser, C. M., Arakawa, S., McCombie, W. R., Venter, J. C. (1989) Cloning, sequence analysis, and permanent expression of a human α2-adrenergic receptor in Chinese hamster ovary cells. Evidence for independent pathways of receptor coupling to adenylate cyclase attenuation and activation. Journal of Biological Chemistry, 264 (20). pp. 11754-11761. ISSN 00219258 (ISSN)

G

Ghosh, S. S., Fahy, E., Gingeras, T. R. (1995) The self-sustained sequence replication (3SR) reaction: Its practice and applications. In: Molecular Methods for Virus Detection. Academic Press, San Diego, pp. 287-313. ISBN 9780080536897

Gilman, M. (2001) Ribonuclease protection assay. In: Current Protocols in Molecular Biology. Wiley InterScience.

Gingeras, T. R. (1980) Restriction endonucleases and their role in genomic analysis. In: Gene structure and expression. Ohio State University Biosciences Colloquia. Ohio State University Press, pp. 3-20.

Gingeras, T. R., Biery, M., Goulden, M., Ghosh, S. S., Fahy, E. (1995) Optimization and Characterization of 3SR-based Assays. In: PCR primer: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pp. 653-666. ISBN 9780879694487

Gladman, Nicholas, Goodwin, Sara, Chougule, Kapeel, Richard McCombie, William, Ware, Doreen (January 2023) Era of gapless plant genomes: innovations in sequencing and mapping technologies revolutionize genomics and breeding. Current Opinion in Biotechnology, 79. p. 102886. ISSN 0958-1669

Grubor, V., Krasnitz, A., Troge, J. E., Meth, J. L., Lakshmi, B., Kendall, J. T., Yamrom, B., Alex, G., Pai, D., Navin, N. E., Hufnagel, L. A., Lee, Y. H., Cook, K., Allen, S. L., Rai, K. R., Damle, R., Calissano, C., Chiorazzi, N., Wigler, M. H., Esposito, D. (November 2008) High-Resolution Array-Based Comparative Genome Hybridization (CGH) Identifies Novel and Recurrent Regions in CLL. Blood, 112 (11). p. 717. ISSN 0006-4971

Grubor, V., Krasnitz, A., Troge, J. E., Meth, J. L., Lakshmi, B., Kendall, J. T., Yamrom, B., Alex, G., Pai, D., Navin, N. E., Hufnagel, L. A., Lee, Y. H., Cook, K., Allen, S. L., Rai, K. R., Damle, R. N., Calissano, C., Chiorazzi, N., Wigler, M. H., Esposito, D. (February 2009) Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA). Blood, 113 (6). pp. 1294-1303. ISSN 0006-4971

Guha, S., Rees, E., Darvasi, A., Ivanov, D., Ikeda, M., Bergen, S. E., Magnusson, P. K., Cormican, P., Morris, D., Gill, M., Cichon, S., Rosenfeld, J. A., Lee, A., Gregersen, P. K., Kane, J. M., Malhotra, A. K., Rietschel, M., Nothen, M. M., Degenhardt, F., Priebe, L., Breuer, R., Strohmaier, J., Ruderfer, D. M., Moran, J. L., Chambert, K. D., Sanders, A. R., Shi, J. X., Kendler, K., Riley, B., O'Neill, T., Walsh, D., Malhotra, D., Corvin, A., Purcell, S., Sklar, P., Iwata, N., Hultman, C. M., Sullivan, P. F., Sebat, J., McCarthy, S., Gejman, P. V., Levinson, D. F., Owen, M. J., O'Donovan, M. C., Lencz, T., Kirov, G. (2013) Implication of a Rare Deletion at Distal 16p11.2 in Schizophrenia. Jama Psychiatry, 70 (3). pp. 253-260. ISSN 2168-622X

H

Haas, Brian J, Dobin, Alexander, Ghandi, Mahmoud, Van Arsdale, Anne, Tickle, Timothy, Robinson, James T, Gillani, Riaz, Kasif, Simon, Regev, Aviv (May 2023) Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector. Cell Reports: Methods, 3 (5). p. 100467. ISSN 2667-2375

Haas, B. J., Dobin, A., Li, B., Stransky, N., Pochet, N., Regev, A. (October 2019) Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. Genome Biol, 20 (1). p. 213. ISSN 1474-7596

Hackett, Jennifer, Pepenella, Sharon, Marco, Cristina Fernandez, Bodt, Louise, Grajales, Lina Ruiz, Petracca, Jeffry, Burke, Justin, Mayle, Allison, Nash, Bruce, Micklos, David A (April 2024) Simple, Robust Invertebrate DNA Barcoding: Chelex-Based DNA Extraction and Optimized COI Amplification. Methods in molecular biology (Clifton, N.J.), 2744. pp. 119-127. ISSN 1064-3745

Harold, D., Connolly, S., Riley, B. P., Kendler, K. S., McCarthy, S. E., McCombie, W. R., Richards, A., Owen, M. J., O'Donovan, M. C., Walters, J., Donohoe, G., Gill, M., Corvin, A., Morris, D. W. (February 2019) Population-based identity-by-descent mapping combined with exome sequencing to detect rare risk variants for schizophrenia. American Journal of Medical Genetics Part B-Neuropsychiatric Genetics, 180 (3). pp. 223-231. ISSN 0148-7299

Harris, Benjamin D, Crow, Megan, Fischer, Stephan, Gillis, Jesse (May 2021) Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain. Cell Systems. ISSN 2405-4712

Heberle, Bernardo Aguzzoli, Brandon, J Anthony, Page, Madeline L, Nations, Kayla A, Dikobe, Ketsile I, White, Brendan J, Gordon, Lacey A, Fox, Grant A, Wadsworth, Mark E, Doyle, Patricia H, Williams, Brittney A, Fox, Edward J, Shantaraman, Anantharaman, Ryten, Mina, Goodwin, Sara, Ghiban, Elena, Wappel, Robert, Mavruk-Eskipehlivan, Senem, Miller, Justin B, Seyfried, Nicholas T, Nelson, Peter T, Fryer, John D, Ebbert, Mark TW (December 2023) Using deep long-read RNAseq in Alzheimer's disease brain to assess medical relevance of RNA isoform diversity. bioRxiv. (Submitted)

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

Ho, Y. J., Anaparthy, N., Molik, D., Mathew, G., Aicher, T., Patel, A., Hicks, J., Gale Hammell, M. (July 2018) Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations. Genome Res, 28 (9). pp. 1353-1363. ISSN 1088-9051

Hsieh, T. C., Mensah, M. A., Pantel, J. T., Aguilar, D., Bar, O., Bayat, A., Becerra-Solano, L., Bentzen, H. B., Biskup, S., Borisov, O., Braaten, O., Ciaccio, C., Coutelier, M., Cremer, K., Danyel, M., Daschkey, S., Eden, H. D., Devriendt, K., Wilson, S., Douzgou, S., Dukic, D., Ehmke, N., Fauth, C., Fischer-Zirnsak, B., Fleischer, N., Gabriel, H., Graul-Neumann, L., Gripp, K. W., Gurovich, Y., Gusina, A., Haddad, N., Hajjir, N., Hanani, Y., Hertzberg, J., Hoertnagel, K., Howell, J., Ivanovski, I., Kaindl, A., Kamphans, T., Kamphausen, S., Karimov, C., Kathom, H., Keryan, A., Knaus, A., Kohler, S., Kornak, U., Lavrov, A., Leitheiser, M., Lyon, G. J., Mangold, E., Reina, P. M., Carrascal, A. M., Mitter, D., Herrador, L. M., Nadav, G., Nothen, M., Orrico, A., Ott, C. E., Park, K., Peterlin, B., Polsler, L., Raas-Rothschild, A., Randolph, L., Revencu, N., Fagerberg, C. R., Robinson, P. N., Rosnev, S., Rudnik, S., Rudolf, G., Schatz, U., Schossig, A., Schubach, M., Shanoon, O., Sheridan, E., Smirin-Yosef, P., Spielmann, M., Suk, E. K., Sznajer, Y., Thiel, C. T., Thiel, G., Verloes, A., Vrecar, I., Wahl, D., Weber, I., Winter, K., Wisniewska, M., Wollnik, B., Yeung, M. W., Zhao, M., Zhu, N., Zschocke, J., Mundlos, S., Horn, D., Krawitz, P. M. (June 2019) PEDIA: prioritization of exome data by image analysis. Genet Med, 21 (12). pp. 2807-2814. ISSN 1098-3600

I

Ibrahim, Ayman M, Moss, Matthew A, Gray, Zane, Rojo, Michelle D, Burke, Caitlin M, Schwertfeger, Kathryn L, Dos Santos, Camila O, Machado, Heather L (2020) Diverse Macrophage Populations Contribute to the Inflammatory Microenvironment in Premalignant Lesions During Localized Invasion. Frontiers in Oncology, 10. p. 569985. ISSN 2234-943X

Iossifov, I. (November 2011) Talk from Ivan Iossifov at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Irvine, D. V., Goto, D. B., Vaughn, M. W., Nakaseko, Y., McCombie, W. R., Yanagida, M., Martienssen, R. (June 2009) Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing. Genome research, 19 (6). pp. 1077-83. ISSN 1088-9051 (Print)1088-9051 (Linking)

Iyer, Shruti V, Kramer, Melissa, Goodwin, Sara, McCombie, W Richard (July 2021) Understanding genetic variation in cancer using nanopore targeted sequencing. In: AACR Annual Meeting 2021.

J

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

Jia, Xiaoming, Goes, Fernando S, Locke, Adam E, Palmer, Duncan, Wang, Weiqing, Cohen-Woods, Sarah, Genovese, Giulio, Jackson, Anne U, Jiang, Chen, Kvale, Mark, Mullins, Niamh, Nguyen, Hoang, Pirooznia, Mehdi, Rivera, Margarita, Ruderfer, Douglas M, Shen, Ling, Thai, Khanh, Zawistowski, Matthew, Zhuang, Yongwen, Abecasis, Gonçalo, Akil, Huda, Bergen, Sarah, Burmeister, Margit, Chapman, Sinéad, DelaBastide, Melissa, Juréus, Anders, Kang, Hyun Min, Kwok, Pui-Yan, Li, Jun Z, Levy, Shawn E, Monson, Eric T, Moran, Jennifer, Sobell, Janet, Watson, Stanley, Willour, Virginia, Zöllner, Sebastian, Adolfsson, Rolf, Blackwood, Douglas, Boehnke, Michael, Breen, Gerome, Corvin, Aiden, Craddock, Nick, DiFlorio, Arianna, Hultman, Christina M, Landen, Mikael, Lewis, Cathryn, McCarroll, Steven A, Richard McCombie, W, McGuffin, Peter, McIntosh, Andrew, McQuillin, Andrew, Morris, Derek, Myers, Richard M, O'Donovan, Michael, Ophoff, Roel, Boks, Marco, Kahn, Rene, Ouwehand, Willem, Owen, Michael, Pato, Carlos, Pato, Michele, Posthuma, Danielle, Potash, James B, Reif, Andreas, Sklar, Pamela, Smoller, Jordan, Sullivan, Patrick F, Vincent, John, Walters, James, Neale, Benjamin, Purcell, Shaun, Risch, Neil, Schaefer, Catherine, Stahl, Eli A, Zandi, Peter P, Scott, Laura J (January 2021) Investigating rare pathogenic/likely pathogenic exonic variation in bipolar disorder. Molecular Psychiatry. ISSN 1359-4184

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

Jin, Y., Hammell, M. (February 2018) Analysis of RNA-Seq Data Using TEtranscripts. Methods Mol Biol, 1751. pp. 153-167. ISSN 1064-3745

Jobanputra, Vaidehi, Andrews, Peter, Felice, Vanessa, Abhyankar, Avinash, Kozon, Lukasz, Robinson, Dino, London, Ferrah, Hakker, Inessa, Wrzeszczynski, Kazimierz, Ronemus, Michael (December 2020) Detection of Copy Number Variants by Short Multiply Aggregated Sequence Homologies. The Journal of Molecular Diagnostics, 22 (12). pp. 1476-1481. ISSN 1525-1578

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

K

Kaminow, Benjamin, Yunusov, Dinar, Dobin, Alexander (2021) STARsolo: accurate, fast and versatile mapping/quantification of single-cell and single-nucleus RNA-seq data. bioRxiv. (Submitted)

Kaminow, Benjamin, Ballouz, Sara, Gillis, Jesse, Dobin, Alexander (March 2022) Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses. Genome Research. gr.275613.121-gr.275613.121. ISSN 1088-9051

Kettner-Buhrow, D., Guenther, B., Kaelble, S., Joshua-Tor, L., Kracht, M. (April 2009) Measurement of in vivo RISC activity using an in vitro non-radioactive RISC assay. Naunyn-Schmiedebergs Archives of Pharmacology, 379 (281 Ab). p. 59. ISSN 0028-1298

Kettner-Buhrow, D., Kaelble, S., Joshua-Tor, L., Kracht, M. (March 2008) Establishment of a non-radioactive assay to measure RISC (RNA-induced silencing complex) activity in vitro. Naunyn-Schmiedebergs Archives of Pharmacology, 377 (Supp 1). p. 64. ISSN 0028-1298

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

Kirsche, Melanie, Prabhu, Gautam, Sherman, Rachel, Ni, Bohan, Battle, Alexis, Aganezov, Sergey, Schatz, Michael C (March 2023) Jasmine and Iris: population-scale structural variant comparison and analysis. Nature Methods, 20 (3). pp. 408-417. ISSN 1548-7091

Koren, Sergey, Bao, Zhigui, Guarracino, Andrea, Ou, Shujun, Goodwin, Sara, Jenike, Katharine M, Lucas, Julian, McNulty, Brandy, Park, Jimin, Rautianinen, Mikko, Rhie, Arang, Roelofs, Dick, Schneiders, Harrie, Vrijenhoek, Ilse, Nijbroek, Koen, Ware, Doreen, Schatz, Michael C, Garrison, Erik, Huang, Sanwen, McCombie, William Richard, Miga, Karen H, Wittenberg, Alexander HJ, Phillippy, Adam M (March 2024) Gapless assembly of complete human and plant chromosomes using only nanopore sequencing. bioRxiv. (Submitted)

Koren, S., Schatz, M. C., Walenz, B. P., Martin, J., Howard, J. T., Ganapathy, G., Wang, Z., Rasko, D. A., McCombie, W. R., Jarvis, E. D., Phillippy, A. M. (July 2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology, 30 (7). pp. 693-700. ISSN 1087-0156

Kramer, Melissa, Goodwin, Sara, Wappel, Robert, Borio, Matilde, Offit, Kenneth, Feldman, Darren R, Stadler, Zsofia K, McCombie, W Richard (July 2024) Exploring the genetic and epigenetic underpinnings of early-onset cancers: Variant prioritization for long read whole genome sequencing from family cancer pedigrees. bioRxiv. (Submitted)

L

Li, S., Kendall, J., Park, S., Wang, Z., Alexander, J., Moffitt, A., Ranade, N., Danyko, C., Gegenhuber, B., Fischer, S., Robinson, B. D., Lepor, H., Tollkuhn, J., Gillis, J., Brouzes, E., Krasnitz, A., Levy, D., Wigler, M. (November 2019) Copolymerization of single-cell nucleic acids into balls of acrylamide gel. Genome Res, 30 (1). pp. 49-61. ISSN 1088-9051 (Public Dataset)

Li, Xinran, Zhou, Jiaqi, Zhao, Wenjuan, Wen, Qing, Wang, Weijie, Peng, Huipai, Gao, Yuan, Bouchonville, Kelly J, Offer, Steven M, Chan, Kuiming, Wang, Zhiquan, Li, Nan, Gan, Haiyun (September 2021) Defining Proximity Proteomics of Histone Modifications by Antibody-mediated Protein A-APEX2 Labeling. Genomics Proteomics and Bioinformatics. ISSN 1672-0229

Lin, K. T., Krainer, A. R. (May 2019) PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis. Bioinformatics, 35 (23). pp. 5048-5054. ISSN 1367-4803

Lisitsyn, N. A., Lisitsina, N. M., Dalbagni, G., Barker, P., Sanchez, C. A., Gnarra, J., Linehan, W. M., Reid, B. J., Wigler, M. H. (January 1995) Comparative genomic analysis of tumors: detection of DNA losses and amplification. Proc Natl Acad Sci U S A, 92 (1). pp. 151-5. ISSN 0027-8424 (Print)

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

Lohia, Ruchi, Hansen, Matthew EB, Brannigan, Grace (March 2022) Contiguously hydrophobic sequences are functionally significant throughout the human exome. Proceedings of the National Academy of Sciences of USA, 119 (12). e2116267119. ISSN 0027-8424

Lucito, R., Nakimura, M., West, J. A., Han, Y., Chin, K., Jensen, K. R., McCombie, R. W., Gray, J. W., Wigler, M. H. (April 1998) Genetic analysis using genomic representations. Proceedings of the National Academy of Sciences of the United States of America, 95 (8). pp. 4487-92. ISSN 0027-8424

Lucito, R., West, J., Reiner, A., Alexander, J., Esposito, D., Mishra, B., Powers, S., Norton, L., Wigler, M. H. (November 2000) Detecting gene copy number fluctuations in tumor cells by microarray analysis of genomic representations. Genome Research, 10 (11). pp. 1726-1736. ISSN 1088-9051

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, Gholson J. (2012) Clinical Issues with the Return of Next-­Generation Sequencing Results. In: The Clinical Genome Conference, June 12th-13th 2012, San Francisco, CA. (Unpublished)

Lyon, Gholson J. (April 2013) Exome and Genome Sequencing. [Teaching Resource] (Unpublished)

Lyon, Gholson J. (May 2013) Exome and Genome Sequencing. [Teaching Resource] (Unpublished)

Lyon, Gholson J. (2011) Finding and Analyzing Human Genetic Variation in Neuropsychiatric Disorders. In: Faculty Recruitment Talk, Dec 2011, Cold Spring Harbor Laboratory. (Unpublished)

Lyon, Gholson J. (April 2013) Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. In: COMPUTATIONAL BIOLOGY & BIOINFORMATICS SEMINAR SERIES, April 10th 2013, Cold Spring Harbor Laboratory. (Unpublished)

Lyon, Gholson J. (November 2012) Software Considerations for Processing, Analyzing and Interpreting Exome & Genome Sequence Data in Clinical Settings. In: World Genome Data Analysis Summit: Pre Conference Workshop, Nov 27th 2012, San Francisco. (Unpublished)

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

M

Maihofer, Adam X, Engchuan, Worrawat, Huguet, Guillaume, Klein, Marieke, MacDonald, Jeffrey R, Shanta, Omar, Thiruvahindrapuram, Bhooma, Jean-Louis, Martineau, Saci, Zohra, Jacquemont, Sebastien, Scherer, Stephen W, Ketema, Elizabeth, Aiello, Allison E, Amstadter, Ananda B, Avdibegović, Esmina, Babic, Dragan, Baker, Dewleen G, Bisson, Jonathan I, Boks, Marco P, Bolger, Elizabeth A, Bryant, Richard A, Bustamante, Angela C, Caldas-de-Almeida, Jose Miguel, Cardoso, Graça, Deckert, Jurgen, Delahanty, Douglas L, Domschke, Katharina, Dunlop, Boadie W, Dzubur-Kulenovic, Alma, Evans, Alexandra, Feeny, Norah C, Franz, Carol E, Gautam, Aarti, Geuze, Elbert, Goci, Aferdita, Hammamieh, Rasha, Jakovljevic, Miro, Jett, Marti, Jones, Ian, Kaufman, Milissa L, Kessler, Ronald C, King, Anthony P, Kremen, William S, Lawford, Bruce R, Lebois, Lauren AM, Lewis, Catrin, Liberzon, Israel, Linnstaedt, Sarah D, Lugonja, Bozo, Luykx, Jurjen J, Lyons, Michael J, Mavissakalian, Matig R, McLaughlin, Katie A, McLean, Samuel A, Mehta, Divya, Mellor, Rebecca, Morris, Charles Phillip, Muhie, Seid, Orcutt, Holly K, Peverill, Matthew, Ratanatharathorn, Andrew, Risbrough, Victoria B, Rizzo, Albert, Roberts, Andrea L, Rothbaum, Alex O, Rothbaum, Barbara O, Roy-Byrne, Peter, Ruggiero, Kenneth J, Rutten, Bart PF, Schijven, Dick, Seng, Julia S, Sheerin, Christina M, Sorenson, Michael A, Teicher, Martin H, Uddin, Monica, Ursano, Robert J, Vinkers, Christiaan H, Voisey, Joanne, Weber, Heike, Winternitz, Sherry, Xavier, Miguel, Yang, Ruoting, McD Young, Ross, Zoellner, Lori A, Psychiatric Genomics Consortium PTSD Working Group, Psychiatric Genomics Consortium CNV Working Group, Salem, Rany M, Shaffer, Richard A, Wu, Tianying, Ressler, Kerry J, Stein, Murray B, Koenen, Karestan C, Sebat, Jonathan, Nievergelt, Caroline M (September 2022) Rare copy number variation in posttraumatic stress disorder. Molecular Psychiatry. ISSN 1359-4184

McCombie, W. R., Heiner, C., Kelley, J. M., Fitzgerald, M. G., Gocayne, J. D. (1992) Rapid and reliable fluorescent cycle sequencing of double-stranded templates. DNA sequence : the journal of DNA sequencing and mapping, 2 (5). pp. 289-296. ISSN 10425179 (ISSN)

Menges, F., Narzisi, G., Mishra, B. (September 2011) TotalReCaller: improved accuracy and performance via integrated alignment and base-calling. Bioinformatics, 27 (17). pp. 2330-2337. ISSN 1367-4803

Milella, M, Luchini, C, Lawlor, RT, Johns, AL, Casolino, R, Yoshino, T, Biankin, AV, Stein, LD, Park, K, Korbel, JO, Zeps, N, Rubin, MA, Marra, MA, Elemento, O, Gallinger, S, Tuveson, D, Trumper, L, Koch, R, Scarpa, A, Brennan, P, Pilarsky, C, Nikolaev, S, Yoon, SS, Lee, ES, Shibata, T, Wu, X, Wu, J, Zhan, Q, Poon, W, Al-Kuraya, KS, Eeles, R, Fitzgerald, R, Caldas, C, Abraham, J, Chang, DK (January 2022) ICGC-ARGO precision medicine: familial matters in pancreatic cancer. The Lancet Oncology, 23 (1). pp. 25-26. ISSN 1470-2045

Moffitt, A. B., Spector, M. S., Andrews, P., Kendall, J., Alexander, J., Stepansky, A., Ma, B., Kolitz, J., Chiorazzi, N., Allen, S.L., Krasnitz, A., Wigler, M., Levy, D., Wang, Z. (February 2020) Multiplex Accurate Sensitive Quantitation (MASQ) With Application to Minimal Residual Disease in Acute Myeloid Leukemia. Nucleic Acids Research, 48 (7). e40. ISSN 0305-1048 (Public Dataset)

Moravec, Jiří C, Lanfear, Robert, Spector, David L, Diermeier, Sarah D, Gavryushkin, Alex (December 2022) Testing for Phylogenetic Signal in Single-Cell RNA-Seq Data. Journal of Computational Biology. ISSN 1066-5277

Moreno, Pablo, Fexova, Silvie, George, Nancy, Manning, Jonathan R, Miao, Zhichiao, Mohammed, Suhaib, Muñoz-Pomer, Alfonso, Fullgrabe, Anja, Bi, Yalan, Bush, Natassja, Iqbal, Haider, Kumbham, Upendra, Solovyev, Andrey, Zhao, Lingyun, Prakash, Ananth, García-Seisdedos, David, Kundu, Deepti J, Wang, Shengbo, Walzer, Mathias, Clarke, Laura, Osumi-Sutherland, David, Tello-Ruiz, Marcela Karey, Kumari, Sunita, Ware, Doreen, Eliasova, Jana, Arends, Mark J, Nawijn, Martijn C, Meyer, Kerstin, Burdett, Tony, Marioni, John, Teichmann, Sarah, Vizcaíno, Juan Antonio, Brazma, Alvis, Papatheodorou, Irene (November 2021) Expression Atlas update: gene and protein expression in multiple species. Nucleic Acids Research. ISSN 0305-1048

N

Navin, N., Hicks, J. B. (May 2011) Future medical applications of single-cell sequencing in cancer. Genome Medicine, 3 (5). ISSN 1756994X (ISSN)

Navin, N. E., Kendall, J. T., Troge, J. E., Andrews, P., Rodgers,  L., McIndoo, J., Cook, K., Stepansky,  A., Levy, D., Esposito, D., Muthuswamy, L., Krasnitz, A., McCombie, W. R., Hicks, J. B., Wigler, M. H. (2011) Tumour evolution inferred by single-cell sequencing. Nature, 472 (7341). pp. 90-94. ISSN 00280836 (ISSN)

Nechooshtan, G., Yunusov, D., Chang, K., Gingeras, T. R. (August 2020) Processing by RNase 1 forms tRNA halves and distinct Y RNA fragments in the extracellular environment. Nucleic Acids Res, 48 (14). pp. 8035-8049. ISSN 0305-1048 (Print)0305-1048

Noyes, Michelle D, Harvey, William T, Porubsky, David, Sulovari, Arvis, Li, Ruiyang, Rose, Nicholas R, Audano, Peter A, Munson, Katherine M, Lewis, Alexandra P, Hoekzema, Kendra, Mantere, Tuomo, Graves-Lindsay, Tina A, Sanders, Ashley D, Goodwin, Sara, Kramer, Melissa, Mokrab, Younes, Zody, Michael C, Hoischen, Alexander, Korbel, Jan O, McCombie, W Richard, Eichler, Evan E (March 2022) Familial long-read sequencing increases yield of de novo mutations. American Journal of Human Genetics. ISSN 0002-9297

Ntakirutimana, Fabrice, Tranchant-Dubreuil, Christine, Cubry, Philippe, Chougule, Kapeel, Zhang, Jianwei, Wing, Rod A, Adam, Hélène, Lorieux, Mathias, Jouannic, Stefan (August 2023) Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud. G3: Genes, Genomes, Genetics. jkad174. ISSN 2160-1836 (Public Dataset)

Nurk, Sergey, Koren, Sergey, Rhie, Arang, Rautiainen, Mikko, Bzikadze, Andrey V, Mikheenko, Alla, Vollger, Mitchell R, Altemose, Nicolas, Uralsky, Lev, Gershman, Ariel, Aganezov, Sergey, Hoyt, Savannah J, Diekhans, Mark, Logsdon, Glennis A, Alonge, Michael, Antonarakis, Stylianos E, Borchers, Matthew, Bouffard, Gerard G, Brooks, Shelise Y, Caldas, Gina V, Chen, Nae-Chyun, Cheng, Haoyu, Chin, Chen-Shan, Chow, William, de Lima, Leonardo G, Dishuck, Philip C, Durbin, Richard, Dvorkina, Tatiana, Fiddes, Ian T, Formenti, Giulio, Fulton, Robert S, Fungtammasan, Arkarachai, Garrison, Erik, Grady, Patrick GS, Graves-Lindsay, Tina A, Hall, Ira M, Hansen, Nancy F, Hartley, Gabrielle A, Haukness, Marina, Howe, Kerstin, Hunkapiller, Michael W, Jain, Chirag, Jain, Miten, Jarvis, Erich D, Kerpedjiev, Peter, Kirsche, Melanie, Kolmogorov, Mikhail, Korlach, Jonas, Kremitzki, Milinn, Li, Heng, Maduro, Valerie V, Marschall, Tobias, McCartney, Ann M, McDaniel, Jennifer, Miller, Danny E, Mullikin, James C, Myers, Eugene W, Olson, Nathan D, Paten, Benedict, Peluso, Paul, Pevzner, Pavel A, Porubsky, David, Potapova, Tamara, Rogaev, Evgeny I, Rosenfeld, Jeffrey A, Salzberg, Steven L, Schneider, Valerie A, Sedlazeck, Fritz J, Shafin, Kishwar, Shew, Colin J, Shumate, Alaina, Sims, Ying, Smit, Arian FA, Soto, Daniela C, Sović, Ivan, Storer, Jessica M, Streets, Aaron, Sullivan, Beth A, Thibaud-Nissen, Françoise, Torrance, James, Wagner, Justin, Walenz, Brian P, Wenger, Aaron, Wood, Jonathan MD, Xiao, Chunlin, Yan, Stephanie M, Young, Alice C, Zarate, Samantha, Surti, Urvashi, McCoy, Rajiv C, Dennis, Megan Y, Alexandrov, Ivan A, Gerton, Jennifer L, O'Neill, Rachel J, Timp, Winston, Zook, Justin M, Schatz, Michael C, Eichler, Evan E, Miga, Karen H, Phillippy, Adam M (April 2022) The complete sequence of a human genome. Science, 376 (6588). pp. 44-53. ISSN 0036-8075

O

O'Neill, K., Brocks, D., Hammell, M. G. (March 2020) Mobile Genomics: Tools and Techniques for Tackling Transposons. Philos Trans R Soc Lond B Biol Sci, 375 (1795). ISSN 0962-8436

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. (May 2013) Supplemental figure 3 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 4 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 5 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 10 for "Integrating precision medicine in the study and clinical treatment of a severely mentally ill person.". [Dataset] (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 11 for "Integrating precision medicine in the study and clinical treatment of a severely mentally ill person.". UNSPECIFIED. (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, Fang, Han, Rynearson, Shawn, Robison, Reid J., Kiruluta, Edward S., Higgins, Gerald, Eilbeck, Karen, Reese, Martin G., Lyon, Gholson J. (August 2013) Supplemental file 2 for "Integrating precision medicine in the study and clinical treatment of a severely mentally ill person.". [Dataset] (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 3 for "Integrating precision medicine in the study and clinical treatment of a severely mentally ill person.". [Dataset] (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 4 for "Integrating precision medicine in the study and clinical treatment of a severely mentally ill person.". [Dataset] (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 5 for "Integrating precision medicine in the study and clinical treatment of a severely mentally ill person.". [Dataset] (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 6 for "Integrating precision medicine in the study and clinical treatment of a severely mentally ill person.". [Dataset] (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 7 for "Integrating precision medicine in the study and clinical treatment of a severely mentally ill person.". [Dataset] (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 8 for "Integrating precision medicine in the study and clinical treatment of a severely mentally ill person.". [Dataset] (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 9 for "Integrating precision medicine in the study and clinical treatment of a severely mentally ill person.". [Dataset] (Unpublished)

Olson, Andrew J, Ware, Doreen (July 2021) Ranked Choice Voting for Representative Transcripts with TRaCE. Bioinformatics. ISSN 1367-4803

Omary, Moutasem, Gil-Yarom, Naama, Yahav, Chen, Steiner, Evyatar, Hendelman, Anat, Efroni, Idan (March 2022) A conserved superlocus regulates above- and belowground root initiation. Science, 375 (6584). eabf4368. ISSN 0036-8075

Onai, T., FitzGerald, M. G., Arakawa, S., Gocayne, J. D., Urquhart, D. A., Hall, L. M., Fraser, C. M., McCombie, W. R., Venter, J. C. (1989) Cloning, sequence analysis and chromosome localization of a Drosophila muscarinic acetylcholine receptor. FEBS Letters, 255 (2). pp. 219-225. ISSN 00145793 (ISSN)

Oppenheim, S., Cao, X., Rueppel, O., Krongdang, S., Phokasem, P., DeSalle, R., Goodwin, S., Xing, J., Chantawannakul, P., Rosenfeld, J. A. (January 2020) Whole Genome Sequencing and Assembly of the Asian Honey Bee Apis dorsata. Genome Biol Evol, 12 (1). pp. 3677-3683. ISSN 1759-6653 (Public Dataset)

Ortiz-Ramírez, Carlos, Guillotin, Bruno, Xu, Xiaosa, Rahni, Ramin, Zhang, Sanqiang, Yan, Zhe, Coqueiro Dias Araujo, Poliana, Demesa-Arevalo, Edgar, Lee, Laura, Van Eck, Joyce, Gingeras, Thomas R, Jackson, David, Gallagher, Kimberly L, Birnbaum, Kenneth D (December 2021) Ground tissue circuitry regulates organ complexity in maize and Setaria. Science, 374 (6572). pp. 1247-1252. ISSN 0036-8075

P

Parla, J, Kramer, M, McCombie, WR (January 2010) High-Throughput Sequencing. In: Microbial Forensics, Second Edition. UNSPECIFIED, pp. 461-478. ISBN 9780123820068

Parla, J., Kramer, M. R., McCombie, W. R. (2011) High-Throughput Sequencing. In: Microbial Forensics (Second Edition). Academic Press, San Diego, pp. 461-478.

Parla, J. S., Iossifov, I., Grabill, I., Spector, M. S., Kramer, M., McCombie, W. R. (September 2011) A comparative analysis of exome capture. Genome Biology, 12 (9). R97. ISSN 1474-7596

Patel, B, Kleeman, SO, Neavin, D, Powell, J, Baskozos, G, Ng, M, Ahmed, WUR, Bennett, DL, Schmid, AB, Furniss, D, Wiberg, A (August 2022) Shared genetic susceptibility between trigger finger and carpal tunnel syndrome: a genome-wide association study. The Lancet Rheumatology, 4 (8). e556-e565. ISSN 2665-9913

Peng, Hanchuan, Xie, Peng, Liu, Lijuan, Kuang, Xiuli, Wang, Yimin, Qu, Lei, Gong, Hui, Jiang, Shengdian, Li, Anan, Ruan, Zongcai, Ding, Liya, Yao, Zizhen, Chen, Chao, Chen, Mengya, Daigle, Tanya L, Dalley, Rachel, Ding, Zhangcan, Duan, Yanjun, Feiner, Aaron, He, Ping, Hill, Chris, Hirokawa, Karla E, Hong, Guodong, Huang, Lei, Kebede, Sara, Kuo, Hsien-Chi, Larsen, Rachael, Lesnar, Phil, Li, Longfei, Li, Qi, Li, Xiangning, Li, Yaoyao, Li, Yuanyuan, Liu, An, Lu, Donghuan, Mok, Stephanie, Ng, Lydia, Nguyen, Thuc Nghi, Ouyang, Qiang, Pan, Jintao, Shen, Elise, Song, Yuanyuan, Sunkin, Susan M, Tasic, Bosiljka, Veldman, Matthew B, Wakeman, Wayne, Wan, Wan, Wang, Peng, Wang, Quanxin, Wang, Tao, Wang, Yaping, Xiong, Feng, Xiong, Wei, Xu, Wenjie, Ye, Min, Yin, Lulu, Yu, Yang, Yuan, Jia, Yuan, Jing, Yun, Zhixi, Zeng, Shaoqun, Zhang, Shichen, Zhao, Sujun, Zhao, Zijun, Zhou, Zhi, Huang, Z Josh, Esposito, Luke, Hawrylycz, Michael J, Sorensen, Staci A, Yang, X William, Zheng, Yefeng, Gu, Zhongze, Xie, Wei, Koch, Christof, Luo, Qingming, Harris, Julie A, Wang, Yun, Zeng, Hongkui (October 2021) Morphological diversity of single neurons in molecularly defined cell types. Nature, 598 (7879). pp. 174-181. ISSN 0028-0836

Pond, S. K., Wadhawan, S., Chiaromonte, F., Ananda, G., Chung, W. Y., Taylor, J., Nekrutenko, A. (October 2009) Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome Research, 19 (11). pp. 2144-2153.

R

Razaghi, Roham, Hook, Paul, Ou, Shujun, Schatz, Michael, Hansen, Kasper, Jain, Miten, Timp, Winston (2022) Modbamtools: Analysis of single-molecule epigenetic data for long-range profiling, heterogeneity, and clustering. bioRxiv. (Submitted)

Roux de Bézieux, Hector, Street, Kelly, Fischer, Stephan, Van den Berge, Koen, Chance, Rebecca, Risso, Davide, Gillis, Jesse, Ngai, John, Purdom, Elizabeth, Dudoit, Sandrine (May 2024) Improving replicability in single-cell RNA-Seq cell type discovery with Dune. BMC Bioinformatics, 25 (1). p. 198. ISSN 1471-2105 (Public Dataset)

Rozowsky, Joel, Gao, Jiahao, Borsari, Beatrice, Yang, Yucheng T, Galeev, Timur, Gürsoy, Gamze, Epstein, Charles B, Xiong, Kun, Xu, Jinrui, Li, Tianxiao, Liu, Jason, Yu, Keyang, Berthel, Ana, Chen, Zhanlin, Navarro, Fabio, Sun, Maxwell S, Wright, James, Chang, Justin, Cameron, Christopher JF, Shoresh, Noam, Gaskell, Elizabeth, Drenkow, Jorg, Adrian, Jessika, Aganezov, Sergey, Aguet, François, Balderrama-Gutierrez, Gabriela, Banskota, Samridhi, Corona, Guillermo Barreto, Chee, Sora, Chhetri, Surya B, Cortez Martins, Gabriel Conte, Danyko, Cassidy, Davis, Carrie A, Farid, Daniel, Farrell, Nina P, Gabdank, Idan, Gofin, Yoel, Gorkin, David U, Gu, Mengting, Hecht, Vivian, Hitz, Benjamin C, Issner, Robbyn, Jiang, Yunzhe, Kirsche, Melanie, Kong, Xiangmeng, Lam, Bonita R, Li, Shantao, Li, Bian, Li, Xiqi, Lin, Khine Zin, Luo, Ruibang, Mackiewicz, Mark, Meng, Ran, Moore, Jill E, Mudge, Jonathan, Nelson, Nicholas, Nusbaum, Chad, Popov, Ioann, Pratt, Henry E, Qiu, Yunjiang, Ramakrishnan, Srividya, Raymond, Joe, Salichos, Leonidas, Scavelli, Alexandra, Schreiber, Jacob M, Sedlazeck, Fritz J, See, Lei Hoon, Sherman, Rachel M, Shi, Xu, Shi, Minyi, Sloan, Cricket Alicia, Strattan, J Seth, Tan, Zhen, Tanaka, Forrest Y, Vlasova, Anna, Wang, Jun, Werner, Jonathan, Williams, Brian, Xu, Min, Yan, Chengfei, Yu, Lu, Zaleski, Christopher, Zhang, Jing, Ardlie, Kristin, Cherry, J Michael, Mendenhall, Eric M, Noble, William S, Weng, Zhiping, Levine, Morgan E, Dobin, Alexander, Wold, Barbara, Mortazavi, Ali, Ren, Bing, Gillis, Jesse, Myers, Richard M, Snyder, Michael P, Choudhary, Jyoti, Milosavljevic, Aleksandar, Schatz, Michael C, Bernstein, Bradley E, Guigó, Roderic, Gingeras, Thomas R, Gerstein, Mark (March 2023) The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell, 186 (7). 1493-1511.e40. ISSN 0092-8674

Ruiz-Ortiz, Jenelys, Tollkuhn, Jessica (January 2021) Specificity in sociogenomics: Identifying causal relationships between genes and behavior. Hormones and Behaviour, 127. p. 104882. ISSN 0018-506X

Russnes, H. G., Navin, N., Hicks, J. B., Borresen-Dale, A. L. (October 2011) Insight into the heterogeneity of breast cancer through next-generation sequencing. Journal of Clinical Investigation, 121 (10). pp. 3810-3818. ISSN 0021-9738

Russnes, H. G., Sorlie, T., Krasnitz, A., Zetterberg, A., Naume, B., Borgen, E., Nesland, J. M., Wigler, M. H., Borresen-Dale, A. L., Hicks, J. B. (July 2008) Molecular subclassification of breast carcinomas based on aCGH, gene expression, IHC and ploidy - relevance for clinical outcome. European Journal of Cancer Supplements, 6 (9). p. 9. ISSN 1359-6349

S

Sabot, F., Picault, N., Elbaidouri, M., Llauro, C., Chaparro, C., Piegu, B., Roulin, A., Guiderdoni, E., Delabastide, M., McCombie, W. R., Panaud, O. (January 2011) Transpositional landscape of rice genome revealed by Paired-End Mapping of high-throughput resequencing data. Plant Journal, 66 (2). pp. 241-246. ISSN 0960-7412

Scharner, J., Ma, W. K., Zhang, Q., Lin, K. T., Rigo, F., Bennett, C. F., Krainer, A. R. (December 2019) Hybridization-mediated off-target effects of splice-switching antisense oligonucleotides. Nucleic Acids Res, 48 (2). ISSN 0305-1048 (Public Dataset)

Schmitz, A. A., Lucito, R., Van Aelst, L. (2002) Using cDNA-representational difference analysis (cDNA-RDA) in combination with microarrays to identify Rac regulated genes. Methods Mol Biol, 189. pp. 25-43. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Senn, Savanah, Bhattacharyya, Sharmodeep, Presley, Gerald, Taylor, Anne E, Nash, Bruce, Enke, Ray A, Barnard-Kubow, Karen B, Ford, Jillian, Jasinski, Brandon, Badalova, Yekaterina (June 2022) The Functional Biogeography of eDNA Metacommunities in the Post-Fire Landscape of the Angeles National Forest. Microorganisms, 10 (6). p. 1218. ISSN 2076-2607

Shih, M. M., Davis, F. P., Henry, G. L., Dubnau, J. (January 2019) Nuclear Transcriptomes of the Seven Neuronal Cell Types That Constitute the Drosophila Mushroom Bodies. G3 (Bethesda), 9 (1). pp. 81-94. ISSN 2160-1836

Smith, J.C., Sausville, E. L., Girish, V., Yuan, M.L., Vasudevan, A., John, K.M., Sheltzer, J. M. (May 2020) Cigarette Smoke Exposure and Inflammatory Signaling Increase the Expression of the SARS-CoV-2 Receptor ACE2 in the Respiratory Tract. Dev Cell, 53 (5). 514-529.e3. ISSN 1534-5807

Spector, M. S., Iossifov, I., Kritharis, A., He, C., Kolitz, J. E., Lowe, S. W., Allen, S. L. (June 2012) Mast-cell leukemia exome sequencing reveals a mutation in the IgE mast-cell receptor beta chain and KIT V654A. Leukemia, 26 (6). pp. 1422-1425. ISSN 0887-6924

Steele, Nina G, Biffi, Giulia, Kemp, Samantha B, Zhang, Yaqing, Drouillard, Donovan, Syu, LiJyun, Hao, Yuan, Oni, Tobiloba E, Brosnan, Erin, Elyada, Ela, Doshi, Abhishek, Hansma, Christa, Espinoza, Carlos, Abbas, Ahmed, The, Stephanie, Irizarry-Negron, Valerie, Halbrook, Christopher J, Franks, Nicole E, Hoffman, Megan T, Brown, Kristee, Carpenter, Eileen S, Nwosu, Zeribe C, Johnson, Craig, Lima, Fatima, Anderson, Michelle A, Park, Youngkyu, Crawford, Howard C, Lyssiotis, Costas A, Frankel, Timothy L, Rao, Arvind, Bednar, Filip, Dlugosz, Andrzej A, Preall, Jonathan B, Tuveson, David A, Allen, Benjamin L, Pasca di Magliano, Marina (April 2021) Inhibition of Hedgehog Signaling Alters Fibroblast Composition in Pancreatic Cancer. Clinical Cancer Research, 27 (7). pp. 2023-2037. ISSN 1078-0432

Sun, Lijuan, Han, Xiao, Egeblad, Mikala (December 2022) Isolation of mouse mammary carcinoma-derived macrophages and cancer cells for co-culture assays. STAR Protocols, 3 (4). p. 101833. ISSN 2666-1667 (In Press)

T

Tajima, Nami, Simorowski, Noriko, Yovanno, Remy A, Regan, Michael C, Michalski, Kevin, Gómez, Ricardo, Lau, Albert Y, Furukawa, Hiro (February 2022) Development and characterization of functional antibodies targeting NMDA receptors. Nature Communications, 13 (1). p. 923. ISSN 2041-1723

Tareen, Ammar, Kooshkbaghi, Mahdi, Posfai, Anna, Ireland, William T, McCandlish, David M, Kinney, Justin B (April 2022) MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect. Genome Biology, 23 (1). p. 98. ISSN 1474-7596

Thacker, Gatha, Henry, Samantha, Nandi, Ajeya, Debnath, Rahul, Singh, Snahlata, Nayak, Anupma, Susnik, Barbara, Boone, Melinda M, Zhang, Qing, Kesmodel, Susan B, Gumber, Sanjeev, Das, Gokul M, Kambayashi, Taku, Dos Santos, Camila O, Chakrabarti, Rumela (March 2023) Immature natural killer cells promote progression of triple-negative breast cancer. Science Translational Medicine, 15 (686). eabl4414. ISSN 1946-6234

U

Ustav, M., Stenlund, A. (February 1991) Transient Replication of Bpv-1 Requires 2 Viral Polypeptides Encoded by the E1 and E2 Open Reading Frames. Embo Journal, 10 (2). pp. 449-457. ISSN 0261-4189

W

Wagner, J, Olson, ND, Harris, L, Khan, Z, Farek, J, Mahmoud, M, Stankovic, A, Kovacevic, V, Yoo, B, Miller, N, Rosenfeld, JA, Ni, B, Zarate, S, Kirsche, M, Aganezov, S, Schatz, MC, Narzisi, G, Byrska-Bishop, M, Clarke, W, Evani, US, Markello, C, Shafin, K, Zhou, X, Sidow, A, Bansal, V, Ebert, P, Marschall, T, Lansdorp, P, Hanlon, V, Mattsson, CA, Barrio, AM, Fiddes, IT, Xiao, C, Fungtammasan, A, Chin, CS, Wenger, AM, Rowell, WJ, Sedlazeck, FJ, Carroll, A, Salit, M, Zook, JM (May 2022) Benchmarking challenging small variants with linked and long reads. Cell Genomics, 2 (5). p. 100128. ISSN 2666-979X

Wang, B., Kumar, V., Olson, A., Ware, D. (April 2019) Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing. Front Genet, 10. Article no.384. ISSN 1664-8021 (Print)1664-8021

Wang, B., Tseng, E., Baybayan, P., Eng, K., Regulski, M., Jiao, Y., Wang, L., Olson, A., Chougule, K., Buren, P. V., Ware, D. (February 2020) Variant phasing and haplotypic expression from long-read sequencing in maize. Commun Biol, 3 (1). p. 78. ISSN 2399-3642 (Public Dataset)

Wang, Kejun, Hu, Haifei, Tian, Yadong, Li, Jingyi, Scheben, Armin, Zhang, Chenxi, Li, Yiyi, Wu, Junfeng, Yang, Lan, Fan, Xuewei, Sun, Guirong, Li, Donghua, Zhang, Yanhua, Han, Ruili, Jiang, Ruirui, Huang, Hetian, Yan, Fengbin, Wang, Yanbin, Li, Zhuanjian, Li, Guoxi, Liu, Xiaojun, Li, Wenting, Edwards, David, Kang, Xiangtao (July 2021) The chicken pan-genome reveals gene content variation and a promoter region deletion in IGF2BP1 affecting body size. Molecular Biology and Evolution. ISSN 0737-4038

Wang, Zihua, Sew, Pui-Hoon, Chong, Samuel S, Lee, Caroline GL (December 2009) Realtime exonuclease-mediated allelic discrimination (READ): a simple homogeneous genotyping assay for SNPs at the ABC gene loci. Pharmacogenomics, 10 (12). pp. 1995-2001. ISSN 1462-2416

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

Williams, Jason, Nash, Bruce, Ghiban, Cornel, Khalfan, Mohammed, Hilgert, Uwe, Lauter, Susan, Yang, Chun-Hua, Micklos, David Andrew (April 2024) Analysis of DNA Barcodes Using DNA Subway. Methods in molecular biology (Clifton, N.J.), 2744. pp. 551-560. ISSN 1064-3745

Williams, Jason (2022) CyVerse for Reproducible Research: RNA-Seq Analysis. Methods in Molecular Biology, 2443. pp. 57-79. ISSN 1064-3745

X

Xiang Neik, Ting, Ghanbarnia, Kaveh, Ollivier, Bénédicte, Scheben, Armin, Severn-Ellis, Anita, Larkan, Nicholas J, Haddadi, Parham, Fernando, Dilantha WG, Rouxel, Thierry, Batley, Jacqueline, Borhan, Hossein M, Balesdent, Marie-Hélène (March 2022) Two independent approaches converge to the cloning of a new Leptosphaeria maculans avirulence effector gene, AvrLmS-Lep2. Molecular Plant Pathology. ISSN 1464-6722

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.

Xu, X., Crow, M., Rice, B. R., Li, F., Harris, B., Liu, L., Demesa-Arevalo, E., Lu, Z., Wang, L., Fox, N., Wang, X., Drenkow, J., Luo, A., Char, S. N., Yang, B., Sylvester, A. W., Gingeras, T. R., Schmitz, R. J., Ware, D., Lipka, A. E., Gillis, J., Jackson, D. (December 2020) Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery. Dev Cell, S1534- (20). pp. 31021-31022. ISSN 1534-5807

Xue, Alexander, Huang, Yi-Fei, Siepel, Adam (2024) Inferring polygenic negative selection underlying an individual trait as a distribution of fitness effects (DFEs) from GWAS summary statistics. bioRxiv. (Submitted)

Y

Yan, Stephanie M, Sherman, Rachel M, Taylor, Dylan J, Nair, Divya R, Bortvin, Andrew N, Schatz, Michael C, McCoy, Rajiv C (September 2021) Local adaptation and archaic introgression shape global diversity at human structural variant loci. eLife, 10. ISSN 2050-084X

Yang, T, Alessandri-Haber, N, Fury, W, Schaner, M, Breese, R, LaCroix-Fralish, M, Kim, J, Adler, C, Macdonald, LE, Atwal, GS, Bai, Y (October 2021) AdRoit is an accurate and robust method to infer complex transcriptome composition. Communications Biology, 4 (1). ISSN 2399-3642 (In Press)

Yu, D., Sul, J. H., Tsetsos, F., Nawaz, M. S., Huang, A. Y., Zelaya, I., Illmann, C., Osiecki, L., Darrow, S. M., Hirschtritt, M. E., Greenberg, E., Muller-Vahl, K. R., Stuhrmann, M., Dion, Y., Rouleau, G., Aschauer, H., Stamenkovic, M., Schlogelhofer, M., Sandor, P., Barr, C. L., Grados, M., Singer, H. S., Nothen, M. M., Hebebrand, J., Hinney, A., King, R. A., Fernandez, T. V., Barta, C., Tarnok, Z., Nagy, P., Depienne, C., Worbe, Y., Hartmann, A., Budman, C. L., Rizzo, R., Lyon, G. J., McMahon, W. M., Batterson, J. R., Cath, D. C., Malaty, I. A., Okun, M. S., Berlin, C., Woods, D. W., Lee, P. C., Jankovic, J., Robertson, M. M., Gilbert, D. L., Brown, L. W., Coffey, B. J., Dietrich, A., Hoekstra, P. J., Kuperman, S., Zinner, S. H., Luethvigsson, P., Saemundsen, E., Thorarensen, O., Atzmon, G., Barzilai, N., Wagner, M., Moessner, R., Ophoff, R., Pato, C. N., Pato, M. T., Knowles, J. A., Roffman, J. L., Smoller, J. W., Buckner, R. L., Willsey, A. J., Tischfield, J. A., Heiman, G. A., Stefansson, H., Stefansson, K., Posthuma, D., Cox, N. J., Pauls, D. L., Freimer, N. B., Neale, B. M., Davis, L. K., Paschou, P., Coppola, G., Mathews, C. A., Scharf, J. M. (March 2019) Interrogating the Genetic Determinants of Tourette's Syndrome and Other Tic Disorders Through Genome-Wide Association Studies. The American Journal of Psychiatry, 176 (3). pp. 217-227. ISSN 0002-953x

Yuan, Chengxiang (March 2023) Applications of oligonucleotide ligation in sequencing. PhD thesis, Cold Spring Harbor Laboratory.

Yuste, R., Hawrylycz, M., Aalling, N., Aguilar-Valles, A., Arendt, D., Arnedillo, R. A., Ascoli, G. A., Bielza, C., Bokharaie, V., Bergmann, T. B., Bystron, I., Capogna, M., Chang, Y., Clemens, A., de Kock, C. P. J., DeFelipe, J., Dos Santos, S. E., Dunville, K., Feldmeyer, D., Fiáth, R., Fishell, G. J., Foggetti, A., Gao, X., Ghaderi, P., Goriounova, N. A., Güntürkün, O., Hagihara, K., Hall, V. J., Helmstaedter, M., Herculano, S., Hilscher, M. M., Hirase, H., Hjerling-Leffler, J., Hodge, R., Huang, J., Huda, R., Khodosevich, K., Kiehn, O., Koch, H., Kuebler, E. S., Kühnemund, M., Larrañaga, P., Lelieveldt, B., Louth, E. L., Lui, J. H., Mansvelder, H. D., Marin, O., Martinez-Trujillo, J., Moradi Chameh, H., Nath, A., Nedergaard, M., Němec, P., Ofer, N., Pfisterer, U. G., Pontes, S., Redmond, W., Rossier, J., Sanes, J. R., Scheuermann, R., Serrano-Saiz, E., Steiger, J. F., Somogyi, P., Tamás, G., Tolias, A. S., Tosches, M. A., García, M. T., Vieira, H. M., Wozny, C., Wuttke, T. V., Yong, L., Yuan, J., Zeng, H., Lein, E. (August 2020) A community-based transcriptomics classification and nomenclature of neocortical cell types. Nat Neurosci, 23 (12). pp. 1456-1468. ISSN 1097-6256

Z

Zador, A. M., Dubnau, J., Oyibo, H. K., Zhan, H., Cao, G., Peikon, I. D. (October 2012) Sequencing the Connectome. PLoS Biology, 10 (10). ISSN 1544-9173

Zender, L., Xue, W., Zuber, J., Semighini, C. P., Krasnitz, A., Ma, B., Zender, P., Kubicka, S., Luk, J. M., Schirmacher, P., McCombie, W. R., Wigler, M. H., Hicks, J. B., Hannon, G. J., Powers, S., Lowe, S. W. (November 2008) An Oncogenomics-Based In Vivo RNAi Screen Identifies Tumor Suppressors in Liver Cancer. Cell, 135 (5). pp. 852-864. ISSN 0092-8674

Zhang, R, Atwal, GS, Lim, WK (March 2021) Noise regularization removes correlation artifacts in single-cell RNA-seq data preprocessing. Patterns, 2 (3). p. 100211. ISSN 2666-3899

Zhao, Qi, Molina-Portela, Maria Del Pilar, Parveen, Asma, Adler, Alexander, Adler, Christina, E, Hock, Wang, Wei, Ni, Min, Wei, Yi, Atwal, Gurinder, Mohrs, Markus, Thurston, Gavin, Eichten, Alexandra (November 2020) Heterogeneity and chimerism of endothelial cells revealed by single-cell transcriptome in orthotopic liver tumors. Angiogenesis, 23 (4). pp. 581-597. ISSN 0969-6970

Zhou, Jessica, Guruvayurappan, Karthik, Toneyan, Shushan, Chen, Hsiuyi V, Chen, Aaron R, Koo, Peter, McVicker, Graham (July 2024) Analysis of single-cell CRISPR perturbations indicates that enhancers act multiplicatively and provides limited evidence for epistatic-like interactions. bioRxiv. (Public Dataset) (Submitted)

Zou, C., Karn, A., Reisch, B., Nguyen, A., Sun, Y., Bao, Y., Campbell, M. S., Church, D., Williams, S., Xu, X., Ledbetter, C. A., Patel, S., Fennell, A., Glaubitz, J. C., Clark, M., Ware, D., Londo, J. P., Sun, Q., Cadle-Davidson, L. (January 2020) Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus. Nat Commun, 11 (1). p. 413. ISSN 2041-1723 (Public Dataset)