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--- publications [2023/01/31 09:52] – david
+++ publications [2026/05/22 14:27] (current) – christi
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 |~~=row()~~.| Alexander, J., Kendall, J., McIndoo, J., Rodgers, L., Aboukhalil, R., Levy, D., Stepansky, A., Sun, G., Riggs, M., Cox, H., Hakker, I., Nowak, D., Laze, J., Lukani, E., Srivastava, A., Gruschow, S., Yadav, S., Robinson, B., Atwal, G., Trotman, L., Lepor, H., Hicks, J., Wigler, M. and Krasnitz, A. | 2017 | Utility of single cell genomic evaluation of prostate cancer.  Cancer Research, 78: 348-358. PMCID: 5771881 | {{:Alexander_et_al_Cancer_Res_2017.pdf|PDF}} |
 |~~=row()~~.| Buja, A., Volfovsky, N., Krieger, A., Lord, C., Lash, A.E., Wigler, M., and Iossifov, I. | 2017 | Damaging de novo mutations diminish motor skills in children on the autism spectrum.  PNAS, 15: E1859-E1866.  PMCID: 5828599 | {{:Buja et al PNAS 2018.pdf|PDF}} |
-|~~=row()~~.| Buja, A., Volfovsky, N., Krieger, A., Lord, C., Lash, A.E., Wigler, M., and Iossifov, I. | 2017 | Damaging mutations are associated with diminished motor skills and IQ in children on the autism spectrum. bioRxiv/2017/141200. | {{Buja et al bioRxiv 2017.pdf|PDF}} |
 |~~=row()~~.| Munoz, A., Yamrom, B., Lee, Y-h., Marks, S., Lin, K-T., Wang, Z., Krainer, A.R., Darnell, R.B., Wigler, M. and Iossifov, I. | 2017 | //De novo// indels within introns comtribute to ASD incidence.  bioRxiv/2017/137471. | {{:Munoz et al bioRxiv 2017.pdf|PDF}} |
 |~~=row()~~.| Kumar, V., Rosembaum, J., Wang, Z., Forcier, T., Ronemus, M., Wigler, M. and Levy, D. | 2018 | Partial bisulfite conversion for unique template sequencing.  Nucleic Acids Research, 46: e10.  PMCID: 5778454 | {{:Kumar_et_al_Nucleic_Acids_Res_2017.pdf|PDF}} |
 |~~=row()~~.| 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. and Wigler, M. | 2019 | Copolymerization of single-cell nucleic acids into balls of acrylamide gel. Genome Research, 30: 49-61.  PMCID: 6961581 | {{:Li_et_al_Genome_Res_2019.pdf|PDF}} |
+|~~=row()~~.| Andrews, Peter A., Alexander, J., Kendall, J. and Wigler, M. | 2019 | G-Graph: An interactive genomic graph viewer. bioRxiv/2019/803015 | {{ :andrews_et_al_biorxiv_2019.pdf |PDF}} |
 |~~=row()~~.| Moffitt, A.B., Spector., M.S., Andrews, P., Kendall, J., Alexander, J., Stepansky, A., Ma, B.C., Kolitz, J., Chiorazzi, N., Allen, S.L., Krasnitz, A., Wigler, M., Levy, D. and Wang, Z. | 2020 | Multiplex accurate sensitive quantitation (MASQ) with application to minimal residual disease in acute myeloid leukemia.  Nucleic Acids Research, 48: e40.  PMCID: 7144909 | {{:Moffitt_et_al_nar_2020.pdf|PDF}} |
 |~~=row()~~.| Chorbadjiev, L., Kendall, J., Alexander, J., Zhygulin, V., Song, J., Wigler, M. and Krasnitz, A. |2020| An integrated computational pipeline for single-cell genomic profiling. JCO Clin. Cancer Inform., 4: 464-471. | {{: Chorbadjiev_et_al_jcoclincaninform_2020.pdf|PDF}} |
 |~~=row()~~.| 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.,  Merida, R.G., Chadalavada, K., Nanjangud, G., Varadan, V., Gordon, A., Curtis, C., Krasnitz, A., Dimitrova, N., Harris, L., Wigler, M., and Hicks, J. |2020| Novel insights into breast cancer copy number genetic heterogeneity revealed by single-cell genome sequencing. eLife Science, 9: 51480. | {{: Baslan_et_al_eLife_2020.pdf.|PDF}} |
 |~~=row()~~.| Vasudevan, A., Baruah, P.S., Smith, J.C., Wang, Z., Sayles, N.M., Andrews, P., Kendall, J., Leu, J., Chunduri, N.K., Levy, D., Wigler, M., Storchová, Z., Sheltzer, J.M. |2020| Single-Chromosomal Gains Can Function as Metastasis Suppressors and Promoters in Colon Cancer. Dev Cell. 4: 413-428.e6. | {{:Vasudevan_et_al_developmental_cell_2020.pdf|PDF}} |
-|~~=row()~~.| Miyabayashi, K, Baker, LA, Deschênes, A,Traub, B, Caligiuri, G, Plenker, D, Alagesan, B, Belleau, P, Li, S, Kendall, J, Jang, GH, Kawaguchi, RK, Somerville, TDD, Tiriac, H, Hwang, CI, Burkhart, RA, Roberts, NJ, Wood, LD, Hruban, RH, Gillis, J, Krasnitz, A, Vakoc, CR, Wigler, M. Notta, F, Gallinger, S, Park, Y, Tuveson, DA. |2020| Intraductal Transplantation Models of Human Pancreatic Ductal Adenocarcinoma Reveal Progressive Transition of Molecular Subtypes. Cancer Discovery, 10: 1566-1589.  PMCID:  PMC7664990  |  {{:Miyabayashi_et_al_cancer_discovery_2020.pdf|PDF}} |
+|~~=row()~~.| Miyabayashi, K, Baker, LA, Deschênes, A,Traub, B, Caligiuri, G, Plenker, D, Alagesan, B, Belleau, P, Li, S, Kendall, J, Jang, GH, Kawaguchi, RK, Somerville, TDD, Tiriac, H, Hwang, CI, Burkhart, RA, Roberts, NJ, Wood, LD, Hruban, RH, Gillis, J, Krasnitz, A, Vakoc, CR, Wigler, M. Notta, F, Gallinger, S, Park, Y, Tuveson, DA. |2020| Intraductal Transplantation Models of Human Pancreatic Ductal Adenocarcinoma Reveal Progressive Transition of Molecular Subtypes. Cancer Discovery, 10: 1566-1589.  PMCID:  PMC7664990  | {{:Miyabayashi_et_al_cancer_discovery_2020.pdf|PDF}} |
 |~~=row()~~.| Yoon S, Munoz A, Yamrom B, Lee Y-h, Andrews P, Marks S, Wang Z, Reeves C, Winterkorn L, Krieger AM, Buja, A, Pradhan K. Ronemus M, Baldwin KK, Levy D, Wigler M, Iossifov I. |2021| Rates of contributory de novo mutation in high and low risk autism families. Nature Communications Biology, 4: 1026.  PMCID:  PMC8410909 | {{:Yoon_et_al_commun_biol_2021.pdf|PDF}} |
 |~~=row()~~.| Li S, Park S, Ye C, Danyko C, Wroten M, Andrews P, Wigler M, and Levy D. |2022| Targeted de novo phasing and long-range assembly by template mutagenesis.  Nucleic Acids Research, 50: e103.  PMCID: PMC9561374 | {{: Li_et_al_NAR_2022.pdf|PDF}} |
 |~~=row()~~.| Wang Z, Moffitt A, Andrews P, Wigler M, Levy D. |2022| Accurate measurement of microsatellite length by disrupting its tandem repeat structure.  Nucleic Acids Research 50: e116. PMC9723644 | {{:Wang_et_al_NAR_2022.pdf|PDF}} |
-|~~=row()~~.| Li S, Alexander J, Kendall J, Andrews P, Rose E, Orjuela H, Park S, Podszus C, Shanley L, Ma R, Rishi A, Donoho DL, Goldberg GL, Levy D, and Wigler M. |2022| High-throughput single-nucleus hybrid sequencing reveals genome-transcriptome correlations in cancer.  In progress. |
+|~~=row()~~.| Wroten M, Yoon S, Andrews P, Yamrom B, Ronemus M, Buja A, Krieger AM, Levy D, Ye K, Wigler M, and Iossifov I. |2023| Sharing parental genomes by siblings concordant or discordant for autism. Cell Genomics 3: 100319. PMCID: PMC10300587 | {{:Wroten_et_al_Cell_Genomics_2023.pdf|PDF}} |
+|~~=row()~~.| Lammertse E, Li S, Kendall J, Kim C, Morris P, Ranade N, Levy D, Wigler M, Brouzes E. |2023| Magnetically functionalized hydrogels for high-throughput genomic applications. Adv Mater Technol 9: (2):2301155. PMCID: PMC11029686. | {{:brouzes_et_al_adv_materials_technologies_2023.pdf|PDF}} |
+|~~=row()~~.| Swamynathan MM, Kuang S, Watrud KE, Doherty MR, Gineste C, Mathew G, Gong GQ, Cox H, Cheng E, Reiss D, Kendall J, Ghosh D, Reczek CR, Zhao X, Herzka T, Kim S, Klingbeil O, Liu J, Nowak DG, Alsudani H, Wee T-L, Park Y, Minicozzi F, Rivera K,  Almeida AS, Chang K, Chakrabarty RP, Wilkinson JE, Gimotty PA, Diermeier SD, Egeblad M, Vakoc CR, Locasale JW, Hicks JB, Wigler M, Chandel NS, Janowitz T, Pappin DJ, Williams RL, Cifani P, Tuveson DA, Laporte J, Trotman, LC. |2024| Pro-oxidant therapy by a vitamin K precursor targets PI 3-Kinase VPS34 function. Science, 386: eadk9167. doi: 10.1126/science.adk9167. | {{:swamynathan_et_al_science.2024.pdf|PDF}} |
+|~~=row()~~.| Li S, Alexander J, Kendall J, Andrews P, Rose E, Orjuela H, Park S, Podszus C, Shanley L, Ranade N, Morris P, Stauder D, Bradford D, Laster Z, Ronemus M, Rishi A, Frimer M, Ma R, Donoho DL, Goldberg GL, Wigler M, Levy D. |2025| Hybrid BAG-seq: DNA and RNA from the same single nucleus reveals interactions between genomic and transcriptomic landscapes in human tumor samples. Genome Biol. 2025 Sep 27;26(1):314. doi: 10.1186/s13059-025-03790-5. PMID: 41015771; PMCID: PMC12476631. | {{:li_et_al_genome_biology_2025.pdf|PDF}} |
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