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Paper

Somerville, T. D. D., Xu, Y., Miyabayashi, K., Tiriac, H., Cleary, C. R., Maia-Silva, D., Milazzo, J. P., Tuveson, D. A., Vakoc, C. R. (November 2018) TP63-Mediated Enhancer Reprogramming Drives the Squamous Subtype of Pancreatic Ductal Adenocarcinoma. Cell Rep, 25 (7). 1741-1755.e7. ISSN 2211-1247

Tran, Ngoc, Kepple, Daniel, Shuvaev, Sergey A., Koulakov, Alexei A. (November 2018) DeepNose: Using artificial neural networks to represent the space of odorants. bioRxiv. (Unpublished)

Kebschull, J. M., Zador, A. M. (November 2018) Cellular barcoding: lineage tracing, screening and beyond. Nat Methods, 15 (11). pp. 871-879. ISSN 1548-7091

Maharjan, D. M., Dai, Y. Y., Glantz, E. H., Jadhav, S. P. (November 2018) Disruption of dorsal hippocampal – prefrontal interactions using chemogenetic inactivation impairs spatial learning. Neurobiology of Learning and Memory, 155. pp. 351-360. ISSN 10747427 (ISSN)

Odoemene, O., Pisupati, S., Nguyen, H., Churchland, A. K. (October 2018) Visual evidence accumulation guides decision-making in unrestrained mice. J Neurosci, 38 (47). pp. 10143-10155. ISSN 0270-6474

O'Neill, K., Liao, W. W., Patel, A., Hammell, M. G. (October 2018) TEsmall Identifies Small RNAs Associated With Targeted Inhibitor Resistance in Melanoma. Frontiers in Genetics, 9. Article Number: 461 . ISSN 1664-8021

Kepple, D. R., Giaffar, H., Rinberg, D., Koulakov, A. A. (October 2018) Primacy coding in dual olfactory networks. 51st Asilomar Conference on Signals, Systems, and Computers, 2017-O. pp. 587-592.

Albrengues, J., Shields, M. A., Ng, D., Park, C. G., Ambrico, A., Poindexter, M. E., Upadhyay, P., Uyeminami, D. L., Pommier, A., Kuttner, V., Bruzas, E., Maiorino, L., Bautista, C., Carmona, E. M., Gimotty, P. A., Fearon, D. T., Chang, K., Lyons, S. K., Pinkerton, K. E., Trotman, L. C., Goldberg, M. S., Yeh, J. T., Egeblad, M. (September 2018) Neutrophil extracellular traps produced during inflammation awaken dormant cancer cells in mice. Science, 361 (6409). ISSN 0036-8075

Huang, Longwen, Kebschull, Justus, Furth, Daniel, Musall, Simon, Kaufman, Matthew T., Churchland, Anne K., Zador, Anthony (September 2018) High-throughput mapping of mesoscale connectomes in individual mice. bioRxiv.

Skopelitis, D. S., Hill, K., Klesen, S., Marco, C. F., von Born, P., Chitwood, D. H., Timmermans, M. C. P. (August 2018) Gating of miRNA movement at defined cell-cell interfaces governs their impact as positional signals. Nat Commun, 9 (1). p. 3107. ISSN 2041-1723

Wang, Q., Yan, R., Pinnell, N., McCarter, A. C., Oh, Y., Liu, Y., Sha, C., Garber, N. F., Chen, Y., Wu, Q., Ku, C. J., Tran, I., Serna Alarcon, A., Kuick, R., Engel, J. D., Maillard, I., Cierpicki, T., Chiang, M. Y. (August 2018) Stage-specific roles for Zmiz1 in Notch-dependent steps of early T-cell development. Blood. ISSN 0006-4971

Nattestad, M., Goodwin, S., Ng, K., Baslan, T., Sedlazeck, F., Rescheneder, P., Garvin, T., Fang, H., Gurtowski, J., Hutton, E., Tseng, E., Chin, J., Beck, T., Sundaravadanam, Y., Kramer, M., Antoniou, E., McPherson, J., Hicks, J., McCombie, W. R., Schatz, M. C. (August 2018) Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome Res, 28 (8). pp. 1126-1135. ISSN 1088-9051

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

Sedlazeck, F. J., Rescheneder, P., Smolka, M., Fang, H., Nattestad, M., von Haeseler, A., Schatz, M. C. (June 2018) Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods, 15 (6). pp. 461-468. ISSN 1548-7091

Pommier, A., Anaparthy, N., Memos, N., Kelley, Z. L., Gouronnec, A., Yan, R., Auffray, C., Albrengues, J., Egeblad, M., Iacobuzio-Donahue, C. A., Lyons, S. K., Fearon, D. T. (May 2018) Unresolved endoplasmic reticulum stress engenders immune-resistant, latent pancreatic cancer metastases. Science. ISSN 0036-8075

Aznarez, Isabel, Nomakuchi, Tomoki T., Tetenbaum-Novatt, Jaclyn, Rahman, Mohammad Alinoor, Fregoso, Oliver, Rees, Holly, Krainer, Adrian R. (May 2018) Mechanism of Nonsense-Mediated mRNA Decay Stimulation by Splicing Factor SRSF1. Cell Reports, 23 (7). pp. 2186-2198. ISSN 2211-1247

Fein, M. R., He, X. Y., Almeida, A. S., Pommier, A., Bruzas, E., Eberhardt, A., Wilkinson, J. E., dos Santos, C., Egeblad, M. (May 2018) Targeting cancer cell CCR2 enhances synergistic immune surveillance in breast cancer. Cancer Research, 78 (10 Sup). pp. 75-76. ISSN 0008-5472

Han, Y., Kebschull, J. M., Campbell, R. A. A., Cowan, D., Imhof, F., Zador, A. M., Mrsic-Flogel, T. D. (April 2018) The logic of single-cell projections from visual cortex. Nature, 556 (7699). pp. 51-56. ISSN 0028-0836

Naguib, A., Mathew, G., Reczek, C. R., Watrud, K., Ambrico, A., Herzka, T., Salas, I. C., Lee, M. F., El-Amine, N., Zheng, W., Di Francesco, M. E., Marszalek, J. R., Pappin, D. J., Chandel, N. S., Trotman, L. C. (April 2018) Mitochondrial Complex I Inhibitors Expose a Vulnerability for Selective Killing of Pten-Null Cells. Cell Rep, 23 (1). pp. 58-67. ISSN 2211-1247 (Electronic)

Underwood, C. J., Choi, K., Lambing, C., Zhao, X., Serra, H., Borges, F., Simorowski, J., Ernst, E., Jacob, Y., Henderson, I. R., Martienssen, R. A. (April 2018) Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation. Genome Res, 28 (4). pp. 519-531. ISSN 1088-9051

Choi, K., Zhao, X., Tock, A. J., Lambing, C., Underwood, C. J., Hardcastle, T. J., Serra, H., Kim, J., Cho, H. S., Kim, J., Ziolkowski, P. A., Yelina, N. E., Hwang, I., Martienssen, R. A., Henderson, I. R. (April 2018) Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions. Genome Res, 28 (4). pp. 532-546. ISSN 1088-9051

Bružas, Emilis, Egeblad, Mikala (March 2018) Bone Talk: Activated Osteoblasts Promote Lung Cancer Growth. Trends in Molecular Medicine, 24 (3). pp. 237-239. ISSN 1471-4914

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

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

Batut, P. J., Gingeras, T. R. (December 2017) Conserved noncoding transcription and core promoter regulatory code in early Drosophila development. Elife, 6. ISSN 2050-084x

Lee, M., Naguib, A., Trotman, L. C., El-Amine, N. (December 2017) Endocytosis and PTEN in Tumor Suppression. Molecular Biology of the Cell, 28 (26 ASC). Abstract M257. ISSN 1059-15241939-4586

Albrengues, J., Wysocki, R. W., Maiorino, L., Egeblad, M. (November 2017) Re-cyclin' Cell-Cycle Components to Make NETs. Dev Cell, 43 (4). pp. 379-380. ISSN 1534-5807

Delas, M. J., Sabin, L. R., Dolzhenko, E., Knott, S. R., Munera Maravilla, E., Jackson, B. T., Wild, S. A., Kovacevic, T., Stork, E. M., Zhou, M., Erard, N., Lee, E., Kelley, D. R., Roth, M., Barbosa, I. S. A., Zuber, J., Rinn, J. L., Smith, A. D., Hannon, G. J. (September 2017) lncRNA requirements for mouse acute myeloid leukemia and normal differentiation. Elife, 6. e25607. ISSN 2050-084x

Roe, J. S., Hwang, C. I., Somerville, T. D. D., Milazzo, J. P., Lee, E. J., Da Silva, B., Maiorino, L., Tiriac, H., Young, C. M., Miyabayashi, K., Filippini, D., Creighton, B., Burkhart, R. A., Buscaglia, J. M., Kim, E. J., Grem, J. L., Lazenby, A. J., Grunkemeyer, J. A., Hollingsworth, M. A., Grandgenett, P. M., Egeblad, M., Park, Y., Tuveson, D. A., Vakoc, C. R. (August 2017) Enhancer Reprogramming Promotes Pancreatic Cancer Metastasis. Cell, 170 (5). pp. 875-888. ISSN 0092-8674

Faehnle, C. R., Walleshauser, J., Joshua-Tor, L. (August 2017) Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis. Nat Struct Mol Biol, 24 (8). pp. 658-665. ISSN 1545-9985 (Public Dataset)

Vurture, G. W., Sedlazeck, F. J., Nattestad, M., Underwood, C. J., Fang, H., Gurtowski, J., Schatz, M. C. (July 2017) GenomeScope: Fast reference-free genome profiling from short reads. Bioinformatics, 33 (14). pp. 2202-2204. ISSN 1367-4803

Romero-Hernandez, A., Furukawa, H. (July 2017) Novel mode of antagonist binding in NMDA receptors revealed by the crystal structure of the GluN1-GluN2A ligand-binding domain complexed to NVP-AAM077. Mol Pharmacol, 92 (1). pp. 22-29. ISSN 0026-895x (Public Dataset)

Delas, M. J., Hannon, G. J. (July 2017) lncRNAs in development and disease: from functions to mechanisms. Open Biol, 7 (7). ISSN 2046-2441

Schorn, A. J., Gutbrod, M. J., LeBlanc, C., Martienssen, R. (June 2017) LTR-Retrotransposon Control by tRNA-Derived Small RNAs. Cell, 170 (1). 61-71.e11. ISSN 0092-8674 (Public Dataset)

Chang, An-Yun, Castel, Stephane E., Ernst, Evan, Kim, Hyun Soo, Martienssen, Robert A. (June 2017) The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly. Cell Reports, 19 (12). pp. 2477-2489. ISSN 2211-1247

Chalk, M., Masset, P., Gutkin, B., Deneve, S. (June 2017) Sensory noise predicts divisive reshaping of receptive fields. PLoS Comput Biol, 13 (6). e1005582. ISSN 1553-734x

Soyk, Sebastian, Lemmon, Zachary H., Oved, Matan, Fisher, Josef, Liberatore, Katie L., Park, Soon Ju, Goren, Anna, Jiang, Ke, Ramos, Alexis, van der Knaap, Esther, Van Eck, Joyce, Zamir, Dani, Eshed, Yuval, Lippman, Zachary B. (June 2017) Bypassing Negative Epistasis on Yield in Tomato Imposed by a Domestication Gene. Cell, 169 (6). pp. 1142-1155. ISSN 0092-8674

Feigin, M. E., Garvin, T., Bailey, P., Waddell, N., Chang, D. K., Kelley, D. R., Shuai, S., Gallinger, S., McPherson, J. D., Grimmond, S. M., Khurana, E., Stein, L. D., Biankin, A. V., Schatz, M. C., Tuveson, D. A. (June 2017) Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma. Nat Genet, 49 (6). pp. 825-833. ISSN 1061-4036

Oberauer, K., Stoneking, C., Wabersich, D., Lin, H. Y. (May 2017) Hierarchical Bayesian measurement models for continuous reproduction of visual features from working memory. J Vis, 17 (5). p. 11. ISSN 1534-7362

Peikon, I. D., Kebschull, J. M., Vagin, V. V., Ravens, D. I., Sun, Y. C., Brouzes, E., Correa, I. R., Bressan, D., Zador, A. M. (April 2017) Using high-throughput barcode sequencing to efficiently map connectomes. Nucleic Acids Res. ISSN 0305-1048

Underwood, Charles J., Henderson, Ian R., Martienssen, Robert A. (April 2017) Genetic and epigenetic variation of transposable elements in Arabidopsis. Current Opinion in Plant Biology, 36. pp. 135-141. ISSN 1369-5266

Chen, M., Nowak, D. G., Narula, N., Robinson, B., Watrud, K., Ambrico, A., Herzka, T. M., Zeeman, M. E., Minderer, M., Zheng, W., Ebbesen, S. H., Plafker, K. S., Stahlhut, C., Wang, V. M., Wills, L., Nasar, A., Castillo-Martin, M., Cordon-Cardo, C., Wilkinson, J. E., Powers, S., Sordella, R., Altorki, N. K., Mittal, V., Stiles, B. M., Plafker, S. M., Trotman, L. C. (March 2017) The nuclear transport receptor Importin-11 is a tumor suppressor that maintains PTEN protein. J Cell Biol, 216 (3). pp. 641-656. ISSN 0021-9525

Pal, D., Pertot, A., Shirole, N. H., Yao, Z., Anaparthy, N., Garvin, T., Cox, H., Chang, K., Rollins, F., Kendall, J., Edwards, L., Singh, V. A., Stone, G. C., Schatz, M. C., Hicks, J., Hannon, G., Sordella, R. (January 2017) TGF-beta reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24- cancer cells. Elife, 6. ISSN 2050-084X (Electronic)2050-084X (Linking)

Romero-Hernandez, Annabel, Simorowski, Noriko, Karakas, Erkan, Furukawa, Hiro (December 2016) Molecular Basis for Subtype Specificity and High-Affinity Zinc Inhibition in the GluN1-GluN2A NMDA Receptor Amino-Terminal Domain. Neuron, 92 (6). pp. 1324-1336. ISSN 0896-6273 (Public Dataset)

Chin, C. S., Peluso, P., Sedlazeck, F. J., Nattestad, M., Concepcion, G. T., Clum, A., Dunn, C., O'Malley, R., Figueroa-Balderas, R., Morales-Cruz, A., Cramer, G. R., Delledonne, M., Luo, C., Ecker, J. R., Cantu, D., Rank, D. R., Schatz, M. C. (December 2016) Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods, 13 (12). pp. 1050-1054. ISSN 1548-7105 (Electronic)1548-7091 (Linking)

Delevich, K., Abi-Dargham, A., Hall, J., Sawa, A. (October 2016) Studying schizophrenia in the post-genomic era: perspectives from the 2016 summer Banbury Workshop at Cold Spring Harbor Laboratory. Mol Psychiatry. ISSN 1476-5578 (Electronic)1359-4184 (Linking)

Park, J., Wysocki, R. W., Amoozgar, Z., Maiorino, L., Fein, M. R., Jorns, J., Schott, A. F., Kinugasa-Katayama, Y., Lee, Y., Won, N. H., Nakasone, E. S., Hearn, S. A., Kuttner, V., Qiu, J., Almeida, A. S., Perurena, N., Kessenbrock, K., Goldberg, M. S., Egeblad, M. (October 2016) Cancer cells induce metastasis-supporting neutrophil extracellular DNA traps. Sci Transl Med, 8 (361). 361ra138. ISSN 1946-6242 (Electronic)1946-6234 (Linking)

Nattestad, M., Schatz, M. C. (October 2016) Assemblytics: a web analytics tool for the detection of variants from an assembly. Bioinformatics, 32 (19). pp. 3021-3023. ISSN 1367-4811 (Electronic)1367-4803 (Linking)

Pisupati, S., Chartarifsky, L., Churchland, A. K. (September 2016) Decision Activity in Parietal Cortex - Leader or Follower? Trends Cogn Sci. ISSN 1879-307X (Electronic)1364-6613 (Linking)

Kebschull, Justus M, Garcia da Silva, Pedro, Reid, Ashlan P, Peikon, Ian D, Albeanu, Dinu F, Zador, Anthony M (September 2016) High-Throughput Mapping of Single-Neuron Projections by Sequencing of Barcoded RNA. Neuron, 91 (5). pp. 975-987. ISSN 0896-6273 (Public Dataset)

Otazu, G. H., Masset, P. P., Albeanu, D. F. (September 2016) A Computational Role for Cortical Feedback in Odor Detection in Natural Scenes. Chemical Senses, 41 (7). E101-E102. ISSN 0379-864X

Hohmann, A. F., Martin, L. J., Minder, J. L., Roe, J. S., Shi, J., Steurer, S., Bader, G., McConnell, D., Pearson, M., Gerstberger, T., Gottschamel, T., Thompson, D., Suzuki, Y., Koegl, M., Vakoc, C. R. (September 2016) Sensitivity and engineered resistance of myeloid leukemia cells to BRD9 inhibition. Nat Chem Biol, 12 (9). pp. 672-9. ISSN 1552-4469 (Electronic)1552-4450 (Linking) (Public Dataset)

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)

Fagegaltier, D., Falciatori, I., Czech, B., Castel, S., Perrimon, N., Simcox, A., Hannon, G. J. (July 2016) Oncogenic transformation of Drosophila somatic cells induces a functional piRNA pathway. Genes Dev, 30 (14). pp. 1623-35. ISSN 1549-5477 (Electronic)0890-9369 (Linking)

Choi, K., Reinhard, C., Serra, H., Ziolkowski, P. A., Underwood, C. J., Zhao, X., Hardcastle, T. J., Yelina, N. E., Griffin, C., Jackson, M., Mezard, C., McVean, G., Copenhaver, G. P., Henderson, I. R. (July 2016) Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes. PLoS Genet, 12 (7). e1006179. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

Manchado, E., Weissmueller, S., Morris, J. P., Chen, C. C., Wullenkord, R., Lujambio, A., de Stanchina, E., Poirier, J. T., Gainor, J. F., Corcoran, R. B., Engelman, J. A., Rudin, C. M., Rosen, N., Lowe, S. W. (June 2016) A combinatorial strategy for treating KRAS-mutant lung cancer. Nature, 534. pp. 647-51. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Martin, L. J., Koegl, M., Bader, G., Cockcroft, X. L., Fedorov, O., Fiegen, D., Gerstberger, T., Hofmann, M. H., Hohmann, A. F., Kessler, D., Knapp, S., Knesl, P., Kornigg, S., Muller, S., Nar, H., Rogers, C., Rumpel, K., Schaaf, O., Steurer, S., Tallant, C., Vakoc, C. R., Zeeb, M., Zoephel, A., Pearson, M., Boehmelt, G., McConnell, D. (May 2016) Structure-Based Design of an in Vivo Active Selective BRD9 Inhibitor. J Med Chem, 59 (10). pp. 4462-75. ISSN 1520-4804 (Electronic)0022-2623 (Linking)

Kebschull, J. M., Garcia da Silva, P., Zador, A. M. (May 2016) A New Defective Helper RNA to Produce Recombinant Sindbis Virus that Infects Neurons but does not Propagate. Front Neuroanat, 10. p. 56. ISSN 1662-5129 (Electronic)1662-5129 (Linking)

Sanders, Joshua I, Hangya, Balázs, Kepecs, Adam (May 2016) Signatures of a Statistical Computation in the Human Sense of Confidence. Neuron, 90 (3). pp. 499-506. ISSN 0896-6273

Bhagwat, A. S., Roe, J. S., Mok, B. Y., Hohmann, A. F., Shi, J., Vakoc, C. R. (April 2016) BET Bromodomain Inhibition Releases the Mediator Complex from Select cis-Regulatory Elements. Cell Rep, 15 (3). pp. 519-30. ISSN 2211-1247 (Electronic)

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)

Christov-Moore, L., Sugiyama, T., Grigaityte, K., Iacoboni, M. (April 2016) Increasing generosity by disrupting prefrontal cortex. Soc Neurosci, 12 (2). pp. 174-181. ISSN 1747-0927 (Electronic)1747-0919 (Linking)

Ebbesen, S. H., Scaltriti, M., Bialucha, C. U., Morse, N., Kastenhuber, E. R., Wen, H. Y., Dow, L. E., Baselga, J., Lowe, S. W. (March 2016) Pten loss promotes MAPK pathway dependency in HER2/neu breast carcinomas. Proc Natl Acad Sci U S A, 113 (11). pp. 3030-3035. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Plavskin, Yevgeniy, Nagashima, Akitomo, Perroud, Pierre-François, Hasebe, Mitsuyasu, Quatrano, Ralph S, Atwal, Gurinder S, Timmermans, Marja C P. (February 2016) Ancient trans-Acting siRNAs Confer Robustness and Sensitivity onto the Auxin Response. Developmental Cell, 36 (3). pp. 276-289. ISSN 1534-5807

Kim, Y., Perova, Z., Mirrione, M. M., Pradhan, K., Henn, F. A., Shea, S., Osten, P., Li, B. (February 2016) Whole-Brain Mapping of Neuronal Activity in the Learned Helplessness Model of Depression. Front Neural Circuits, 10. ISSN 1662-5110 (Electronic)1662-5110 (Linking)

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)

Zepeda-Mendoza, C. J., Mukhopadhyay, S., Wong, E. S., Harder, N., Splinter, E., de Wit, E., Eckersley-Maslin, M. A., Ried, T., Eils, R., Rohr, K., Mills, A., de Laat, W., Flicek, P., Sengupta, A. M., Spector, D. L. (November 2015) Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2. BMC Genomics, 16 (1). p. 982. ISSN 1471-2164 (Electronic)1471-2164 (Linking)

Zhou, X., Battistoni, G., El Demerdash, O., Gurtowski, J., Wunderer, J., Falciatori, I., Ladurner, P., Schatz, M. C., Hannon, G. J., Wasik, K. A. (November 2015) Dual functions of Macpiwi1 in transposon silencing and stem cell maintenance in the flatworm Macrostomum lignano. RNA, 21 (11). pp. 1885-1897. ISSN 1469-9001 (Electronic)1355-8382 (Linking)

Garvin, T., Aboukhalil, R., Kendall, J., Baslan, T., Atwal, G. S., Hicks, J., Wigler, M., Schatz, M. C. (November 2015) Interactive analysis and assessment of single-cell copy-number variations. Nat Methods, 12. pp. 1058-1060. ISSN 1548-7105 (Electronic)1548-7091 (Linking) (Public Dataset)

Yu, Y., Gu, J., Jin, Y., Luo, Y., Preall, J. B., Ma, J., Czech, B., Hannon, G. J. (October 2015) Panoramix enforces piRNA-dependent cotranscriptional silencing. Science, 350 (6258). pp. 339-42. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Wasik, K., Gurtowski, J., Zhou, X., Ramos, O. M., Delas, M. J., Battistoni, G., El Demerdash, O., Falciatori, I., Vizoso, D. B., Smith, A. D., Ladurner, P., Scharer, L., McCombie, W. R., Hannon, G. J., Schatz, M. (September 2015) Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano. Proc Natl Acad Sci U S A, 112 (40). pp. 12462-12467. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Dong, J., Panchakshari, R. A., Zhang, T., Zhang, Y., Hu, J., Volpi, S. A., Meyers, R. M., Ho, Y. J., Du, Z., Robbiani, D. F., Meng, F., Gostissa, M., Nussenzweig, M. C., Manis, J. P., Alt, F. W. (September 2015) Orientation-specific joining of AID-initiated DNA breaks promotes antibody class switching. Nature, 525 (7567). pp. 134-9. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Chae, H. G., Kepple, D., Koulakov, A. A., Murthy, V. N., Albeanu, D. F. (September 2015) Mosaic representation of odors in the output layer of the mouse olfactory bulb. Chemical Senses, 40 (7). p. 564. ISSN 0379-864X

Regan, Michael C., Romero-Hernandez, Annabel, Furukawa, Hiro (August 2015) A structural biology perspective on NMDA receptor pharmacology and function. Current Opinion in Structural Biology, 33. pp. 68-75. ISSN 0959-440X

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Chiang, A. S., Blum, A., Barditch, J., Chen, Y. H., Chiu, S. L., Regulski, M., Armstrong, J. D., Tully, T., Dubnau, J. T. (February 2004) radish encodes a phospholipase-A2 and defines a neural circuit involved in anesthesia-resistant memory. Current Biology, 14 (4). pp. 263-272. ISSN 0960-9822

Bastow, R., Mylne, J. S., Lister, C., Lippman, Z., Martienssen, R. A., Dean, C. (January 2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Nature, 427 (6970). pp. 164-7. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

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Book Section

Campbell, R. A. A., Honegger, K. S., Gruntman, E., Turner, G. C. (2012) Two-Photon Imaging of Population Activity with Genetically Encoded Calcium Indicators in Living Flies. In: Genetically Encoded Functional Indicators. Neuromethods, 72 . Humana Press, pp. 113-124. ISBN 978-1-62703-013-7

Paddison, P. J., Caudy, A. A., Sachidanandam, R., Hannon, G. J. (2004) Short hairpin activated gene silencing in mammalian cells. In: RNA Interference, Editing and Modification: methods and protocols. Methods Mol Biol, 265 . Springer, pp. 85-100.

Hall, I. M., Grewal, S. I. S. (2003) Structure and function of heterochromatin: implications for epigenetic gene silencing and genome organization. In: RNAi : a guide to gene silencing. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. , pp. 205-232. ISBN 978-087969641-2

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