Items where Year is 2011

Up a level
Export as [feed] Atom [feed] RSS 1.0 [feed] RSS 2.0
Group by: Authors | Item Type | No Grouping
Jump to: A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | V | W | X | Y | Z
Number of items: 308.

A

Adams, B., Golding, S., Biddlestone-Thorpe, L., Beckta, J., Saleh, H., Enikopolov, G., Valerie, K. (2011) In Vivo and In Vitro Human Brain Tumor Models for Improving the Therapeutic Ratio of Ionizing Radiation and DNA Repair Inhibitors. International Journal of Radiation Oncology Biology Physics, 81 (S2). S741-S742. ISSN 0360-3016

Akst, J. (2011) Chromosomes and Cancer. The Scientist.

Al-Balool, H. H., Weber, D., Liu, Y., Wade, M., Guleria, K., Nam, P. L. P., Clayton, J., Rowe, W., Coxhead, J., Irving, J., Elliott, D. J., Hall, A. G., Santibanez-Koref, M., Jackson, M. S. (2011) Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant. Genome Research, 21 (11). pp. 1788-1799. ISSN 10889051 (ISSN)

Albers, C., Illert, A. L., Miething, C., Leischner, H., Thiede, M., Peschel, C., Duyster, J. (2011) An RNAi-based system for loss-of-function analysis identifies Raf1 as a crucial mediator of BCR-ABL - Driven leukemogenesis. Blood, 118 (8). pp. 2200-2210. ISSN 00064971 (ISSN)

Albert, F. W., Hodges, E., Jensen, J. D., Besnier, F., Xuan, Z. Y., Rooks, M., Bhattacharjee, A., Brizuela, L., Good, J. M., Green, R. E., Burbano, H. A., Plyusnina, I. Z., Trut, L., Andersson, L., Schoneberg, T., Carlborg, O., Hannon, G. J., Paabo, S. (2011) Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection. Heredity, 107 (3). pp. 205-214. ISSN 0018-067X

Amador-Arjona, A., Elliott, J., Miller, A., Ginbey, A., Pazour, G. J., Enikolopov, G. N., Roberts, A. J., Terskikh, A. V. (2011) Primary cilia regulate proliferation of amplifying progenitors in adult hippocampus: implications for learning and memory. J Neurosci, 31 (27). pp. 9933-44. ISSN 1529-2401 (Electronic) 0270-6474 (Linking)

Argout, X., Salse, J., Aury, J. M., Guiltinan, M. J., Droc, G., Gouzy, J., Allegre, M., Chaparro, C., Legavre, T., Maximova, S. N., Abrouk, M., Murat, F., Fouet, O., Poulain, J., Ruiz, M., Roguet, Y., Rodier-Goud, M., Barbosa-Neto, J. F., Sabot, F., Kudrna, D., Ammiraju, J. S. S., Schuster, S. C., Carlson, J. E., Sallet, E., Schiex, T., Dievart, A., Kramer, M. R., Gelley, L., Shi, Z., Bérard, A., Viot, C., Boccara, M., Risterucci, A. M., Guignon, V., Sabau, X., Axtell, M. J., Ma, Z., Zhang, Y, Brown, S., Bourge, M., Golser, W., Song, X., Clement, D., Rivallan, R., Tahi, M., Akaza, J. M., Pitollat, B., Gramacho, K., D'Hont, A., Brunel, D., Infante, D., Kebe, I., Costet, P., Wing, R., McCombie, W. R., Guiderdoni, E., Quetier, F., Panaud, O., Wincker, P., Bocs, S., Lanaud, C. (2011) The genome of Theobroma cacao. Nature Genetics, 43 (2). pp. 101-108. ISSN 10614036

B

Balagula, Y., Pulitzer, M. P., Maki, R. G., Myskowski, P. L. (2011) Pigmentary changes in a patient treated with imatinib. J Drugs Dermatol, 10 (9). pp. 1062-6. ISSN 1545-9616 (Print)1545-9616 (Linking)

Banks, J. A., Nishiyama, T., Hasebe, M., Bowman, J. L., Gribskov, M., Depamphilis, C., Albert, V. A., Aono, N., Aoyama, T., Ambrose, B. A., Ashton, N. W., Axtell, M. J., Barker, E., Barker, M. S., Bennetzen, J. L., Bonawitz, N. D., Chapple, C., Cheng, C., Correa, L. G. G., Dacre, M., Debarry, J., Dreyer, I., Elias, M., Engstrom, E. M., Estelle, M., Feng, L., Finet, C., Floyd, S. K., Frommer, W. B., Fujita, T., Gramzow, L., Gutensohn, M., Harholt, J., Hattori, M., Heyl, A., Hirai, T., Hiwatashi, Y., Ishikawa, M., Iwata, M., Karol, K. G., Koehler, B., Kolukisaoglu, U., Kubo, M., Kurata, T., Lalonde, S., Li, K., Li, Y., Litt, A., Lyons, E., Manning, G., Maruyama, T., Michael, T. P., Mikami, K., Miyazaki, S., Morinaga, S., Murata, T., Mueller-roeber, B., Nelson, D. R., Obara, M., Oguri, Y., Olmstead, R. G., Onodera, N., Petersen, B. L., Pils, B., Prigge, M., Rensing, S. A., Riaño-Pachón, D. M., Roberts, A. W., Sato, Y., Scheller, H. V., Schulz, B., Schulz, C., Shakirov, E. V., Shibagaki, N., Shinohara, N., Shippen, D. E., Sørensen, I., Sotooka, R., Sugimoto, N., Sugita, M., Sumikawa, N., Tanurdzic, M., Theiben, G., Ulvskov, P., Wakazuki, S., Weng, J., Willats, W. W. G. T., Wipf, D., Wolf, P. G., Yang, L., Zimmer, A. D., Zhu, Q., Mitros, T., Hellsten, U., Loqué, D., Otillar, R., Salamov, A., Schmutz, J., Shapiro, H., Lindquist, E. (2011) The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants. Science, 332 (6032). pp. 963-966. ISSN 00368075

Baumann, U., Targosz, B. S., Lemeer, S., Nikolova, V., Kratzat, S., Fernandez-Saiz, V., Reiter, C., Rudelius, M., Miething, C., Kuster, B., Peschel, C., Keller, U., Bassermann, F. (2011) SCF(Fbxo25) suppresses B cell lymphomagenesis by targeting Hax-1 for ubiquitin mediated proteasomal degradation. Onkologie, 34. p. 190. ISSN 0378-584X

Bell, S., Li, J., Walter, J. (2011) EUKARYOTIC DNA REPLICATION & GENOME MAINTENANCE. In: 2011 meeting on EUKARYOTIC DNA REPLICATION & GENOME MAINTENANCE, September 6–September 10, 2011.

Benitez-Alfonso, Y., Jackson, D. P., Maule, A. (2011) Redox regulation of intercellular transport. Protoplasma, 248 (1). pp. 131-140.

Benitez-Alfonso, Y., Jackson, D. P., Maule, A. (2011) Redox regulation of intercellular transport. Protoplasma, 248 (1). pp. 131-140.

Berezikov, E., Robine, N., Samsonova, A., Westholm, J. O., Naqvi, A., Hung, J. H., Okamura, K., Dai, Q., Bortolamiol-Becet, D., Martin, R., Zhao, Y. J., Zamore, P. D., Hannon, G. J., Marra, M. A., Weng, Z. P., Perrimon, N., Lai, E. C. (2011) Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Research, 21 (2). pp. 203-215. ISSN 1088-9051

Bergmann, J. H., Rodriguez, M. G., Martins, N. M. C., Kimura, H., Kelly, D. A., Masumoto, H., Larionov, V., Jansen, L. E. T., Earnshaw, W. C. (2011) Epigenetic engineering shows H3K4me2 is required for HJURP targeting and CENP-A assembly on a synthetic human kinetochore. EMBO Journal, 30 (2). pp. 328-340.

Bernard Chera, T.H. , Sing Chana, H. , Kleinb, G. F. , Jabkowskib, J. , Schadenböck-Kranzlc, G. , Zachd, O. , Roca, X., Alex Law, S.K. (2011) A novel 3′ splice-site mutation and a novel gross deletion in leukocyte adhesion deficiency (LAD)-1star, open. Biochemical and Biophysical Research Communications, 404 (4). pp. 1099-1104. ISSN 0006-291X

Birbrair, A., Wang, Z. M., Messi, M. L., Enikolopov, G. N. , Delbono, O. (2011) Nestin-GFP transgene reveals neural precursor cells in adult skeletal muscle. PLoS ONE, 6 (2). ISSN 19326203 (ISSN)

Bivona, T. G., Hieronymus, H., Parker, J., Chang, K., Taron, M., Rosell, R., Moonsamy, P., Dahlman, K., Miller, V. A., Costa, C., Hannon, G. J., Sawyers, C. L. (2011) FAS and NF-kappa B signalling modulate dependence of lung cancers on mutant EGFR. Nature, 471 (7339). pp. 523-526. ISSN 0028-0836

Bogdanove, A. J., Koebnik, R., Lu, H., Furutani, A., Angiuoli, S. V., Patil, P. B., Van Sluys, M. A., Ryan, R. P., Meyer, D. F., Han, S. W., Aparna, G., Rajaram, M., Delcher, A. L., Phillippy, A. M., Puiu, D., Schatz, M. C., Shumway, M., Sommer, D. D., Trapnell, C., Benahmed, F., Dimitrov, G., Madupu, R., Radune, D., Sullivan, S., Jha, G., Ishihara, H., Lee, S. W., Pandey, A., Sharma, V., Sriariyanun, M., Szurek, B., Vera-Cruz, C. M., Dorman, K. S., Ronald, P. C., Verdier, V., Dow, J. M., Sonti, R. V., Tsuge, S., Brendel, V. P., Rabinowicz, P. D., Leach, J. E., White, F. F., Salzberg, S. L. (2011) Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. Journal of Bacteriology, 193 (19). pp. 5450-5464. ISSN 00219193 (ISSN)

Borges, F., Pereira, P. A., Slotkin, R. K., Martienssen, R. A., Becker, J. D. (2011) MicroRNA activity in the Arabidopsis male germline. Journal of Experimental Botany, 62 (5). pp. 1611-1620. ISSN 0022-0957

Botcheva, K., McCorkle, S. R., McCombie, W. R., Dunn, J. J., Anderson, C. W. (2011) Distinct p53 genomic binding patterns in normal and cancer-derived human cells. Cell Cycle, 10 (24). pp. 4237-4249. ISSN 1538-4101

Brady, S. M., Zhang, L., Megraw, M., Martinez, N. J., Jiang, E., Yi, C. S., Liu, W., Zeng, A., Taylor-Teeples, M., Kim, D., Ahnert, S., Ohler, U., Ware, D. H., Walhout, A. J. M., Benfey, P. N. (2011) A stele-enriched gene regulatory network in the Arabidopsis root. Molecular Systems Biology, 7. p. 459.

Brennand, K. J., Simone, A., Jou, J., Gelboin-Burkhart, C., Tran, N., Sangar, S., Li, Y., Mu, Y., Chen, G., Yu, D., McCarthy, S. E., Sebat, J., Gage, F. H. (2011) Modelling schizophrenia using human induced pluripotent stem cells. Nature, 473 (7346). 221 - 225. ISSN 00280836 (ISSN)

Brumby, A. M., Goulding, K. R., Schlosser, T., Loi, S., Galea, R., Khoo, P., Bolden, J. E., Aigaki, T., Humbert, P. O., Richardson, H. E. (2011) Identification of novel Ras-cooperating oncogenes in Drosophila melanogaster: A RhoGEF/Rho-family/JNK pathway is a central driver of tumorigenesis. Genetics, 188 (1). pp. 105-125. ISSN 00166731 (ISSN)

Bush, K., Courvalin, P., Dantas, G., Davies, J., Eisenstein, B., Huovinen, P., Jacoby, G. A., Kishony, R., Kreiswirth, B. N., Kutter, E., Lerner, S. A., Levy, S., Lewis, K., Lomovskaya, O., Miller, J. H., Mobashery, S., Piddock, L. J. V., Projan, S., Thomas, C. M., Tomasz, A., Tulkens, P. M., Walsh, T. R., Watson, J. D., Witkowski, J., Witte, W., Wright, G., Yeh, P., Zgurskaya, H. I. (2011) Tackling antibiotic resistance. Nature Reviews Microbiology, 9 (12). pp. 894-896. ISSN 17401526 (ISSN)

C

Cabal, R., Khanin, R., Viali, A., Socci, N., Lucito, R., Olshen, A., Zhang, J., Gerald, W., Powers, S., Ladanyi, M. (2011) Testing and Validating High Throughput Genomic Analysis of FFPE Samples: Systematic Gene Expression Differences between Matched Frozen and FFPE Samples Due to Rapid mRNA Degradation Signals. Modern Pathology, 24. p. 1875. ISSN 0893-3952

Calarco, J. P., Martienssen, R. A. (2011) Genome reprogramming and small interfering RNA in the Arabidopsis germline. Curr Opin Genet Dev, 21 (2). pp. 134-9. ISSN 1879-0380 (Electronic) 0959-437X (Linking)

Chan, C. S., Glajch, K. E., Gertler, T. S., Guzman, J. N., Mercer, J. N., Lewis, A. S., Goldberg, A. B., Tkatch, T., Shigemoto, R., Fleming, S. M., Chetkovich, D. M., Osten, P., Kita, H., Surmeier, D. J. (2011) HCN channelopathy in external globus pallidus neurons in models of Parkinson's disease. Nature Neuroscience, 14 (1). 85-U117. ISSN 1097-6256

Chen, M. H., Pratt, C. P., Zeeman, M. E., Schultz, N., Taylor, B. S., O'Neill, A., Castillo-Martin, M., Nowak, D. G., Naguib, A., Grace, D. M., Murn, J., Navin, N., Atwal, G. S., Sander, C., Gerald, W. L., Cordon-Cardo, C., Newton, A. C., Carver, B. S., Trotman, L. C. (2011) Identification of PHLPP1 as a Tumor Suppressor Reveals the Role of Feedback Activation in PTEN-Mutant Prostate Cancer Progression. Cancer Cell, 20 (2). pp. 173-186. ISSN 1535-6108

Cheng, J., Zhu, Y., He, S., Lu, Y., Chen, J., Han, B., Petrillo, M., Wrzeszczynski, K. O., Yang, S., Dai, P., Zhai, S., Han, D., Zhang, M. Q., Li, W., Liu, X., Li, H., Chen, Z. Y., Yuan, H. (2011) Functional Mutation of SMAC/DIABLO, Encoding a Mitochondrial Proapoptotic Protein, Causes Human Progressive Hearing Loss DFNA64. The American Journal of Human Genetics, 89 (1). pp. 56-66. ISSN 0002-9297

Cherbas, L., Willingham, A., Zhang, D., Yang, L., Zou, Y., Eads, B. D., Carlson, J. W., Landolin, J. M., Kapranov, P., Dumais, J., Samsonova, A., Choi, J. H., Roberts, J., Davis, C. A., Tang, H., Van Baren, M. J., Ghosh, S., Dobin, A., Bell, K. G., Lin, W., Langton, L., Duff, M. O., Tenney, A. E., Zaleski, C., Brent, M. R., Hoskins, R. A., Kaufman, T. C., Andrews, J., Graveley, B. R., Perrimon, N., Celniker, S. E., Gingeras, T. R., Cherbas, P. (2011) The transcriptional diversity of 25 Drosophila cell lines. Genome Research, 21 (2). pp. 301-314. ISSN 10889051 (ISSN)

Chia, J. M., Ware, D. H. (2011) Sequencing for the cream of the crop. Nature Biotechnology, 29 (2). pp. 138-9. ISSN 1546-1696 (Electronic) 1087-0156 (Linking)

Chien, Y., Scuoppo, C., Wang, X., Fang, X., Balgley, B., Bolden, J. E., Premsrirut, P., Luo, W., Chicas, A., Lee, C. S., Kogan, S. C., Lowe, S. W. (2011) Control of the senescence-associated secretory phenotype by NF-kappaB promotes senescence and enhances chemosensitivity. Genes Dev, 25 (20). pp. 2125-36. ISSN 1549-5477 (Electronic) 0890-9369 (Linking)

Cho, S. Y., Hoang, A., Sinha, R., Zhong, X. Y., Fu, X. D., Krainer, A. R., Ghosh, G. (2011) Interaction between the RNA binding domains of Ser-Arg splicing factor 1 and U1-70K snRNP protein determines early spliceosome assembly. Proceedings of the National Academy of Sciences of the United States of America, 108 (20). pp. 8233-8238. ISSN 0027-8424

Choi, Y. J., Lin, C. P., Ho, J. J., He, X., Okada, N., Bu, P., Zhong, Y., Kim, S. Y., Bennett, M. J., Chen, C., Ozturk, A., Hicks, G. G., Hannon, G. J., He, L. (2011) MiR-34 miRNAs provide a barrier for somatic cell reprogramming. Nature Cell Biology, 13 (11). pp. 1353-1360. ISSN 14657392 (ISSN)

Churchland, A. K. (2011) Normalizing relations between the senses. Nature Neuroscience, 14 (6). pp. 672-3. ISSN 1097-6256

Churchland, A. K. (2011) Talk from Anne Churchland at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Churchland, A. K., Kiani, R., Chaudhuri, R., Wang, X. J., Pouget, A., Shadlen, M. N. (2011) Variance as a Signature of Neural Computations during Decision Making. Neuron, 69 (4). pp. 818-831.

Clark, M. B., Amaral, P. P., Schlesinger, F. J., Dinger, M. E., Taft, R. J., Rinn, J. L., Ponting, C. P., Stadler, P. F., Morris, K. V., Morillon, A., Rozowsky, J. S., Gerstein, M. B., Wahlestedt, C., Hayashizaki, Y., Carninci, P., Gingeras, T. R., Mattick, J. S. (2011) The reality of pervasive transcription. Plos Biology, 9 (7). ISSN 15449173

Comte, I., Kim, Y., Young, C. C., van der Harg, J. M., Hockberger, P., Bolam, P. J., Poirier, F., Szele, F. G. (2011) Galectin-3 maintains cell motility from the subventricular zone to the olfactory bulb. Journal of Cell Science, 124 (14). pp. 2438-2447. ISSN 00219533 (ISSN)

Consortium, Arabidopsis Interactome Mapping (2011) Evidence for Network Evolution in an Arabidopsis Interactome Map. Science, 333 (6042). pp. 601-607.

Creasey, K. M., Martienssen, R. A. (2011) Germline Reprogramming of Heterochromatin in Plants. Cold Spring Harbor Symposia on Quantitative Biology, 75. pp. 269-274. ISSN 00917451 (ISSN)

Croft, D., O'Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Gopinath, G., Jassal, B., Jupe, S., Kalatskaya, I., MayMahajan, S., May, B., Ndegwa, N., Schmidt, E., Shamovsky, V., Yung, C., Birney, E., Hermjakob, H., D'Eustachio, P., Stein, L. D. (2011) Reactome: A database of reactions, pathways and biological processes. Nucleic Acids Research, 39 (SUPPL.).

Czech, B., Hannon, G. J. (2011) Small RNA sorting: matchmaking for Argonautes. Nat Rev Genet, 12 (1). pp. 19-31. ISSN 1471-0064 (Electronic) 1471-0056 (Linking)

D

Daher, M., Lacouture, M. E., Rathkopf, D., Maki, R. G., Keohan, M. L., Gansukh, B., Chen, H., Abou-Alfa, G. K. (2011) Case series of dermatologic events associated with the insulin-like growth factor receptor 1 inhibitor cixutumumab. J Clin Oncol, 29 (21). e638-40. ISSN 1527-7755 (Electronic)0732-183X (Linking)

Darnell, J. C., Van Driesche, S. J., Zhang, C., Hung, K. Y. S., Mele, A., Fraser, C. E., Stone, E. F., Chen, C., Fak, J. J., Chi, S. W., Licatalosi, D. D., Richter, J. D., Darnell, R. B. (2011) FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism. Cell, 146 (2). pp. 247-261. ISSN 00928674 (ISSN)

DeNicola, G. M., Karreth, F. A., Humpton, T. J., Gopinathan, A., Wei, C., Frese, K., Mangal, D., Yu, K. H., Yeo, C. J., Calhoun, E. S., Scrimieri, F., Winter, J. M., Hruban, R. H., Iacobuzio-Donahue, C., Kern, S. E., Blair, I. A., Tuveson, D. A. (2011) Oncogene-induced Nrf2 transcription promotes ROS detoxification and tumorigenesis. Nature, 475 (7354). pp. 106-9. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Delmore, J. E., Issa, G. C., Lemieux, M. E., Rahl, P. B., Shi, J. W., Jacobs, H. M., Kastritis, E., Gilpatrick, T., Paranal, R. M., Qi, J., Chesi, M., Schinzel, A. C., McKeown, M. R., Heffernan, T. P., Vakoc, C. R., Bergsagel, P.  , Ghobrial, I. M., Richardson, P. G., Young, R. A., Hahn, W. C., Anderson, K. C., Kung, A. L., Bradner, J. E., Mitsiades, C. S. (2011) BET Bromodomain Inhibition as a Therapeutic Strategy to Target c-Myc. Cell, 146 (6). pp. 904-917. ISSN 00928674 (ISSN)

Deng, X., Hiatt, J. B., Nguyen, D. K., Ercan, S., Sturgill, D., Hillier, L. W., Schlesinger, F., Davis, C. A., Reinke, V. J., Gingeras, T. R., Shendure, J., Waterston, R. H., Oliver, B., Lieb, J. D., Disteche, C. M. (2011) Balance of the x restored: evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nature Genetics, 43 (12). pp. 1179-85. ISSN 10614036 (ISSN)

Depge-Fargeix, N., Javelle, M., Chambrier, P., Frangne, N., Gerentes, D., Perez, P., Rogowsky, P. M., Vernoud, V. (2011) Functional characterization of the HD-ZIP IV transcription factor OCL1 from maize. Journal of Experimental Botany, 62 (1). pp. 293-305.

Ding, Z. H., Wu, C. J., Chu, G. C., Xiao, Y. H., Ho, D., Zhang, J. F., Perry, S. R., Labrot, E. S., Wu, X. Q., Lis, R., Hoshida, Y., Hiller, D., Hu, B. L., Jiang, S., Zheng, H. W., Stegh, A. H., Scott, K. L., Signoretti, S., Bardeesy, N., Wang, Y. A., Hill, D. E., Golub, T. R., Stampfer, M. J., Wong, W. H., Loda, M., Mucci, L., Chin, L., DePinho, R. A. (2011) SMAD4-dependent barrier constrains prostate cancer growth and metastatic progression. Nature, 470 (7333). pp. 269-73. ISSN 0028-0836

Donia, M. S., Fricke, W. F., Partensky, F., Cox, J., Elshahawi, S. I., White, J. R., Phillippy, A. M., Schatz, M. C., Piel, J., Haygood, M. G., Ravel, J., Schmidt, E. W. (2011) Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis. Proceedings of the National Academy of Sciences of the United States of America, 108 (51). E1423-E1432. ISSN 00278424 (ISSN)

d'Alencon, E., Negre, N., Stanojcic, S., Alassoeur, B., Gimenez, S., Leger, A., Abd-Alla, A., Juliant, S., Fournier, P. (2011) Characterization of a CENP-B homolog in the holocentric Lepidoptera Spodoptera frugiperda. Gene, 485 (2). pp. 91-101. ISSN 0378-1119

E

Earl, D., Bradnam, K., St. John, J., Darling, A., Lin, D., Fass, J., Yu, H. O. K., Buffalo, V., Zerbino, D. R., Diekhans, M., Nguyen, N., Ariyaratne, P. N., Sung, W. K., Ning, Z., Haimel, M., Simpson, J. T., Fonseca, N. A., Birol, I., Docking, T. R., Ho, I. Y., Rokhsar, D. S., Chikhi, R., Lavenier, D., Chapuis, G., Naquin, D., Maillet, N., Schatz, M. C., Kelley, D. R., Phillippy, A. M., Koren, S., Yang, S. P., Wu, W., Chou, W. C., Srivastava, A., Shaw, T. I., Ruby, J. G., Skewes-Cox, P., Betegon, M., Dimon, M. T., Solovyev, V., Seledtsov, I., Kosarev, P., Vorobyev, D., Ramirez-Gonzalez, R., Leggett, R., MacLean, D., Xia, F., Luo, R., Li, Z., Xie, Y., Liu, B., Gnerre, S., MacCallum, I., Przybylski, D., Ribeiro, F. J., Sharpe, T., Hall, G., Kersey, P. J., Durbin, R., Jackman, S. D., Chapman, J. A., Huang, X., DeRisi, J. L., Caccamo, M., Li, Y., Jaffe, D. B., Green, R. E., Haussler, D., Korf, I., Paten, B. (2011) Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Research, 21 (12). pp. 2224-2241. ISSN 10889051 (ISSN)

Egeblad, M. (2011) Talk from Mikala Egeblad at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Encinas, J. M., Hamani, C., Lozano, A. M., Enikolopov, G. N. (2011) Neurogenic hippocampal targets of deep brain stimulation. Journal of Comparative Neurology, 519 (1). pp. 6-20. ISSN 1096-9861 (Electronic) 0021-9967 (Linking)

Encinas, J. M., Michurina, T. V., Peunova, N., Park, J.H., Tordo, J., Peterson, D. A., Fishell, G., Koulakov, A. A., Enikolopov, G. N. (2011) Division-Coupled Astrocytic Differentiation and Age-Related Depletion of Neural Stem Cells in the Adult Hippocampus. Cell Stem Cell, 8 (5). pp. 566-579. ISSN 1934-5909

Enikolopov, G. N. (2011) Talk from Grigori Enikolopov at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Erlich, Y., Edvardson, S., Hodges, E., Zenvirt, S., Thekkat, P., Shaag, A., Dor, T., Hannon, G. J., Elpeleg, O. (2011) Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis. Genome Research, 21 (5). pp. 658-664. ISSN 1088-9051

Errani, C., Zhang, L., Sung, Y. S., Hajdu, M., Singer, S., Maki, R. G., Healey, J. H., Antonescu, C. R. (2011) A novel WWTR1-CAMTA1 gene fusion is a consistent abnormality in epithelioid hemangioendothelioma of different anatomic sites. Genes Chromosomes Cancer, 50 (8). pp. 644-53. ISSN 1098-2264 (Electronic)1045-2257 (Linking)

Ewald, A. J., Werb, Z., Egeblad, M. (2011) Dynamic, Long-Term In Vivo Imaging of Tumor–Stroma Interactions in Mouse Models of Breast Cancer Using Spinning-Disk Confocal Microscopy. Cold Spring Harbor Protocols, 2011 (2).

Ewald, A. J., Werb, Z., Egeblad, M. (2011) Monitoring of vital signs for long-term survival of mice under anesthesia. Cold Spring Harbor Protocols, 2011 (2). ISSN 1559-6095

Ewald, A. J., Werb, Z., Egeblad, M. (2011) Preparation of mice for long-term intravital imaging of the mammary gland. Cold Spring Harbor Protocols, 2011 (2). ISSN 1559-6095

F

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

Fellmann, C., Zuber, J., McJunkin, K., Chang, K. , Malone, C. D., Dickins, R. A., Xu, Q., Hengartner, M. O., Elledge, S. J., Hannon, G. J., Lowe, S. W. (2011) Functional Identification of Optimized RNAi Triggers Using a Massively Parallel Sensor Assay. Molecular Cell, 41 (6). pp. 733-746. ISSN 1097-2765

Feng, W., Jacob, Y., Veley, K. M., Ding, L., Yu, X., Choe, G., Michaels, S. D. (2011) Hypomorphic alleles reveal FCA-independent roles for FY in the regulation of FLOWERING LOCUS C. Plant Physiology, 155 (3). pp. 1425-1434. ISSN 00320889 (ISSN)

Feng, X., Grossman, R., Stein, L. D. (2011) PeakRanger: A cloud-enabled peak caller for ChIP-seq data. Bmc Bioinformatics, 12. ISSN 1471-2105

Fesen, R. A., Zastrow, J. A., Hammell, M. C., Shull, J. M., Silvia, D. W. (2011) Ejecta Knot Flickering, Mass Ablation, and Fragmentation in Cassiopeia A. Astrophysical Journal, 736 (2). p. 13. ISSN 0004-637X

Fields, R. C., Hameed, M., Qin, L. X., Moraco, N., Jia, X., Maki, R. G., Singer, S., Brennan, M. F. (2011) Dermatofibrosarcoma protuberans (DFSP): predictors of recurrence and the use of systemic therapy. Ann Surg Oncol, 18 (2). pp. 328-36. ISSN 1534-4681 (Electronic)1068-9265 (Linking)

Finigan, P. (2011) The origin of novel phenotypic variation in Arabidopsis allopolyploids. PhD thesis, Cold Spring Harbor Laboratory.

Forgeard, M. J. C., Haigh, E. A. P., Beck, A. T., Davidson, R. J., Henn, F. A., Maier, S. F., Mayberg, H. S., Seligman, M. E. P. (2011) Beyond depression: Toward a process-based approach to research, diagnosis, and treatment. Clinical Psychology: Science and Practice, 18 (4). pp. 275-299. ISSN 09695893 (ISSN)

Furukawa, H. (2011) Talk from Hiro Furukawa at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

G

Gerbasi, V. R., Preall, J. B., Golden, D. E., Powell, D. W., Cummins, T. D., Sontheimer, E. J. (2011) Blanks, a nuclear siRNA/dsRNA-binding complex component, is required for Drosophila spermiogenesis. Proceedings of the National Academy of Sciences of the United States of America, 108 (8). pp. 3204-3209. ISSN 00278424 (ISSN)

Gillis, J., Pavlidis, P. (2011) Figure data from "The role of indirect connections in gene networks in predicting function" Gillis, J. and Pavlidis, P. (2011) Bioinformatics, 27 (13). pp. 1860-1866. [Dataset]

Gillis, J., Pavlidis, P. (2011) Gene Ontology matrices from The role of indirect connections in gene networks in predicting function Gillis, J. and Pavlidis, P. (2011) Bioinformatics, 27 (13). pp. 1860-1866. [Dataset]

Gillis, J., Pavlidis, P. (2011) Gene lists from The role of indirect connections in gene networks in predicting function Gillis, J. and Pavlidis, P. (2011) Bioinformatics, 27 (13). pp. 1860-1866. [Dataset]

Gillis, J., Pavlidis, P. (2011) Network data from The role of indirect connections in gene networks in predicting function Gillis, J. and Pavlidis, P. (2011)Bioinformatics, 27 (13). pp. 1860-1866. [Dataset]

Gillis, J., Pavlidis, P. (2011) The impact of multifunctional genes on guilt "by association "analysis. PLoS One, 6 (2). ISSN 19326203 (ISSN)

Gillis, J., Pavlidis, P. (2011) The role of indirect connections in gene networks in predicting function. Bioinformatics, 27 (13). pp. 1860-1866. ISSN 13674803 (ISSN)

Gilman, S. R, Iossifov, I., Levy, D., Ronemus, M., Wigler, M. H., Vitkup, D. (2011) Rare De Novo Variants Associated with Autism Implicate a Large Functional Network of Genes Involved in Formation and Function of Synapses. Neuron, 70 (5). pp. 898-907. ISSN 0896-6273

Goff, S. A, Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E, Gessler, D. , Matasci, N., Wang, L., Hanlon, M., Lenards, A., Muir, A., Merchant, N., Lowry, S., Mock, S., Helmke, M., Kubach, A., Narro, M., Hopkins, N., Micklos, D., Hilgert, U., Gonzales, M, Jordan, C., Skidmore, E., Dooley, R., Cazes, J., McLay, R., Lu, Z., Pasternak, S., Koesterke, L., Piel, W. H., Grene, R., Noutsos, C., Gendler, K., Feng, X., Tang, C., Lent, M., Kim, S. J., Kvilekval, K., Manjunath, B.S., Tannen, V., Stamatakis, A., Sanderson, M. J., Welch, S. M., Cranston, K. , Soltis, P. , Soltis, D., O'Meara, B., Ane, C., Brutnell, T., Kleibenstein, D. J., White, J. W., Leebens-Mack, J., Donoghue, M. J., Spalding, E. P., Vision, T. J., Myers, C. R., Lowenthal, D., Enquist, B. J., Boyle, B., Akoglu, A., Andrews, G., Ram, S., Ware, D., Stein, L., Stanzione, D. (2011) The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers in Plant Science, 2. ISSN 1664-462X

Gottipati, S., Arbiza, L., Siepel, A., Clark, A. G., Keinan, A. (2011) Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing. Nat Genet, 43 (8). pp. 741-3. ISSN 1061-4036

Gounder, M. M., Lefkowitz, R. A., Keohan, M. L., D'Adamo, D. R., Hameed, M., Antonescu, C. R., Singer, S., Stout, K., Ahn, L., Maki, R. G. (2011) Activity of Sorafenib against desmoid tumor/deep fibromatosis. Clin Cancer Res, 17 (12). pp. 4082-90. ISSN 1078-0432 (Print)1078-0432 (Linking)

Govek, E. E., Hatten, M. E., Van Aelst, L. (2011) The role of Rho GTPase proteins in CNS neuronal migration. Developmental Neurobiology, 71 (6). pp. 528-553. ISSN 19328451 (ISSN)

Graveley, B. R., Brooks, A. N., Carlson, J., Duff, M. O., Landolin, J. M., Yang, L., Artieri, C. G., van Baren, M. J., Boley, N., Booth, B. W., Brown, J. B., Cherbas, L., Davis, C. A., Dobin, A., Li, R. H., Lin, W., Malone, J. H., Mattiuzzo, N. R., Miller, D., Sturgill, D., Tuch, B. B., Zaleski, C., Zhang, D. Y., Blanchette, M., Dudoit, S., Eads, B., Green, R. E., Hammonds, A., Jiang, L. C., Kapranov, P., Langton, L., Perrimon, N., Sandler, J. E., Wan, K. H., Willingham, A., Zhang, Y., Zou, Y., Andrews, J., Bickel, P. J., Brenner, S. E., Brent, M. R., Cherbas, P., Gingeras, T. R., Hoskins, R. A., Kaufman, T. C., Oliver, B., Celniker, S. E. (2011) The developmental transcriptome of Drosophila melanogaster. Nature, 471 (7339). pp. 473-479. ISSN 0028-0836

Grellscheid, S., Dalgliesh, C., Storbeck, M., Best, A., Liu, Y., Jakubik, M., Mende, Y., Ehrmann, I., Curk, T., Rossbach, K., Bourgeois, C. F., Stévenin, J., Grellscheid, D., Jackson, M. S., Wirth, B., Elliott, D. J. (2011) Identification of evolutionarily conserved exons as regulated targets for the splicing activator Tra2β in development. PLoS Genetics, 7 (12). ISSN 15537390 (ISSN)

Grodzicker, T., Stewart, D., Stillman, B. (2011) Metabolism and Disease. In: Cold Spring Harbor Symposia on Quantitative Biology LXXVI: Metabolism and Disease, Cold Spring Harbor.

Gronau, I., Hubisz, M. J., Gulko, B., Danko, C. G., Siepel, A. (2011) Bayesian inference of ancient human demography from individual genome sequences. Nat Genet, 43 (10). pp. 1031-4. ISSN 1061-4036

Guberman, J. M., Ai, J., Arnaiz, O., Baran, J., Blake, A., Baldock, R., Chelala, C., Croft, D., Cros, A., Cutts, R. J., Di Génova, A., Forbes, S., Fujisawa, T., Gadaleta, E., Goodstein, D. M., Gundem, G., Haggarty, B., Haider, S., Hall, M., Harris, T., Haw, R., Hu, S., Hubbard, S., Hsu, J., Iyer, V., Jones, P., Katayama, T., Kinsella, R., Kong, L., Lawson, D., Liang, Y., Lopez-Bigas, N., Luo, J., Lush, M., Mason, J., Moreews, F., Ndegwa, N., Oakley, D., Perez-Llamas, C., Primig, M., Rivkin, E., Rosanoff, S., Shepherd, R., Simon, R., Skarnes, B., Smedley, D., Sperling, L., Spooner, W., Stevenson, P., Stone, K., Teague, J., Wang, J., Whitty, B., Wong, D. T., Wong-Erasmus, M., Yao, L., Youens-Clark, K., Yung, C., Zhang, J., Kasprzyk, A. (2011) BioMart Central Portal: an open database network for the biological community. Database : the journal of biological databases and curation, 2011. ISSN 17580463 (ISSN)

Guo, T., Zhang, L., Chang, N. E., Singer, S., Maki, R. G., Antonescu, C. R. (2011) Consistent MYC and FLT4 gene amplification in radiation-induced angiosarcoma but not in other radiation-associated atypical vascular lesions. Genes Chromosomes Cancer, 50 (1). pp. 25-33. ISSN 1098-2264 (Electronic)1045-2257 (Linking)

Gutmann, D. H., Stiles, C. D., Lowe, S. W., Bollag, G. E., Furnari, F. B., Charest, A. (2011) Report from the fifth national cancer institute mouse models of human cancers consortium nervous system tumors workshop. Neuro-Oncology, 13 (7). pp. 692-699. ISSN 15228517 (ISSN)

Gymrek, M., Erlich, Y. (2011) Using DNA sequencers as stethoscopes. Genome Med, 3 (11). p. 73. ISSN 1756-994X (Electronic)

H

Hah, N., Danko, C. G., Core, L., Waterfall, J. J., Siepel, A., Lis, J. T., Kraus, W. L. (2011) A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell, 145 (4). pp. 622-34. ISSN 0092-8674

Hammell, M. (2011) Talk from Molly Hammell at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Hangya, B., Tihanyi, B. T., Entz, L., Fabo, D., Eross, L., Wittner, L., Jakus, R., Varga, V., Freund, T. F., Ulbert, I. (2011) Complex Propagation Patterns Characterize Human Cortical Activity during Slow-Wave Sleep. Journal of Neuroscience, 31 (24). pp. 8770-8779. ISSN 0270-6474

Hansen, K. R., Hazan, I., Shanker, S., Watt, S., Verhein-Hansen, J., Bahler, J., Martienssen, R. A., Partridge, J. F., Cohen, A., Thon, G. (2011) H3K9me-Independent Gene Silencing in Fission Yeast Heterochromatin by Clr5 and Histone Deacetylases. Plos Genetics, 7 (1). ISSN 1553-7390

Haque, Aftabul, Andersen, J. N., Salmeen, A., Barford, D., Tonks, N. K. (2011) Conformation-Sensing Antibodies Stabilize the Oxidized Form of PTP1B and Inhibit Its Phosphatase Activity. Cell, 147 (1). pp. 185-198. ISSN 0092-8674

Harder, N., Bodnar, M., Eils, R., Spector, D. L., Rohr, K. (2011) 3D segmentation and quantification of mouse embryonic stem cells in fluorescence microscopy images. 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Macro. pp. 216-219.

Haseltine, W. A. (2011) Interview: Commercial translation of cell-based therapies and regenerative medicine: learning by experience. Regen Med, 6 (4). pp. 431-5. ISSN 1746-076X (Electronic) 1746-0751 (Linking)

Hattangadi, S. M., Wong, P., Zhang, L., Flygare, J., Lodish, H. F. (2011) From stem cell to red cell: regulation of erythropoiesis at multiple levels by multiple proteins, RNAs, and chromatin modifications. Blood, 118 (24). pp. 6258-68. ISSN 1528-0020 (Electronic)0006-4971 (Linking)

Haw, R., Hermjakob, H., D'Eustachio, P., Stein, L. D. (2011) Reactome pathway analysis to enrich biological discovery in proteomics data sets. Proteomics, 11 (18). pp. 3598-3613. ISSN 16159853 (ISSN)

Haw, R. A., Croft, D., Yung, C. K., Ndegwa, N., D'Eustachio, P., Hermjakob, H., Stein, L. D. (2011) The Reactome BioMart. Database : the journal of biological databases and curation, 2011. ISSN 17580463 (ISSN)

Hein, N., Bywater, M. J., Stanley, K., Verbrugge, I., Cullinane, C., Baker, A., Zuber, H., Rappaport, A., Drygin, D., Huser, N., Bliesath, J., Ryckman, D. M., Rice, W. G., Lowe, S. W., Johnstone, R. W., Pearson, R. B., McArthur, G. A., Hannan, R. D. (2011) Inhibition of RNA Polymerase I Transcription by CX-5461 As a Therapeutic Strategy for the Cancer-Specific Activation of p53 in MLL-Rearranged Acute Myeloid Leukemias. Blood, 118 (21). p. 673. ISSN 0006-4971

Henn, F. A. (2011) Dopamine: A Marker of Psychosis and Final Common Driver of Schizophrenia Psychosis. American Journal of Psychiatry, 168 (12). pp. 1239-1240. ISSN 0002-953X

Herrmann, H., Blatt, K., Shi, J. W., Rappaport, A. R., Gleixner, K. V., Cerny-Reiterer, S., Peter, B., Wang, E., Sperr, W. R., Bradner, J. E., Lowe, S. W., Vakoc, C. R., Zuber, J., Valent, P. (2011) Small-Molecule Inhibition of BRD4 Is a Novel Promising Approach to Therapeutically Target Leukemia Stem Cells in AML. Blood, 118 (21). p. 1487. ISSN 0006-4971

Hirokawa, J., Sadakane, O., Sakata, S., Bosch, M., Sakurai, Y., Yamamori, T. (2011) Multisensory information facilitates reaction speed by enlarging activity difference between superior colliculus hemispheres in rats. PLoS ONE, 6 (9). ISSN 1932-6203 (Electronic)

Hodges, E., Molaro, A., Dos Santos, C. O., Thekkat, P., Song, Q., Uren, P. J., Park, J. H., Butler, J., Rafii, S., McCombie, W. R., Smith, A. D., Hannon, G. J. (2011) Directional DNA Methylation Changes and Complex Intermediate States Accompany Lineage Specificity in the Adult Hematopoietic Compartment. Molecular Cell, 44 (1). pp. 17-28. ISSN 1097-2765

Hoek, M., Myers, M. P., Stillman, B. (2011) An analysis of CAF-1 interacting proteins reveals dynamic and direct interactions with the ku complex and 14-3-3 proteins. Journal of Biological Chemistry, 286 (12). pp. 10876-10887. ISSN 0021-9258

Honegger, K. S., Campbell, R. A. A., Turner, G. C. (2011) Cellular-Resolution Population Imaging Reveals Robust Sparse Coding in the Drosophila Mushroom Body. Journal of Neuroscience, 31 (33). pp. 11772-11785. ISSN 0270-6474

Horev, G., Ellegood, J., Lerch, J. P., Son, Y. E., Muthuswamy, L., Vogel, H., Krieger, A. M., Buja, A., Henkelman, R. M., Wigler, M. H., Mills, A. A. (2011) Dosage-dependent phenotypes in models of 16p11.2 lesions found in autism. Proceedings of the National Academy of Sciences of the United States of America, 108 (41). pp. 17076-81. ISSN 0027-8424

Horev, G., Saig, A., Knutsen, P. M., Pietr, M., Yu, C. X., Ahissar, E. (2011) Motor-sensory convergence in object localization: a comparative study in rats and humans. Philosophical Transactions of the Royal Society B-Biological Sciences, 366 (1581). pp. 3070-3076. ISSN 0962-8436

Hrecka, K., Hao, C., Gierszewska, M., Swanson, S. K., Kesik-Brodacka, M., Srivastava, S., Florens, L., Washburn, M. P., Skowronski, J. (2011) Vpx relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein. Nature, 474 (7353). pp. 658-61. ISSN 1476-4687 (Electronic) 0028-0836 (Linking)

Hua, Y., Sahashi, K., Rigo, F., Hung, G., Horev, G., Bennett, C. F., Krainer, A. R. (2011) Peripheral SMN restoration is essential for long-term rescue of a severe spinal muscular atrophy mouse model. Nature, 478 (7367). pp. 123-6. ISSN 1476-4687 (Electronic) 0028-0836 (Linking)

Hubisz, M. J., Lin, M. F., Kellis, M., Siepel, A. (2011) Error and error mitigation in low-coverage genome assemblies. PLoS One, 6 (2). e17034. ISSN 1932-6203

Hubisz, M. J., Pollard, K. S., Siepel, A. (2011) PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform, 12 (1). pp. 41-51. ISSN 1467-5463

Hyun, S. W., Anglin, I. E., Liu, A., Yang, S., Sorkin, J. D., Lillehoj, E., Tonks, N. K., Passaniti, A., Goldblum, S. E. (2011) Diverse injurious stimuli reduce protein tyrosine phosphatase-μ expression and enhance epidermal growth factor receptor signaling in human airway epithelia. Experimental Lung Research, 37 (6). pp. 327-343. ISSN 01902148 (ISSN)

I

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

Issa, G. C., Delmore, J. E., McKeown, M. R., Lemieux, M. E., Rahl, P. B., Jacobs, H. M., Kastritis, E., Gilpatrick, T., Paranal, R. M., Qi, J., Shi, J. W., Chesi, M., Schinzel, A. C., Vakoc, C. R., Bergsagel, P. L., Richardson, P. G., Young, R., Hahn, W. C., Ghobrial, I. M., Anderson, K. C., Kung, A. L., Mitsiades, C. S., Bradner, J. E. (2011) Inhibition of c-Myc Expression and Function in Hematologic Malignancies. Blood, 118 (21). pp. 613-614. ISSN 0006-4971

J

Jacob, Y., Martienssen, R. A. (2011) Chromatin reprogramming: gender equality during Arabidopsis germline differentiation. Current biology, 21 (1). R20-2. ISSN 1879-0445 (Electronic)0960-9822 (Linking)

Janas, J. A., Van Aelst, L. (2011) Oncogenic tyrosine kinases target Dok-1 for ubiquitin-mediated proteasomal degradation to promote cell transformation. Molecular and Cellular Biology, 31 (13). pp. 2552-2565. ISSN 0270-7306

Javelle, M., Klein-Cosson, C., Vernoud, V., Boltz, V., Maher, C., Timmermans, M. C. P., Depege-Fargeix, N., Rogowsky, P. M. (2011) Genome-Wide Characterization of the HD-ZIP IV Transcription Factor Family in Maize: Preferential Expression in the Epidermis. Plant Physiology, 157 (2). pp. 790-803. ISSN 0032-0889

Javelle, M., Marco, C. F., Timmermans, M. (2011) In Situ Hybridization for the Precise Localization of Transcripts in Plants. Journal of Visualized Experiments (57). ISSN 1940-087X (Electronic)1940-087X (Linking)

Jiang, L. C., Schlesinger, F. J., Davis, C. A., Zhang, Y., Li, R. H., Salit, M., Gingeras, T. R., Oliver, B. (2011) Synthetic spike-in standards for RNA-seq experiments. Genome Research, 21 (9). pp. 1543-1551. ISSN 1088-9051

Jones, R. L., Constantinidou, A., Thway, K., Ashley, S., Scurr, M., Al-Muderis, O., Fisher, C., Antonescu, C. R., D'Adamo, D. R., Keohan, M. L., Maki, R. G., Judson, I. R. (2011) Chemotherapy in clear cell sarcoma. Med Oncol, 28 (3). pp. 859-63. ISSN 1559-131X (Electronic)1357-0560 (Linking)

Joshua-Tor, L. (2011) Talk from Leemor Joshua-Tor at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Joshua-Tor, L., Hannon, G. J. (2011) Ancestral Roles of Small RNAs: An Ago-Centric Perspective. Cold Spring Harb Perspect Biol, 3 (10). ISSN 1943-0264 (Electronic)

K

Kamalakaran, S., Varadan, V., Giercksky Russnes, H. E., Levy, D., Kendall, J. T., Janevski, A., Riggs, M., Banerjee, N., Synnestvedt, M., Schlichting, E., Kåresen, R., Shama Prasada, K., Rotti, H., Rao, R., Rao, L., Eric Tang, M. H., Satyamoorthy, K., Lucito, R., Wigler, M. H., Dimitrova, N., Naume, B., Borresen-Dale, A. L., Hicks, J. B. (2011) DNA methylation patterns in luminal breast cancers differ from non-luminal subtypes and can identify relapse risk independent of other clinical variables. Molecular Oncology, 5 (1). pp. 77-92.

Kang, B., Pu, M., Hu, G., Wen, W., Dong, Z., Zhao, K., Stillman, B., Zhang, Z. (2011) Phosphorylation of H4 Ser 47 promotes HIRA-mediated nucleosome assembly. Genes and Development, 25 (13). pp. 1359-1364. ISSN 08909369 (ISSN)

Karakas, E., Simorowski, N., Furukawa, H. (2011) Subunit arrangement and phenylethanolamine binding in GluN1/GluN2B NMDA receptors. Nature, 475 (7355). 249- U170. ISSN 00280836

Karni-Schmidt, O., Castillo-Martin, M., HuaiShen, T., Gladoun, N., Domingo-Domenech, J., Sanchez-Carbayo, M., Li, Y., Lowe, S. W., Prives, C., Cordon-Cardo, C. (2011) Distinct Expression Profiles of p63 Variants during Urothelial Development and Bladder Cancer Progression. The American Journal of Pathology, 178 (3). pp. 1350-1360. ISSN 0002-9440

Karp, X., Hammell, M., Ow, M. C., Ambros, V. (2011) Effect of life history on microRNA expression during C. elegans development. RNA, 17 (4). pp. 639-651. ISSN 13558382 (ISSN)

Kees, T., Egeblad, M. (2011) Innate Immune Cells in Breast Cancer - From Villains to Heroes? Journal of Mammary Gland Biology and Neoplasia, 16 (3). pp. 189-203. ISSN 1573-7039 (Electronic)1083-3021 (Linking)

Keller, M. M., Jaillais, Y., Pedmale, U. V., Moreno, J. E., Chory, J., Ballare, C. L. (2011) Cryptochrome 1 and phytochrome B control shade-avoidance responses in Arabidopsis via partially independent hormonal cascades. Plant J, 67 (2). pp. 195-207. ISSN 0960-7412

Kepecs, A. (2011) Neuroscience: My brain made me do it. Nature, 473 (7347). pp. 280-281. ISSN 0028-0836

Kepecs, A. (2011) Talk from Adam Kepecs at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Keyes, W. M. , Pecoraro, M., Aranda, V., Vernersson-Lindahl, E., Li, W., Vogel, H., Guo, X., Garcia, E. L., Michurina, T. V., Enikolopov, G. N., Muthuswamy, S. K., Mills, A. A. (2011) DeltaNp63alpha Is an Oncogene that Targets Chromatin Remodeler Lsh to Drive Skin Stem Cell Proliferation and Tumorigenesis. Cell Stem Cell, 8 (2). pp. 164-76. ISSN 1875-9777 (Electronic)

Khan, Z., Amini, S., Bloom, J. S., Ruse, C., Caudy, A. A., Kruglyak, L., Singh, M., Perlman, D. H., Tavazoie, S. (2011) Accurate proteome-wide protein quantification from high-resolution N-15 mass spectra. Genome Biology, 12 (12). ISSN 1474-7596

Kim, Il-Han, Chen, Yi-Chun M., Spector, David L., Eils, Roland, Rohr, Karl (2011) Nonrigid registration of 2-D and 3-D dynamic cell nuclei images for improved classification of subcellular particle motion. IEEE Trans Image Process., 20 (4). pp. 1011-1022. ISSN 1941-0042

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

Kopec, C. D., Bowers, A. C., Pai, S. , Brody, C. D. (2011) Semi-automated atlas-based analysis of brain histological sections. Journal of Neuroscience Methods, 196 (1). ISSN 0165-0270

Koulakov, A. A., Kolterman, B. E., Enikolopov, A. G., Rinberg, D. (2011) In search of the structure of human olfactory space. Frontiers in Systems Neuroscience, 5. p. 65. ISSN 1662-5137 (Electronic)1662-5137 (Linking)

Koulakov, A. A., Rinberg, D. (2011) Sparse Incomplete Representations: A Potential Role of Olfactory Granule Cells. Neuron, 72 (1). pp. 124-136. ISSN 0896-6273

Krainer, A. R. (2011) Oligonucleotide therapeutics for correcting defective RNA splicing. FEBS Journal, 278 (Issue ). p. 11. ISSN 1742-464X

Krainer, A. R. (2011) Talk from Adrian Krainer at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Krainer, A. R., Hua, Y. M., Sahashi, K., Rigo, F., Hung, G. N., Horev, G., Bennett, C. F. (2011) Systemic Versus CNS Delivery Of MOE Antisense Oligonucleotide to Correct Defective Splicing in a Severe Mouse Model of Spinal Muscular Atrophy. Nucleic Acid Therapeutics, 21 (5). A57-A57. ISSN 2159-3337

Krishnan, N., Fu, C., Pappin, D. J., Tonks, N. K. (2011) H2S-induced sulfhydration of the phosphatase PTP1B and its role in the endoplasmic reticulum stress response. Science Signaling, 4 (203). ISSN 19450877 (ISSN)

Kubota, T., Roca, X., Kimura, T., Kokunai, Y., Nishino, I., Sakoda, S., Krainer, A. R., Takahashi, M. P. (2011) A mutation in a rare type of intron in a sodium-channel gene results in aberrant splicing and causes myotonia. Human Mutation, 32 (7). pp. 773-782. ISSN 10597794 (ISSN)

Kumar, A., Bhandari, A., Sinha, R., Goyal, P., Grapputo, A. (2011) Spliceosomal Intron Insertions in Genome Compacted Ray-Finned Fishes as Evident from Phylogeny of MC Receptors, Also Supported by a Few Other GPCRs. PLoS ONE, 6 (8). ISSN 1932-6203

L

Lachke, S. A., Alkuraya, F. S., Kneeland, S. C., Ohn, T., Aboukhalil, A., Howell, G. R., Saadi, I., Cavallesco, R., Yue, Y. Z., Tsai, A. C. H., Nair, K. S., Cosma, M. I., Smith, R. S., Hodges, E., AlFadhli, S. M., Al-Hajeri, A., Shamseldin, H. E., Behbehani, A., Hannon, G. J., Bulyk, M. L., Drack, A. V., Anderson, P. J., John, S. W. M., Maas, R. L. (2011) Mutations in the RNA Granule Component TDRD7 Cause Cataract and Glaucoma. Science, 331 (6024). pp. 1571-1576. ISSN 0036-8075

Lasa, I., Toledo-Arana, A., Dobin, A., Villanueva, M., de los Mozos, I. R., Vergara-Irigaray, M., Segura, V., Fagegaltier, D., Penades, J. R., Valle, J., Solano, C., Gingeras, T. R. (2011) Genome-wide antisense transcription drives mRNA processing in bacteria. Proceedings of the National Academy of Sciences of the United States of America, 108 (50). pp. 20172-20177. ISSN 0027-8424

Lazarus, M. S., Huang, Z. J. (2011) Distinct maturation profiles of perisomatic and dendritic targeting GABAergic interneurons in the mouse primary visual cortex during the critical period of ocular dominance plasticity. Journal of Neurophysiology, 106 (2). pp. 775-787. ISSN 0022-3077

Lee, E. K., Cibrian-Jaramillo, A., Kolokotronis, S. O., Katari, M. S., Stamatakis, A., Ott, M., Chiu, J. C., Little, D. P., Stevenson, D. W., McCombie, W. R., Martienssen, R. A., Coruzzi, G., Desalle, R. (2011) A functional phylogenomic view of the seed plants. PLoS genetics, 7 (12). e1002411. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

Lee, P. T., Lin, H. W., Chang, Y. H., Fu, T. F., Dubnau, J. T., Hirsh, J., Lee, T., Chiang, A. S. (2011) Serotonin-mushroom body circuit modulating the formation of anesthesia-resistant memory in Drosophila. Proceedings of the National Academy of Sciences of the United States of America, 108 (33). pp. 13794-13799. ISSN 0027-8424

Lee, S., Paulson, K. G., Murchison, E. P., Afanasiev, O. K., Alkan, C., Leonard, J. H., Byrd, D. R., Hannon, G. J., Nghiem, P. (2011) Identification and validation of a novel mature microRNA encoded by the Merkel cell polyomavirus in human Merkel cell carcinomas. Journal of Clinical Virology, 52 (3). pp. 272-275. ISSN 13866532 (ISSN)

Leung, A., Cajigas, I., Jia, P., Ezhkova, E., Brickner, J. H., Zhao, Z., Geng, F., Tansey, W. P. (2011) Histone H2B ubiquitylation and H3 lysine 4 methylation prevent ectopic silencing of euchromatic loci important for the cellular response to heat. Mol Biol Cell, 22 (15). pp. 2741-2753. ISSN 1939-4586 (Electronic)1059-1524 (Linking)

Levy, D., Ronemus, M., Yamrom, B., Lee, Y. H., Leotta, A., Kendall, J. T., Marks, S., Lakshmi, B., Pai, D., Ye, Kenny, Buja, Andreas, Krieger, Abba, Yoon, S., Troge, J. E., Rodgers,  L., Iossifov, I., Wigler, M. H. (2011) Rare De Novo and Transmitted Copy-Number Variation in Autistic Spectrum Disorders. Neuron, 70 (5). pp. 886-897. ISSN 0896-6273

Levy, Dan, Pachter, Lior (2011) The neighbor-net algorithm. Advances in Applied Mathematics, 47 (2). pp. 240-258. ISSN 0196-8858

Li, B. (2011) SYNAPTIC AND CIRCUITRY MECHANISMS UNDERLYING COGNITIVE ABERRATIONS IN MICE DEFICIENT IN GENES LINKED TO SCHIZOPHRENIA. Schizophrenia Bulletin, 37. p. 37. ISSN 1745-1701

Li, B., Piriz, J., Mirrione, M., Chung, C. H., Proulx, C. D., Schulz, D., Henn, F. A., Malinow, R. (2011) Synaptic potentiation onto habenula neurons in the learned helplessness model of depression. Nature, 470 (7335). 535-U125. ISSN 0028-0836

Li, F., Martienssen, R. A., Cande, W. Z. (2011) Coordination of DNA replication and histone modification by the Rik1-Dos2 complex. Nature, 475 (7355). 244-U2562. ISSN 0028-0836

Lin, G., Aranda, V., Muthuswamy, S. K., Tonks, N. K. (2011) Identification of PTPN23 as a novel regulator of cell invasion in mammary epithelial cells from a loss-of-function screen of the 'PTP-ome'. Genes & Development, 25 (13). pp. 1412-1425. ISSN 0890-9369

Lindblad-Toh, K., Garber, M., Zuk, O., Lin, M. F., Parker, B. J., Washietl, S., Kheradpour, P., Ernst, J., Jordan, G., Mauceli, E., Ward, L. D., Lowe, C. B., Holloway, A. K., Clamp, M., Gnerre, S., Alfoldi, J., Beal, K., Chang, J., Clawson, H., Cuff, J., Di Palma, F., Fitzgerald, S., Flicek, P., Guttman, M., Hubisz, M. J., Jaffe, D. B., Jungreis, I., Kent, W. J., Kostka, D., Lara, M., Martins, A. L., Massingham, T., Moltke, I., Raney, B. J., Rasmussen, M. D., Robinson, J., Stark, A., Vilella, A. J., Wen, J., Xie, X., Zody, M. C., Baldwin, J., Bloom, T., Chin, C. W., Heiman, D., Nicol, R., Nusbaum, C., Young, S., Wilkinson, J., Worley, K. C., Kovar, C. L., Muzny, D. M., Gibbs, R. A., Cree, A., Dihn, H. H., Fowler, G., Jhangiani, S., Joshi, V., Lee, S., Lewis, L. R., Nazareth, L. V., Okwuonu, G., Santibanez, J., Warren, W. C., Mardis, E. R., Weinstock, G. M., Wilson, R. K., Delehaunty, K., Dooling, D., Fronik, C., Fulton, L., Fulton, B., Graves, T., Minx, P., Sodergren, E., Birney, E., Margulies, E. H., Herrero, J., Green, E. D., Haussler, D., Siepel, A., Goldman, N., Pollard, K. S., Pedersen, J. S., Lander, E. S., Kellis, M. (2011) A high-resolution map of human evolutionary constraint using 29 mammals. Nature, 478 (7370). pp. 476-82. ISSN 0028-0836

Liu-Sullivan, N., Zhang, J., Bakleh, A., Marchica, J., Li, J., Siolas, D., Laquerre, S., Degenhardt, Y. Y., Wooster, R., Chang, K., Hannon, G. J., Powers, S. (2011) Pooled shRNA screen for sensitizers to inhibition of the mitotic regulator polo-like kinase (PLK1). Oncotarget, 2 (12). pp. 1254-64. ISSN 1949-2553 (Electronic) 1949-2553 (Linking)

Locke, D. P., Hillier, L. W., Warren, W. C., Worley, K. C., Nazareth, L. V., Muzny, D. M., Yang, S. P., Wang, Z., Chinwalla, A. T., Minx, P., Mitreva, M., Cook, L., Delehaunty, K. D., Fronick, C., Schmidt, H., Fulton, L. A., Fulton, R. S., Nelson, J. O., Magrini, V., Pohl, C., Graves, T. A., Markovic, C., Cree, A., Dinh, H. H., Hume, J., Kovar, C. L., Fowler, G. R., Lunter, G., Meader, S., Heger, A., Ponting, C. P., Marques-Bonet, T., Alkan, C., Chen, L., Cheng, Z., Kidd, J. M., Eichler, E. E., White, S., Searle, S., Vilella, A. J., Chen, Y., Flicek, P., Ma, J., Raney, B., Suh, B., Burhans, R., Herrero, J., Haussler, D., Faria, R., Fernando, O., Darre, F., Farre, D., Gazave, E., Oliva, M., Navarro, A., Roberto, R., Capozzi, O., Archidiacono, N., Della Valle, G., Purgato, S., Rocchi, M., Konkel, M. K., Walker, J. A., Ullmer, B., Batzer, M. A., Smit, A. F., Hubley, R., Casola, C., Schrider, D. R., Hahn, M. W., Quesada, V., Puente, X. S., Ordonez, G. R., Lopez-Otin, C., Vinar, T., Brejova, B., Ratan, A., Harris, R. S., Miller, W., Kosiol, C., Lawson, H. A., Taliwal, V., Martins, A. L., Siepel, A., Roychoudhury, A., Ma, X., Degenhardt, J., Bustamante, C. D., Gutenkunst, R. N., Mailund, T., Dutheil, J. Y., Hobolth, A., Schierup, M. H., Ryder, O. A., Yoshinaga, Y., de Jong, P. J., Weinstock, G. M., Rogers, J., Mardis, E. R., Gibbs, R. A. (2011) Comparative and demographic analysis of orang-utan genomes. Nature, 469 (7331). pp. 529-33. ISSN 0028-0836

Lowe, C. B., Kellis, M., Siepel, A., Raney, B. J., Clamp, M., Salama, S. R., Kingsley, D. M., Lindblad-Toh, K., Haussler, D. (2011) Three periods of regulatory innovation during vertebrate evolution. Science, 333 (6045). pp. 1019-24. ISSN 0036-8075

Lu, Y., Xue, C. (2011) The power of the purse and budgetary accountability: Experiences from subnational governments in china. Public Administration and Development, 31 (5). pp. 351-362. ISSN 02712075 (ISSN)

Lucito, R. (2011) Talk from Rob Lucito at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Luo, W. J., Friedman, M. S., Hankenson, K. D., Woolf, P. J. (2011) Time series gene expression profiling and temporal regulatory pathway analysis of BMP6 induced osteoblast differentiation and mineralization. BMC Systems Biology, 5 (82). ISSN 1752-0509

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. (2011) Personal account of the discovery of a new disease using next-generation sequencing. Interview by Natalie Harrison. Pharmacogenomics, 12 (11). pp. 1519-1523. ISSN 1744-8042

Lyon, Gholson J. (2011) Returning Research Results from Next‐Generation Sequencing and Analysis to Patients with Idiopathic Disorders? In: Personal Genomes Meeting, Sept 30th - Oct 2nd 2011, Cold Spring Harbor Laboratory. (Unpublished)

Lyon, Gholson J., Abi-Dargham, Anissa, Moore, Holly, Lieberman, Jeffrey A., Javitch, Jonathan A., Sulzer, David (2011) Presynaptic regulation of dopamine transmission in schizophrenia. Schizophrenia Bulletin, 37 (1). pp. 108-117. ISSN 1745-1701

Lyon, Gholson J., Jiang, Tao, Van Wijk, Richard, Wang, Wei, Bodily, Paul Mark, Xing, Jinchuan, Tian, Lifeng, Robison, Reid J., Clement, Mark, Lin, Yang, Zhang, Peng, Liu, Ying, Moore, Barry, Glessner, Joseph T., Elia, Josephine, Reimherr, Fred, van Solinge, Wouter W., Yandell, Mark, Hakonarson, Hakon, Wang, Jun, Johnson, William Evan, Wei, Zhi, Wang, Kai (2011) Exome sequencing and unrelated findings in the context of complex disease research: ethical and clinical implications. Dscovery Medicine, 12 (62). pp. 41-55. ISSN 1944-7930

Lyon, Gholson J. (2011) The 2011 William Allan Award of the American Society of Human Genetics to the Right Person "J.M. Opitz"? [Teaching Resource] (Unpublished)

M

MacAlister, C. A., Bergmann, D. C. (2011) Sequence and function of basic helix-loop-helix proteins required for stomatal development in Arabidopsis are deeply conserved in land plants. Evolution & Development, 13 (2). pp. 182-192. ISSN 1520-541X

Mager, E. M., Brix, K. V., Gerdes, R. M., Ryan, A. C., Grosell, M. (2011) Effects of water chemistry on the chronic toxicity of lead to the cladoceran, Ceriodaphnia dubia. Ecotoxicology and Environmental Safety, 74 (3). pp. 238-243. ISSN 01476513 (ISSN)

Makino, H., Malinow, R. (2011) Compartmentalized versus global synaptic plasticity on dendrites controlled by experience. Neuron, 72 (6). pp. 1001-1011. ISSN 08966273 (ISSN)

Malhotra, D., McCarthy, S., Michaelson, J. J., Vacic, V., Burdick, K. E., Yoon, S., Cichon, S., Corvin, A., Gary, S., Gershon, E. S., Gill, M., Karayiorgou, M., Kelsoe, J. R., Krastoshevsky, O., Krause, V., Leibenluft, E., Levy, D. L., Makarov, V., Bhandari, A., Malhotra, A. K., McMahon, F. J., Nöthen, M. M., Potash, J. B., Rietschel, M., Schulze, T. G., Sebat, J. (2011) High frequencies of de novo cnvs in bipolar disorder and schizophrenia. Neuron, 72 (6). pp. 951-963. ISSN 08966273 (ISSN)

Mao, Y. S., Sunwoo, H., Zhang, B., Spector, D. L. (2011) Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs. Nature Cell Biology, 13 (1). pp. 95-9101. ISSN 1465-7392

Mao, Y. S., Zhang, B., Spector, D. L. (2011) Biogenesis and function of nuclear bodies. Trends in Genetics, 27. pp. 295-306. ISSN 0168-9525

McCandlish, D. M. (2011) Visualizing fitness landscapes. Evolution, 65 (6). pp. 1544-58. ISSN 1558-5646 (Electronic)0014-3820 (Linking)

McGinty, V. B., Hayden, B. Y., Heilbronner, S. R., Dumont, E. C., Graves, S. M., Mirrione, M. M., Hoffman, J. d., Sartor, G. C., España, R. A., Millan, E. Z., DiFeliceantonio, A. G., Marchant, N. J., Napier, T. C., Root, D. H., Borgland, S. L., Treadway, M. T., Floresco, S. B., McGinty, J. F., Haber, S. N. (2011) Emerging, Reemerging, and Forgotten Brain Areas of the Reward Circuit: Notes from the 2010 Motivational and Neural Networks Conference. Behavioural Brain Research, 225 (1). pp. 348-357. ISSN 0166-4328

McJunkin, K., Mazurek, A., Premsrirut, P. K., Zuber, J., Dow, L. E., Simon, J., Stillman, B., Lowe, S. W. (2011) Reversible suppression of an essential gene in adult mice using transgenic RNA interference. Proceedings of the National Academy of Sciences of the United States of America, 108 (17). pp. 7113-7118. ISSN 0027-8424

Mehta, M. S., Vazquez, A., Kulkarni, D. A., Kerrigan, J. E., Atwal, G. S., Metsugi, S., Toppmeyer, D. L., Levine, A. J., Hirshfield, K. M. (2011) Polymorphic variants in TSC1 and TSC2 and their association with breast cancer phenotypes. Breast Cancer Research and Treatment, 125 (3). pp. 861-868.

Meiler, S. E., Dynan, W. S., Porteus, M., Spector, D. L., Bao, G., Chen, Z., Pandey, J., Goyal, D., Kumaran, R. I., Wade, M., Agyekum, D. G. (2011) A Biological Delivery Platform for Zinc Finger Nucleases Using Transferrin-Mediated Endocytosis. Blood, 118 (21). pp. 492-493. ISSN 0006-4971

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

Menon, R. K., Bhat, G. P., Schatz, M. C. (2011) Rapid parallel genome indexing with MapReduce. 2nd International Workshop on MapReduce and Its Applications, MapReduce'11, Co-located with 20th International ACM Symposium on High-Performance Parallel and Distributed Computing, HPDC 2011 . ACM, pp. 51-58. ISBN 9781450307000 (ISBN)

Micklos, D., Lauter, S., Nisselle, A. (2011) Essays on science and society. Lessons from a science education portal. Science, 334 (6063). pp. 1657-1658. ISSN 00368075 (ISSN)

Mills, A. A. (2011) Talk from Alea Mills at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Mirrione, M. M., Li, B., Henn, F. A. (2011) Lateral Habenula Circuit Activity Following High Frequency Deep Brain Stimulation. Biological Psychiatry, 69 (9). 127S-128S. ISSN 0006-3223

Mitchell, K. J., Huang, Z. J., Moghaddam, B., Sawa, A. (2011) Following the genes: A framework for animal modeling of psychiatric disorders. BMC Biology, 9 (11). Article 76. ISSN 17417007

Mitra, P. P. (2011) Talk from Partha Mitra at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Molaro, A., Hodges, E., Fang, F., Song, Q., McCombie, W. R., Hannon, G. J., Smith, A. D. (2011) Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates. Cell, 146 (6). pp. 1029-1041. ISSN 0092-8674

Mukhopadhyay, S., Schedl, P., Studitsky, V. M., Sengupta, A. M. (2011) Theoretical analysis of the role of chromatin interactions in long-range action of enhancers and insulators. Proceedings of the National Academy of Sciences of the United States of America, 108 (50). pp. 19919-19924. ISSN 0027-8424

Muthuswamy, S. K. (2011) 3D culture reveals a signaling network. Breast Cancer Research, 13 (1). ISSN 1465-542X

Muthuswamy, S. K. (2011) Trastuzumab resistance: all roads lead to SRC. Nature Medicine, 17 (4). pp. 416-8. ISSN 1078-8956

Myers, R. M., Stamatoyannopoulos, J., Snyder, M., Dunham, I., Hardison, R. C., Bernstein, B. E., Gingeras, T. R., Kent, W. J., Birney, E., Wold, B., Crawford, G. E., Epstein, C. B., Shoresh, N., Ernst, J., Mikkelsen, T. S., Kheradpour, P., Zhang, X. L., Wang, L., Issner, R., Coyne, M. J., Durham, T., Ku, M. C., Truong, T., Ward, L. D., Altshuler, R. C., Lin, M. F., Kellis, M., Davis, C. A., Kapranov, P., Dobin, A., Zaleski, C., Schlesinger, F., Batut, P., Chakrabortty, S., Jha, S., Lin, W., Drenkow, J., Wang, H. E., Bell, K. G., Gao, H., Bell, I., Dumais, E., Dumais, J., Antonarakis, S. E., Ucla, C., Borel, C., Guigo, R., Djebali, S., Lagarde, J., Kingswood, C., Ribeca, P., Sammeth, M., Alioto, T., Merkel, A., Tilgner, H., Carninci, P., Hayashizaki, Y., Lassmann, T., Takahashi, H., Abdelhamid, R. F., Hannon, G., Fejes-Toth, K., Preall, J., Gordon, A., Sotirova, V., Reymond, A., Howald, C., Graison, E. A. Y., Chrast, J., Ruan, Y. J., Ruan, X. A., Shahab, A., Poh, W. T., Wei, C. L., Furey, T. S., Boyle, A. P., Sheffield, N. C., Song, L. Y., Shibata, Y., Vales, T., Winter, D., Zhang, Z. C., London, D., Wang, T. Y., Keefe, D., Iyer, V. R., Lee, B. K., McDaniell, R. M., Liu, Z., Battenhouse, A., Bhinge, A. A., Lieb, J. D., Grasfeder, L. L., Showers, K. A., Giresi, P. G., Kim, S. K. C., Shestak, C., Pauli, F., Reddy, T. E., Gertz, J. (2011) A User's Guide to the Encyclopedia of DNA Elements (ENCODE). Plos Biology, 9 (4). ISSN 1544-9173

Myles, S., Boyko, A. R., Owens, C. L., Brown, P. J., Grassi, F., Aradhya, M. K., Prins, B., Reynolds, A., Chia, J. M., Ware, D. H., Bustamante, C. D., Buckler, E. S. (2011) Genetic structure and domestication history of the grape. Proceedings of the National Academy of Sciences of the United States of America, 108 (9). pp. 3530-3535. ISSN 0027-8424

N

Nadif Kasri, N., Nakano-Kobayashi, A., Van Aelst, L. (2011) Rapid Synthesis of the X-Linked Mental Retardation Protein OPHN1 Mediates mGluR-Dependent LTD through Interaction with the Endocytic Machinery. Neuron, 72 (2). pp. 300-315. ISSN 1097-4199 (Electronic)0896-6273 (Linking)

Nakano, S., Stillman, B., Horvitz, H. R. (2011) Replication-coupled chromatin assembly generates a neuronal bilateral asymmetry in C. elegans. Cell, 147 (7). pp. 1525-1536. ISSN 00928674 (ISSN)

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

Navin, N. E., Hicks, J. B. (2011) Corrigendum to "Tracing the tumor lineage" [Mol. Oncol. 4 (2010) 267-283]. Molecular Oncology, 5 (3). p. 302. ISSN 1574-7891

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)

Ni, J. Q., Zhou, R., Czech, B., Liu, L. P., Holderbaum, L., Yang-Zhou, D., Shim, H. S., Tao, R., Handler, D., Karpowicz, P., Binari, R., Booker, M., Brennecke, J., Perkins, L. A., Hannon, G. J., Perrimon, N. (2011) A genome-scale shRNA resource for transgenic RNAi in Drosophila. Nature Methods, 8 (5). pp. 405-407. ISSN 15487091 (ISSN)

Nord, A. S., Roeb, W., Dickel, D. E., Walsh, T., Kusenda, M., O'Connor, K. L., Malhotra, D., McCarthy, S. E., Stray, S. M., Taylor, S. M., Sebat, J., King, B., King, M. C., McClellan, J. M. (2011) Reduced transcript expression of genes affected by inherited and de novo CNVs in autism. European Journal of Human Genetics, 19 (6). pp. 727-731. ISSN 10184813 (ISSN)

Nurenberg, A., Kitzing, T. M., Grosse, R. (2011) Nucleating actin for invasion. Nature Reviews Cancer, 11 (3). pp. 177-187. ISSN 1474-175X

O

Obad, S., Dos Santos, C. O., Petri, A., Heidenblad, M., Broom, O., Ruse, C., Fu, C., Lindow, M., Stenvang, J., Straarup, E. M., Hansen, H. F., Koch, T., Pappin, D., Hannon, G. J., Kauppinen, S. (2011) Silencing of microRNA families by seed-targeting tiny LNAs. Nature Genetics, 43 (4). pp. 371-380. ISSN 10614036 (ISSN)

Ou, S. H., Kwak, E. L., Siwak-Tapp, C., Dy, J., Bergethon, K., Clark, J. W., Camidge, D. R., Solomon, B. J., Maki, R. G., Bang, Y. J., Kim, D. W., Christensen, J., Tan, W., Wilner, K. D., Salgia, R., Iafrate, A. J. (2011) Activity of crizotinib (PF02341066), a dual mesenchymal-epithelial transition (MET) and anaplastic lymphoma kinase (ALK) inhibitor, in a non-small cell lung cancer patient with de novo MET amplification. J Thorac Oncol, 6 (5). pp. 942-6. ISSN 1556-1380 (Electronic)1556-0864 (Linking)

P

Pai, S., Erlich, J. C., Kopec, C., Brody, C. D. (2011) Minimal impairment in a rat model of duration discrimination following excitotoxic lesions of primary auditory and prefrontal cortices. Front Syst Neurosci, 5 (74). ISSN 1662-5137

Pappo, A. S., Patel, S. R., Crowley, J., Reinke, D. K., Kuenkele, K. P., Chawla, S. P., Toner, G. C., Maki, R. G., Meyers, P. A., Chugh, R., Ganjoo, K. N., Schuetze, S. M., Juergens, H., Leahy, M. G., Geoerger, B., Benjamin, R. S., Helman, L. J., Baker, L. H. (2011) R1507, a monoclonal antibody to the insulin-like growth factor 1 receptor, in patients with recurrent or refractory Ewing sarcoma family of tumors: results of a phase II Sarcoma Alliance for Research through Collaboration study. J Clin Oncol, 29 (34). pp. 4541-7. ISSN 1527-7755 (Electronic)0732-183X (Linking)

Pardee, T. S., Zuber, J., Lowe, S. W. (2011) Flt3-ITD alters chemotherapy response in vitro and in vivo in a p53-dependent manner. Exp Hematol, 39 (4). 473-485 e4. ISSN 1873-2399 (Electronic)0301-472X (Linking)

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. (2011) A comparative analysis of exome capture. Genome Biology, 12 (9). R97. ISSN 1474-7596

Passini, M. A., Bu, J., Richards, A. M., Kinnecom, C., Sardi, S. P., Stanek, L. M., Hua,  Y., Rigo, F., Matson, J., Hung, G., Kaye, E. M., Shihabuddin, L. S., Krainer, A. R., Bennett, C. F., Cheng, S. H. (2011) Antisense oligonucleotides delivered to the mouse CNS ameliorate symptoms of severe spinal muscular atrophy. Science Translational Medicine, 3 (72). ISSN 19466234 (ISSN)

Pearson, H. B., Perez-Mancera, P. A., Dow, L. E., Ryan, A., Tennstedt, P., Bogani, D., Elsum, I., Greenfield, A., Tuveson, D. A., Simon, R., Humbert, P. O. (2011) SCRIB expression is deregulated in human prostate cancer, and its deficiency in mice promotes prostate neoplasia. Journal of Clinical Investigation, 121 (11). pp. 4257-4267. ISSN 0021-9738

Png, K. J., Yoshida, M., Zhang, X. H. F., Shu, W., Lee, H., Rimner, A., Chan, T. A., Comen, E., Andrade, V. P., Kim, S. W., King, T. A., Hudis, C. A., Norton, L., Hicks, J. B., Massagué, J., Tavazoie, S. F. (2011) MicroRNA-335 inhibits tumor reinitiation and is silenced through genetic and epigenetic mechanisms in human breast cancer. Genes and Development, 25 (3). pp. 226-231. ISSN 08909369

Premsrirut, P. K., Dow, L. E., Kim, S. Y., Camiolo, M., Malone, C. D., Miething, C., Scuoppo, C. , Zuber, J., Dickins, R. A., Kogan, Scott C, Shroyer, Kenneth R, Sordella, R., Hannon, G. J., Lowe, S. W. (2011) A Rapid and Scalable System for Studying Gene Function in Mice Using Conditional RNA Interference. Cell, 145 (1). pp. 145-158. ISSN 0092-8674

R

Rajan, P., Dalgliesh, C., Carling, P. J., Buist, T., Zhang, C. L., Grellscheid, S. N., Armstrong, K., Stockley, J., Simillion, C., Gaughan, L., Kalna, G., Zhang, M. Q., Robson, C. N., Leung, H. Y., Elliott, D. J. (2011) Identification of Novel Androgen-Regulated Pathways and mRNA Isoforms through Genome-Wide Exon-Specific Profiling of the LNCaP Transcriptome. PLoS ONE, 6 (12). ISSN 1932-6203

Rangan, P., Malone, Colin D. , Navarro, C., Newbold, S. P, Hayes, P. S, Sachidanandam, R., Hannon, G. J., Lehmann, R. (2011) piRNA Production Requires Heterochromatin Formation in Drosophila. Current Biology, 21 (16). pp. 1373-1379. ISSN 0960-9822

Rappaport, A. R. (2011) Dissecting tumor suppressor and tumor maintenance genes in poor prognosis AML. PhD thesis, Cold Spring Harbor Laboratory.

Rebbeck, C. A., Leroi, A. M., Burt, A. (2011) Mitochondrial capture by a transmissible cancer. Science, 331 (6015). p. 303.

Rhind, N., Chen, Z., Yassour, M., Thompson, D. A., Haas, B. J., Habib, N., Wapinski, I., Roy, S., Lin, M. F., Heiman, D. I., Young, S. K., Furuya, K., Guo, Y., Pidoux, A., Chen, H. M., Robbertse, B., Goldberg, J. M., Aoki, K., Bayne, E. H., Berlin, A. M., Desjardins, C. A., Dobbs, E., Dukaj, L., Fan, L., FitzGerald, M. G., French, C., Gujja, S., Hansen, K., Keifenheim, D., Levin, J. Z., Mosher, R. A., Muller, C. A., Pfiffner, J., Priest, M., Russ, C., Smialowska, A., Swoboda, P., Sykes, S. M., Vaughn, M., Vengrova, S., Yoder, R., Zeng, Q., Allshire, R., Baulcombe, D., Birren, B. W., Brown, W., Ekwall, K., Kellis, M., Leatherwood, J., Levin, H., Margalit, H., Martienssen, R., Nieduszynski, C. A., Spatafora, J. W., Friedman, N., Dalgaard, J. Z., Baumann, P., Niki, H., Regev, A., Nusbaum, C. (2011) Comparative functional genomics of the fission yeasts. Science, 332 (6032). pp. 930-6. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Riedel, O., Dodel, R., Deuschl, G., Forstl, H., Henn, F., Heuser, I., Oertel, W., Reichmann, H., Riederer, P., Trenkwalder, C., Wittchen, H. U. (2011) [Dementia and depression determine care dependency in Parkinson's disease: analysis of 1,449 outpatients receiving nursing care in Germany]. Nervenarzt, 82 (8). pp. 1012-9. ISSN 0028-2804

Rigo, F., Hua, Y. M., Chun, S. J., Krainer, A. R., Bennett, C. F. (2011) Modulation of Gene Expression By Oligonucleotide Chemistry-Dependent Recruitment of Proteins to RNA Transcripts. Nucleic Acid Therapeutics, 21 (5). A53-A54. ISSN 2159-3337

Roberts, D., Pedmale, U. V., Morrow, J., Sachdev, S., Lechner, E., Tang, X., Zheng, N., Hannink, M., Genschik, P., Liscum, E. (2011) Modulation of phototropic responsiveness in Arabidopsis through ubiquitination of phototropin 1 by the CUL3-Ring E3 ubiquitin ligase CRL3(NPH3). Plant Cell, 23 (10). pp. 3627-40. ISSN 1040-4651

Rollins, F. (2011) The genetics and epigenetics of erlotinib resistance in non-small cell lung cancer. PhD thesis, Cold Spring Harbor Laboratory.

Rope, Alan F., Wang, Kai, Evjenth, Rune, Xing, Jinchuan, Johnston, Jennifer J., Swensen, Jeffrey J., Johnson, W. Evan, Moore, Barry, Huff, Chad D., Bird, Lynne M., Carey, John C., Opitz, John M., Stevens, Cathy A., Jiang, Tao, Schank, Christa, Fain, Heidi Deborah, Robison, Reid, Dalley, Brian, Chin, Steven, South, Sarah T., Pysher, Theodore J., Jorde, Lynn B., Hakonarson, Hakon, Lillehaug, Johan R., Biesecker, Leslie G., Yandell, Mark, Arnesen, Thomas, Lyon, Gholson J. (2011) Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. American Journal of Human Genetics, 89 (1). pp. 28-43. ISSN 0002-9297

Rossmann, M. P., Luo, W., Tsaponina, O., Chabes, A., Stillman, B. (2011) A Common Telomeric Gene Silencing Assay Is Affected by Nucleotide Metabolism. Molecular Cell, 42 (1). pp. 127-136. ISSN 1097-2765

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

Ryu, S., Joshi, N., McDonnell, K., Woo, J., Choi, H., Gao, D., McCombie, W. R., Mittal, V. (2011) Discovery of novel human breast cancer micrornas from deep sequencing data by analysis of pri-microrna secondary structures. PLoS ONE, 6 (2).

S

Sabot, F., Picault, N., Elbaidouri, M., Llauro, C., Chaparro, C., Piegu, B., Roulin, A., Guiderdoni, E., Delabastide, M., McCombie, W. R., Panaud, O. (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

Sawey, E. T., Chanrion, M., Cai, C., Wu, G., Zhang, J., Zender, L., Zhao, A., Busuttil, R. W., Yee, H., Stein, L. D., French, D. M., Finn, Richard S, Lowe, S. W., Powers, S. (2011) Identification of a Therapeutic Strategy Targeting Amplified FGF19 in Liver Cancer by Oncogenomic Screening. Cancer Cell, 19 (3). pp. 347-358. ISSN 1535-6108

Schalch, T., Job, G., Shanker, S., Partridge, J., Joshua-Tor, L. (2011) The Chp1-Tas3 core is a multifunctional platform critical for gene silencing by RITS. Molecular Biology of the Cell, 22. ISSN 1059-1524

Schalch, T., Job, G., Shanker, S., Partridge, J. F., Joshua-Tor, L. (2011) The Chp1-Tas3 core is a multifunctional platform critical for gene silencing by RITS. Nature Structural and Molecular Biology, 18 (12). pp. 1351-1357. ISSN 15459993 (ISSN)

Schoffski, P., Taron, M., Jimeno, J., Grosso, F., Sanfilipio, R., Casali, P. G., Le Cesne, A., Jones, R. L., Blay, J. Y., Poveda, A., Maki, R. G., Nieto, A., Tercero, J. C., Rosell, R. (2011) Predictive impact of DNA repair functionality on clinical outcome of advanced sarcoma patients treated with trabectedin: a retrospective multicentric study. Eur J Cancer, 47 (7). pp. 1006-12. ISSN 1879-0852 (Electronic)0959-8049 (Linking)

Schuck, S., Stenlund, A. (2011) Mechanistic analysis of local ori melting and helicase assembly by the papillomavirus e1 protein. Mol Cell, 43 (5). pp. 776-787. ISSN 1097-4164 (Electronic) 1097-2765 (Linking)

Schulz, D., Southekal, S. S., Junnarkar, S. S., Pratte, J. F., Purschke, M. L., Stoll, S. P., Ravindranath, B., Maramraju, S. H., Krishnamoorthy, S., Henn, F. A., O'Connor, P., Woody, C. L., Schlyer, D. J., Vaska, P. (2011) Simultaneous assessment of rodent behavior and neurochemistry using a miniature positron emission tomograph. Nature Methods, 8 (4). pp. 347-352. ISSN 15487091 (ISSN)

Scuoppo, C. (2011) Architectural Models of Tumor Suppression in Lymphoma. PhD thesis, Cold Spring Harbor Laboratory.

Shakya, R., Reid, L. J., Reczek, C. R., Cole, F., Egli, D., Lin, C. S., DeRooij, D. G., Hirsch, S., Ravi, K., Hicks, J. B., Szabolcs, M., Jasin, M., Baer, R., Ludwig, T. (2011) BRCA1 tumor suppression depends on BRCT phosphoprotein binding, but not its E3 ligase activity. Science, 334 (6055). pp. 525-528. ISSN 00368075 (ISSN)

Shao, L., Shuai, Y., Wang, J., Feng, S., Lu, B., Li, Z., Zhao, Y., Wang, L., Zhong, Y. (2011) Schizophrenia susceptibility gene dysbindin regulates glutamatergic and dopaminergic functions via distinctive mechanisms in Drosophila. Proceedings of the National Academy of Sciences of the United States of America, 108 (46). pp. 18831-18836. ISSN 00278424 (ISSN)

Shaw, Alice T., Yeap, Beow Y., Solomon, Benjamin J., Riely, Gregory J., Gainor, Justin, Engelman, Jeffrey A., Shapiro, Geoffrey I., Costa, Daniel B., Ou, Sai-Hong I., Butaney, Mohit, Salgia, Ravi, Maki, Robert G., Varella-Garcia, Marileila, Doebele, Robert C., Bang, Yung-Jue, Kulig, Kimary, Selaru, Paulina, Tang, Yiyun, Wilner, Keith D., Kwak, Eunice L., Clark, Jeffrey W., Iafrate, A. John, Camidge, D. Ross (2011) Effect of crizotinib on overall survival in patients with advanced non-small-cell lung cancer harbouring ALK gene rearrangement: a retrospective analysis. The Lancet Oncology, 12 (11). pp. 1004-1012. ISSN 1470-2045

Shea, S. D. (2011) Talk from Stephen Shea at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Sheltzer, J. M., Amon, A. (2011) The aneuploidy paradox: costs and benefits of an incorrect karyotype. Trends Genet, 27 (11). pp. 446-53. ISSN 0168-9525 (Print)0168-9525 (Linking)

Sheltzer, J. M., Blank, H. M., Pfau, S. J., Tange, Y., George, B. M., Humpton, T. J., Brito, I. L., Hiraoka, Y., Niwa, O., Amon, A. (2011) Aneuploidy drives genomic instability in yeast. Science, 333 (6045). pp. 1026-30. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Shen, M. L., Eyras, E., Wu, J., Khanna, A., Josiah, S., Rederstorff, M., Zhang, M. Q., Stamm, S. (2011) Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression. Nucleic Acids Research, 39 (22). pp. 9720-9730. ISSN 0305-1048

Sheppard, J. P., Wang, J. P., Wong, P. C. M. (2011) Large-Scale Cortical Functional Organization and Speech Perception across the Lifespan. PLoS ONE, 6 (1). ISSN 1932-6203

Shi, L., Wang, J., Hong, F., Spector, D. L., Fang, Y. (2011) Four amino acids guide the assembly or disassembly of Arabidopsis histone H3.3-containing nucleosomes. Proceedings of the National Academy of Sciences of the United States of America, 108 (26). pp. 10574-10578. ISSN 0027-8424

Shuai, Y. C., Hu, Y., Qin, H. T., Campbell, R. A. A., Zhong, Y. (2011) Distinct molecular underpinnings of Drosophila olfactory trace conditioning. Proceedings of the National Academy of Sciences of the United States of America, 108 (50). pp. 20201-20206. ISSN 0027-8424

Shuai, Y. C., Zhang, Y. S., Gao, L. W., Zhong, Y. (2011) Stress Resistance Conferred by Neuronal Expression of Dominant-Negative Rac in Adult Drosophila melanogaster. Journal of Neurogenetics, 25 (1-2). pp. 35-39. ISSN 0167-7063

Shusterman, R., Smear, M. C., Koulakov, A. A., Rinberg, D. (2011) Precise olfactory responses tile the sniff cycle. Nature Neuroscience, 14 (8). 1039-U136. ISSN 1097-6256

Sierra, A., Encinas, J. M., Deudero, J. J. P., Chancey, J. H., Enikolopov, G., Overstreet-Wadiche, L. S., Tsirka, S. E., Maletic-Savatic, M. (2011) Microglial phagocytosis shapes adult hippocampal neurogenesis. Glia, 59. S17-S17. ISSN 0894-1491

Sierra, A., Encinas, J. M., Deudero, J. J. P., Chancey, J. H., Enikolopov, G. N., Overstreet-Wadiche, L. S., Tsirka, S. E., Maletic-Savatic, M. (2011) Microglia shapes adult hippocampal neurogenesis. Glia, 59 (Supple). S17-S17. ISSN 0894-1491

Simpson, D. R., Yu, M., Zheng, S. Y., Zhao, Z. M., Muthuswamy, S. K., Tansey, W. P. (2011) Epithelial Cell Organization Suppresses Myc Function by Attenuating Myc Expression. Cancer Research, 71 (11). pp. 3822-3830. ISSN 0008-5472

Spector, D. L., Lamond, A. I. (2011) Nuclear Speckles. Cold Spring Harbor Perspectives in Biology, 3 (2). ISSN 1943-0264 (Electronic)

Spector, David L. (2011) Immunofluorescence localization of nuclear proteins. Cold Spring Harbor Protocols, 2011 (10). pp. 1276-1280. ISSN 1559-6095

Spierings, D. C., McGoldrick, D., Hamilton-Easton, A. M., Neale, G., Murchison, E. P., Hannon, G. J., Green, D. R., Withoff, S. (2011) Ordered progression of stage-specific miRNA profiles in the mouse B2 B-cell lineage. Blood, 117 (20). pp. 5340-5349. ISSN 00064971 (ISSN)

Stillman, B. (2011) Talk from Bruce Stillman at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Storm, P., Aits, S., Puthia, M. K., Urbano, A., Northen, T., Powers, S., Bowen, B., Chao, Y., Reindl, W., Lee, D. Y., Sullivan, N. L., Zhang, J., Trulsson, M., Yang, H., Watson, J. D., Svanborg, C. (2011) Conserved features of cancer cells define their sensitivity to HAMLET-induced death; c-Myc and glycolysis. Oncogene, 30 (48). pp. 4765-4779. ISSN 09509232 (ISSN)

Sundaramurthy, P., Sreenivasan, R., Shameer, K., Gakkhar, S., Sowdhamini, R. (2011) Poster: HORIBALFRE: Higher order residue interactions based ALgorithm for fold REcognition. 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011 . IEEE, p. 262. ISBN 9781612848525 (ISBN)

Suzuki, H., Lefebure, T., Hubisz, M. J., Pavinski Bitar, P., Lang, P., Siepel, A., Stanhope, M. J. (2011) Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution. Genome Biol Evol, 3. pp. 168-85. ISSN 1759-6653

T

Tafe, L. J., Janjigian, Y. Y., Zaidinski, M., Hedvat, C. V., Hameed, M. R., Tang, L. H., Hicks, J. B., Shah, M. A., Barbashina, V. (2011) Human epidermal growth factor receptor 2 testing in gastroesophageal cancer: Correlation between immunohistochemistry and fluorescence in situ hybridization. Archives of Pathology and Laboratory Medicine, 135 (11). pp. 1460-1465. ISSN 00039985 (ISSN)

Tamura, T., Horiuchi, D., Chen, Y. C., Sone, M., Miyashita, T., Saitoe, M., Yoshimura, N., Chiang, A. S., Okazawa, H. (2011) Drosophila PQBP1 Regulates Learning Acquisition at Projection Neurons in Aversive Olfactory Conditioning. J Neurosci, 30 (42). pp. 14091-14101. ISSN 1529-2401 (Electronic) 0270-6474 (Linking)

Tanaka, T., Hosokawa, M., Vagin, V. V., Reuter, M., Hayashi, E., Mochizuki, A. L., Kitamura, K., Yamanaka, H., Kondoh, G., Okawa, K., Kuramochi-Miyagawa, S., Nakano, T., Sachidanandam, R., Hannon, G. J., Pillai, R. S., Nakatsuji, N., Chuma, S. (2011) Tudor domain containing 7 (Tdrd7) is essential for dynamic ribonucleoprotein (RNP) remodeling of chromatoid bodies during spermatogenesis. Proceedings of the National Academy of Sciences of the United States of America, 108 (26). pp. 10579-10584. ISSN 00278424 (ISSN)

Tang, M. H. E., Varadan, V., Kamalakaran, S., Zhang, M. Q., Dimitrova, N., Hicks, J. (2011) A method for finding novel associations between genome-wide copy number and dna methylation patterns. 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11 . IEEE, pp. 78-82. ISBN 21503001 (ISSN); 9781467304900 (ISBN)

Taniguchi, H., He, M., Wu, P., Kim, S., Paik, R., Sugino, K., Kvitsani, D., Fu, Y., Lu, J., Lin, Y., Miyoshi, G., Shima, Y., Fishell, G., Nelson, S. B., Huang, Z.  J. (2011) A Resource of Cre Driver Lines for Genetic Targeting of GABAergic Neurons in Cerebral Cortex. Neuron, 71 (6). pp. 995-1013. ISSN 0896-6273

Thorsen, K., Mansilla, F., Schepeler, T., Oster, B., Rasmussen, M. H., Dyrskjot, L., Karni, R., Akerman, M., Krainer, A. R., Laurberg, S., Andersen, C. L., Orntoft, T. F. (2011) Alternative splicing of SLC39A14 in colorectal cancer is regulated by the Wnt pathway. Molecular and Cellular Proteomics, 10 (1).

Triplett, J. W., Pfeiffenberger, C., Yamada, J., Stafford, B. K., Sweeney, N. T., Litke, A. M., Sher, A., Koulakov, A. A., Feldheim, D. A. (2011) Competition is a driving force in topographic mapping. Proceedings of the National Academy of Sciences of the United States of America, 108 (47). pp. 19060-19065. ISSN 00278424

Trotman, L. C. (2011) Calling on the cancer sleuths: how cell biologists will do the detective legwork of the postcancer genome era. Molecular Biology of the Cell, 22 (6). ISSN 10591524

Trotman, L. C. (2011) Talk from Lloyd Trotman at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Tyekucheva, S., Yolken, R. H., McCombie, W. R., Parla, J., Kramer, M., Wheelan, S. J., Sabunciyan, S. (2011) Establishing the baseline level of repetitive element expression in the human cortex. BMC Genomics, 12. article number 495. ISSN 1471-2164

V

Vacic, V., McCarthy, S. E., Malhotra, D., Murray, F., Chou, H. H., Peoples, A., Makarov, V., Yoon, S., Bhandari, A., Corominas, R., Iakoucheva, L. M., Krastoshevsky, O., Krause, V., Larach-Walters, V., Welsh, D. K., Craig, D., Kelsoe, J. R., Gershon, E. S., Leal, S. M., Aquila, M. D., Morris, D. W., Gill, M., Corvin, A., Insel, P. A., McClellan, J., King, M. C., Karayiorgou, M., Levy, D. L., Delisi, L. E., Sebat, J. (2011) Duplications of the neuropeptide receptor gene VIPR2 confer significant risk for schizophrenia. Nature, 471 (7339). pp. 499-503. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Van Aelst, L. (2011) Talk from Linda Van Aelst at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Van Ex, F., Jacob, Y., Martienssen, R. A. (2011) Multiple roles for small RNAs during plant reproduction. Current opinion in plant biology, 14 (5). pp. 588-93. ISSN 1879-0356 (Electronic)1369-5266 (Linking)

Vance, K. M., Simorowski, N., Traynelis, S. F., Furukawa, H. (2011) Ligand-specific deactivation time course of GluN1/GluN2D NMDA receptors. Nature Communications, 2. ISSN 2041-1723

Varshney, L. R., Chen, B. L., Paniagua, E., Hall, D. H., Chklovskii, D. B. (2011) Structural Properties of the Caenorhabditis elegans Neuronal Network. Plos Computational Biology, 7 (2). ISSN 1553-734X

Volpe, T., Martienssen, R. A. (2011) RNA interference and heterochromatin assembly. Cold Spring Harbor perspectives in biology, 3 (9). a003731. ISSN 1943-0264 (Electronic)

W

Wall, C. E., Cozza, S., Riquelme, C. A., McCombie, W. R., Heimiller, J. K., Marr, T. G., Leinwand, L. A. (2011) Whole transcriptome analysis of the fasting and fed Burmese python heart: insights into extreme physiological cardiac adaptation. Physiological Genomics, 43 (2). pp. 69-76. ISSN 1094-8341

Wang, G. H., Krishnamurthy, K., Tangpisuthipongsa, D. (2011) Protection of murine neural progenitor cells by the Hsp90 inhibitor 17-allylamino-17-demethoxygeldanamycin in the low nanomolar concentration range. Journal of Neurochemistry, 117 (4). pp. 703-711. ISSN 0022-3042

Wang, J., Czech, B., Crunk, A., Wallace, A., Mitreva, M., Hannon, G. J., Davis, R. E. (2011) Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles. Genome Research, 21 (9). pp. 1462-1477. ISSN 10889051 (ISSN)

Ware, D. H. (2011) Talk from Doreen Ware at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Wasik, K. A., Rebbeck, C. A. (2011) Keystone Symposia 40th Season: MicroRNAs and Noncoding RNAs in Cancer. Cancer Res, 71 (19). ISSN 0008-5472

Watson, J. D. (2011) Curing "incurable" Cancer. Cancer Discovery, 1 (6). pp. 477-480. ISSN 2159-8274

Watts, J. A., Zhang, C. L., Klein-Szanto, A. J., Kormish, J. D., Fu, J., Zhang, M. Q., Zaret, K. S. (2011) Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development. PLoS Genetics, 7 (9). ISSN 1553-7390

Wei, Zhi, Wang, Wei, Hu, Pingzhao, Lyon, Gholson J., Hakonarson, Hakon (2011) SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data. Nucleic Acids Research, 39 (19). e132. ISSN 03051048 (ISSN)

Whipple, C. J., Kebrom, T. H., Weber, A. L., Yang, F., Hall, D., Meeley, R., Schmidt, R., Doebley, J., Brutnell, T. P., Jackson, D. P. (2011) grassy tillers1 promotes apical dominance in maize and responds to shade signals in the grasses. Proceedings of the National Academy of Sciences of the United States of America, 108 (33). E506-E512. ISSN 0027-8424

Wigler, M. H. (2011) Talk from Mike Wigler at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Wrzeszczynski, K. O., Varadan, V., Byrnes, J., Lum, E., Kamalakaran, S., Levine, D. A., Dimitrova, N., Zhang, M. Q., Lucito, R. (2011) Identification of Tumor Suppressors and Oncogenes from Genomic and Epigenetic Features in Ovarian Cancer. PLoS ONE, 6 (12). ISSN 1932-6203

Wu, C.-L., Shih, M.-F. M., Lai, J. S.-Y., Yang, H.-T., Turner, G. C., Chen, L. , Chiang, A. S. (2011) Heterotypic Gap Junctions between Two Neurons in the Drosophila Brain Are Critical for Memory. Current Biology, 21 (10). pp. 848-854. ISSN 0960-9822

Wu, J., Akerman, M., Sun, S., McCombie, W. R., Krainer, A. R., Zhang, M. Q. (2011) SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics, 27 (21). 3010-3016 . ISSN 1367-4803

Wu, Q., Liu, Y., Chen, C., Ikenoue, T., Qiao, Y., Li, C. S., Li, W. Q., Guan, K. L., Zheng, P. (2011) The Tuberous Sclerosis Complex-Mammalian Target of Rapamycin Pathway Maintains the Quiescence and Survival of Naive T Cells. Journal of Immunology, 187 (3). pp. 1106-1112. ISSN 0022-1767

X

Xie, W. W., Liang, C. Z., Birchler, J. A. (2011) Inhibition of RNA Interference and Modulation of Transposable Element Expression by Cell Death in Drosophila. Genetics, 188 (4). pp. 823-834. ISSN 0016-6731

Xu, M. Z., Chan, S. W., Liu, A. M., Wong, K. F., Fan, S. T., Chen, J., Poon, R. T., Zender, L., Lowe, S. W., Hong, W., Luk, J. M. (2011) AXL receptor kinase is a mediator of YAP-dependent oncogenic functions in hepatocellular carcinoma. Oncogene, 30 (10). pp. 1229-1240.

Xu, X. M., Wang, J., Xuan, Z. Y., Goldshmidt, A., Borrill, P. G. M., Hariharan, N., Kim, J. Y., Jackson, D. P. (2011) Chaperonins Facilitate KNOTTED1 Cell-to-Cell Trafficking and Stem Cell Function. Science, 333 (6046). pp. 1141-1144. ISSN 1095-9203

Y

Yang, J. S., Phillips, M. D., Betel, D., Mu, P., Ventura, A., Siepel, A. C., Chen, K. C., Lai, E. C. (2011) Widespread regulatory activity of vertebrate microRNA* species. Rna, 17 (2). pp. 312-26. ISSN 1355-8382

Ying, H. Q., Elpek, K. G., Vinjamoori, A., Zimmerman, S. M., Chu, G. C., Yan, H. Y., Fletcher-Sananikone, E., Zhang, H. L., Liu, Y. C., Wang, W., Ren, X. J., Zheng, H. W., Kimmelman, A. C., Paik, J. H., Lim, C., Perry, S. R., Jiang, S., Malinn, B., Protopopov, A., Colla, S., Xiao, Y. H., Hezel, A. F., Bardeesy, N., Turley, S. J., Wang, Y. A. A., Chin, L., Thayer, S. P., DePinho, R. A. (2011) PTEN Is a Major Tumor Suppressor in Pancreatic Ductal Adenocarcinoma and Regulates an NF-kappa B-Cytokine Network. Cancer Discovery, 1 (2). pp. 158-169. ISSN 2159-8274

Youens-Clark, K., Buckler, E., Casstevens, T., Chen, C., DeClerck, G., Derwent, P., Dharmawardhana, P., Jaiswal, P., Kersey, P., Karthikeyan, A. S., Lu, J., McCouch, S. R., Ren, L., Spooner, W., Stein, J. C., Thomason, J., Wei, S., Ware, D. H. (2011) Gramene database in 2010: Updates and extensions. Nucleic Acids Research, 39 (SUPPL.).

Youens-Clark, K., Buckler, E., Casstevens, T., Chen, C., Declerck, G., Derwent, P., Dharmawardhana, P., Jaiswal, P., Kersey, P., Karthikeyan, A. S., Lu, J., McCouch, S. R., Ren, L., Spooner, W., Stein, J. C., Thomason, J., Wei, S., Ware, D. H. (2011) Gramene database in 2010: updates and extensions. Nucleic Acids Res, 39. D1085-D1094. ISSN 1362-4962 (Electronic) 0305-1048 (Linking)

Z

Zamparini, A. L., Davis, M. Y., Malone, C. D., Vieira, E., Zavadil, J., Sachidanandam, R., Hannon, G. J., Lehmann, R. (2011) Vreteno, a gonad-specific protein, is essential for germline development and primary pirna biogenesis in Drosophila. Development, 138 (18). pp. 4039-4050. ISSN 09501991 (ISSN)

Zaratiegui, B. M., Vaughn, M. W., Irvine, D. V., Goto, D. , Watt, S., Bahler, J., Arcangioli, B., Martienssen, R. A. (2011) CENP-B preserves genome integrity at replication forks paused by retrotransposon LTR. Nature, 469 (7328). pp. 112-5. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Zaratiegui, M., Castel, S. E., Irvine, D. V., Kloc, A., Ren, J., Li, F., de Castro, E., Marin, L., Chang, A. Y., Goto, D., Cande, W. Z., Antequera, F., Arcangioli, B., Martienssen, R. A. (2011) RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II. Nature, 479 (7371). pp. 135-8. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Zhang, L., Flygare, J., Wong, P., Lim, B., Lodish, H. F. (2011) miR-191 regulates mouse erythroblast enucleation by down-regulating Riok3 and Mxi1. Genes Dev, 25 (2). pp. 119-24. ISSN 1549-5477 (Electronic)0890-9369 (Linking)

Zhao, R., Nakamura, T., Fu, Y., Lazar, Z., Spector, D. L. (2011) Gene bookmarking accelerates the kinetics of post-mitotic transcriptional re-activation. Nature Cell Biology, 13 (11). 1295-1304 . ISSN 1465-7392

Zheng, H. (2011) Talk from Hongwu Zheng at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Zheng, S. Y., Tansey, W. P., Hiebert, S. W., Zhao, Z. M. (2011) Integrative network analysis identified key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma. BMC Medical Genomics, 4 (62). ISSN 1755-8794

Zhong, Y. (2011) Talk from Yi Zhong at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Zuber, J., McJunkin, K., Fellmann, C., Dow, L. E., Taylor, M. J., Hannon, G. J., Lowe, S. W. (2011) Toolkit for evaluating genes required for proliferation and survival using tetracycline-regulated RNA. Nature Biotechnology, 29 (1). pp. 79-85.

Zuber, J., Rappaport, A. R., Luo, W., Wang, E., Chen, C., Vaseva, A. V., Shi, J., Weissmueller, S., Fellman, C., Taylor, M. J., Weissenboeck, M., Graeber, T. G., Kogan, S. C., Vakoc, C. R., Lowe, S. W. (2011) An integrated approach to dissecting oncogene addiction implicates a Myb-coordinated self-renewal program as essential for leukemia maintenance. Genes & Development, 25 (15). pp. 1628-1640. ISSN 0890-9369

Zuber, J., Shi, J., Wang, E., Rappaport, A. R., Herrmann, H., Sison, E. A., Magoon, D., Qi, J., Blatt, K., Wunderlich, M., Taylor, M. J., Johns, C., Chicas, A., Mulloy, J. C., Kogan, S. C., Brown, P., Valent, P., Bradner, J. E., Lowe, S. W., Vakoc, C. R. (2011) RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia. Nature, 478 (7370). pp. 524-528. ISSN 0028-0836

This list was generated on Thu Mar 23 03:28:05 2017 EDT.
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving