Items where Community is "CSHL labs > Iossifov lab"

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Paper

Ye, K., Iossifov, I., Levy, D., Yamrom, B., Buja, A., Krieger, A. M., Wigler, M. (2017) Measuring shared variants in cohorts of discordant siblings with applications to autism. Proc Natl Acad Sci U S A. ISSN 0027-8424

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

Zhang, T., Romanel, A., Kluk, M. J., Eng, K., Iossifov, I., Sboner, A., Lipkin, S., Pritchard, C., Beltran, H., Rubin, M., Demichelis, F., Elemento, O. (2016) Germline Variants and Secondary Findings in a Cancer Precision Medicine Cohort. Laboratory Investigation, 96. 461A-461A. ISSN 0023-6837

Turner, Tychele N, Hormozdiari, Fereydoun, Duyzend, Michael H, McClymont, Sarah A, Hook, Paul W, Iossifov, Ivan, Raja, Archana, Baker, Carl, Hoekzema, Kendra, Stessman, Holly A, Zody, Michael C, Nelson, Bradley J, Huddleston, John, Sandstrom, Richard, Smith, Joshua D, Hanna, David, Swanson, James M, Faustman, Elaine M, Bamshad, Michael J, Stamatoyannopoulos, John, Nickerson, Deborah A, McCallion, Andrew S, Darnell, Robert, Eichler, Evan E (2016) Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA. The American Journal of Human Genetics, 98 (1). pp. 58-74. ISSN 0002-9297

Muñoz, A., Santos Muñoz, D., Zimin, A., Yorke, J. A. (2016) Evolution of transcriptional networks in yeast: Alternative teams of transcriptional factors for different species. BMC Genomics, 17 (Suppl ). p. 826. ISSN 1471-2164

Homsy, J., Zaidi, S., Shen, Y., Ware, J. S., Samocha, K. E., Karczewski, K. J., DePalma, S. R., McKean, D., Wakimoto, H., Gorham, J., Jin, S. C., Deanfield, J., Giardini, A., Porter G.A, Jr., Kim, R., Bilguvar, K., López-Giráldez, F., Tikhonova, I., Mane, S., Romano-Adesman, A., Qi, H., Vardarajan, B., Ma, L., Daly, M., Roberts, A. E., Russell, M. W., Mital, S., Newburger, J. W., Gaynor, J. W., Breitbart, R. E., Iossifov, I., Ronemus, M., Sanders, S. J., Kaltman, J. R., Seidman, J. G., Brueckner, M., Gelb, B. D., Goldmuntz, E., Lifton, R. P., Seidman, C. E., Chung, W. K. (2015) De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies. Science, 350 (6265). pp. 1262-1266. ISSN 00368075

Jiménez-Barrón, Laura T., O'Rawe, Jason A., Wu, Yiyang, Yoon, Margaret, Fang, Han, Iossifov, Ivan, Lyon, Gholson J. (2015) Genome-wide variant analysis of simplex autism families with an integrative clinical-bioinformatics pipeline. Molecular Case Studies, 1 (1).

Iossifov, I., Levy, D., Allen, J., Ye, K., Ronemus, M., Lee, Y. H., Yamrom, B., Wigler, M. (2015) Low load for disruptive mutations in autism genes and their biased transmission. Proc Natl Acad Sci U S A. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Iossifov, I., O'Roak, B. J., Sanders, S. J., Ronemus, M., Krumm, N., Levy, D., Stessman, H. A., Witherspoon, K. T., Vives, L., Patterson, K. E., Smith, J. D., Paeper, B., Nickerson, D. A., Dea, J., Dong, S., Gonzalez, L. E., Mandell, J. D., Mane, S. M., Murtha, M. T., Sullivan, C. A., Walker, M. F., Waqar, Z., Wei, L., Willsey, A. J., Yamrom, B., Lee, Y. H., Grabowska, E., Dalkic, E., Wang, Z., Marks, S., Andrews, P., Leotta, A., Kendall, J., Hakker, I., Rosenbaum, J., Ma, B., Rodgers, L., Troge, J., Narzisi, G., Yoon, S., Schatz, M. C., Ye, K., McCombie, W. R., Shendure, J., Eichler, E. E., State, M. W., Wigler, M. (2014) The contribution of de novo coding mutations to autism spectrum disorder. Nature, 515 (7526). pp. 216-221. ISSN 0028-0836

Glessner, J. T., Bick, A. G., Ito, K., Homsy, J. G., Rodriguez-Murillo, L., Fromer, M., Mazaika, E., Vardarajan, B., Italia, M., Leipzig, J., DePalma, S. R., Golhar, R., Sanders, S. J., Yamrom, B., Ronemus, M., Iossifov, I., Willsey, A. J., State, M. W., Kaltman, J. R., White, P. S., Shen, Y., Warburton, D., Brueckner, M., Seidman, C., Goldmuntz, E., Gelb, B. D., Lifton, R., Seidman, J., Hakonarson, H., Chung, W. K. (2014) Increased frequency of de novo copy number variants in congenital heart disease by integrative analysis of single nucleotide polymorphism array and exome sequence data. Circulation Research, 115 (10). pp. 884-96. ISSN 0009-7330

Yilancioglu, K., Weinstein, Z. B., Meydan, C., Akhmetov, A., Toprak, I., Durmaz, A., Iossifov, I., Kazan, H., Roth, F. P., Cokol, M. (2014) Target-independent prediction of drug synergies using only drug lipophilicity. Journal of Chemical Information and Modeling, 54 (8). pp. 2286-2293. ISSN 15499596

Narzisi, G., O'Rawe, Jason, Iossifov, I., Fang, Han, Lee, Y. H., Wang, Zihua, Wu, Yiyang, Lyon, Gholson J., Wigler, M. H., Schatz, M. C. (2014) Accurate de novo and transmitted indel detection in exome-capture data using microassembly. Nature Methods, 11 (10). pp. 1033-1036.

Cokol, M., Weinstein, Z. B., Yilancioglu, K., Tasan, M., Doak, A., Cansever, D., Mutlu, B., Li, S., Rodriguez-Esteban, R., Akhmedov, M., Guvenek, A., Cokol, M., Cetiner, S., Giaever, G., Iossifov, I., Nislow, C., Shoichet, B., Roth, F. P. (2014) Large-Scale Identification and Analysis of Suppressive Drug Interactions. Chemistry & Biology, 21 (4). pp. 541-551. ISSN 1074-5521

Fang, Han, Wu, Yiyang, Narzisi, G., O'Rawe, Jason, Jimenez Barron, Laura, Rosenbaum, J., Ronemus, M., Iossifov, I., Schatz, M. C., Lyon, Gholson J. (2014) Reducing INDEL calling errors in whole genome and exome sequencing data. Genome Med, 6 (10). p. 89.

Ronemus, M., Iossifov, I., Levy, D., Wigler, M. (2014) The role of de novo mutations in the genetics of autism spectrum disorders. Nature Reviews Genetics, 15 (2). pp. 133-141.

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

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

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

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

Iossifov, I., Rodriguez-Esteban, R., Mayzus, I., Millen, K. J., Rzhetsky, A. (2009) Looking at Cerebellar Malformations through Text-Mined Interactomes of Mice and Humans. PLoS Comput Biol, 5 (11). e1000559.

Rodriguez-Esteban, R., Iossifov, I. (2009) Figure mining for biomedical research. Bioinformatics, 25 (16). pp. 2082-2084.

Liu, J., Ghanim, M., Xue, L., Brown, C. D., Iossifov, I., Angeletti, C., Hua, S., Negre, N., Ludwig, M., Stricker, T., Al-Ahmadie, H. A., Tretiakova, M., Camp, R. L., Perera-Alberto, M., Rimm, D. L., Xu, T., Rzhetsky, A., White, K. P. (2009) Analysis of Drosophila segmentation network identifies a JNK pathway factor overexpressed in kidney cancer. Science, 323 (5918). pp. 1218-22. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Iossifov, I., Zheng, T., Baron, M., Gilliam, T. C., Rzhetsky, A. (2008) Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network. Genome Res, 18 (7). pp. 1150-62. ISSN 1088-9051 (Print)1088-9051 (Linking)

Cokol, M., Iossifov, I., Rodriguez-Esteban, R., Rzhetsky, A. (2007) How many scientific papers should be retracted? EMBO Rep, 8 (5). pp. 422-3. ISSN 1469-221X (Print)1469-221X (Linking)

Rodriguez-Esteban, R., Iossifov, I., Rzhetsky, A. (2006) Imitating manual curation of text-mined facts in biomedicine. PLoS Comput Biol, 2 (9). e118. ISSN 1553-7358 (Electronic)1553-734X (Linking)

Rzhetsky, A., Iossifov, I., Loh, J. M., White, K. P. (2006) Microparadigms: chains of collective reasoning in publications about molecular interactions. Proceedings of the National Academy of Sciences of the United States of America, 103 (13). pp. 4940-5. ISSN 0027-8424

Cheng, R., Juo, S. H., Loth, J. E., Nee, J., Iossifov, I., Blumenthal, R., Sharpe, L., Kanyas, K., Lerer, B., Lilliston, B., Smith, M., Trautman, K., Gilliam, T. C., Endicott, J., Baron, M. (2006) Genome-wide linkage scan in a large bipolar disorder sample from the National Institute of Mental Health genetics initiative suggests putative loci for bipolar disorder, psychosis, suicide, and panic disorder. Mol Psychiatry, 11 (3). pp. 252-60. ISSN 1359-4184 (Print)1359-4184 (Linking)

Cokol, M., Iossifov, I., Weinreb, C., Rzhetsky, A. (2005) Emergent behavior of growing knowledge about molecular interactions. Nat Biotechnol, 23 (10). pp. 1243-7. ISSN 1087-0156 (Print)1087-0156 (Linking)

Iossifov, I., Krauthammer, M., Friedman, C., Hatzivassiloglou, V., Bader, J. S., White, K. P., Rzhetsky, A. (2004) Probabilistic inference of molecular networks from noisy data sources. Bioinformatics, 20 (8). pp. 1205-13. ISSN 1367-4803 (Print)1367-4803 (Linking)

Rzhetsky, A., Iossifov, I., Koike, T., Krauthammer, M., Kra, P., Morris, M., Yu, H., Duboue, P. A., Weng, W., Wilbur, W. J., Hatzivassiloglou, V., Friedman, C. (2004) GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform, 37 (1). pp. 43-53. ISSN 1532-0464 (Print)1532-0464 (Linking)

Krauthammer, M., Kra, P., Iossifov, I., Gomez, S. M., Hripcsak, G., Hatzivassiloglou, V., Friedman, C., Rzhetsky, A. (2002) Of truth and pathways: chasing bits of information through myriads of articles. Bioinformatics, 18 Sup. S249-57. ISSN 1367-4803 (Print)1367-4803 (Linking)

Book Section

Rzhetsky, A., Iossifov, I., Koike, T., Krauthammer, M., Kra, P., Morris, M., Yu, H., Duboue, P. A., Weng, W., Wilbur, W. J., Hatzivassiloglou, V., Friedman, C. (2005) GeneWays: A System for Extracting, Analyzing, Visualizing, and Integrating Molecular Pathway Data. In: Databasing the Brain: From Data to Knowledge (Neuroinformatics). Wiley. ISBN 9780471309215

Conference or Workshop Item

Yu, H., Hatzivassiloglou, V., Friedman, C., Iossifov, I., Rzhetsky, A. (2002) A rule-based approach for automatically identifying gene and protein names in MEDLINE abstracts. In: Proc AMIA Symp.

Video

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

This list was generated on Sat Oct 21 14:37:49 2017 EDT.
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