Ivan Iossifov

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Publications

In PubMed

• Iossifov, I.*, O’Roak, B.J.*, Sanders, S.J.*, Ronemus, M.*, Krumm, N., Levy, D., Stessman, H.A., Witherspoon, ., Vives, L., Patterson, K.E., Smith, J.D., Paeper, B., Nickerson, D.A., Dea, J., Dong, S., Gonzalez, L.E., Mandell, J.E., 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.⁺ The burden of de novo coding mutations in autism spectrum disorder. (2014) Nature (in press) (*,⁺-equal contribution)

• Glessner, J., Bick, A.G., Ito, K., Homsy, J., Rodriguez-Murillo, L., Fromer, M., Mazaika, E.J., Vardarajan, B., Italia, M.J., Leipzig, J., DePalma, S., 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.G., Hakonarson, H., & Chung, W.K. Increased Frequency of De Novo Copy Number Variations in Congenital Heart Disease by Integrative Analysis of SNP Array and Exome Sequence Data. (2014) Circulation Research (Epub) PubMed

• Narzisi, G., O'Rawe, J.A., Iossifov, I., Fang, H., Lee, Y.H., Wang, Z., Wu, Y., Lyon, G.J., Wigler, M., & Schatz, M.C. Accurate de novo and transmitted indel detection in exome-capture data using microassembly. (2014) Nature Methods Epub PubMed | Read the paper

• Yilancioglu, K., Weinstein, Z.B., Meydan, C., Akhmetov, A., Toprak, I., Durmaz, A., Iossifov, I., Kazan, H., Roth, F.P., & Cokol, M. Target-independent prediction of drug synergies using only drug lipophilicity. (2014) J Chem Inf Model 54: 2286 PubMed | Read the paper

• 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. Large-scale identification and analysis of suppressive drug interactions. (2014) Chem Biol 21: 541 PubMed | Read the paper

• Ronemus, M., Iossifov, I., Levy, D., & Wigler, M. The role of de novo mutations in the genetics of autism spectrum disorders. (2014) Nature Reviews Genetics 15: 133 PubMed | Read the paper

• Iossifov, I.*, Ronemus, M.*, Levy, D., Wang, Z., Hakker, I., Rosenbaum, J., Yamrom, B., Lee, Y., Narzisi, G., Leotta, A., Kendall, J., Grabowska, E., Ma, B., Marks, S., Rodgers, L., Stepansky, A., Troge, J., Andrews, P., Bekritsky, M., Pradhan, K., Ghiban, E., Kramer, M., Parla, J., Demeter, R., Fulton, L.L., Fulton, R.S., Magrini, V.J., Ye, K., Darnell, J.C., Darnell, R.B., Mardis, E.R., Wilson, R.K., Schatz, M.C., McCombie, W.R., & Wigler, M. De Novo Gene Disruptions in Children on the Autistic Spectrum. (2012) Neuron 74: 285 (*-equal contribution) PubMed | Read the paper

• Spector, M.S., Iossifov, I., Kritharis, A., He, C., Kolitz, J.E., Lowe, S.W., & Allen, S.L. Mast-cell leukemia exome sequencing reveals a mutation in the IgE mast-cell receptor β chain and KIT V654A. (2011) Leukemia doi:10.1038/leu.2011.354 PubMed | Read the paper

• Parla, J.S.*, Iossifov, I.*, Grabill, I., Spector, M.S., Kramer, M., & McCombie, W.R. A comparative analysis of exome capture. (2011) Genome Biol. 12: R97 (*-equal contribution) PubMed | Read the paper

• Gilman, S.R.*, Iossifov, I.*, Levy, D., Ronemus, M., Wigler, M., & Vitkup, D. Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses. (2011) Neuron 70: 898 (*-equal contribution) PubMed | Read the paper

• Levy, D., Ronemus, M., Yamrom, B., Lee, Y.H., Leotta, A., Kendall, J., Marks, S., Lakshmi, B., Pai, D., Ye, K., Buja, A., Krieger, A., Yoon, S., Troge, J., Rodgers, L., Iossifov, I., & Wigler, M. Rare de novo and transmitted copy-number variation in autistic spectrum disorders. (2011) Neuron 70: 886 PubMed | Read the paper

• Iossifov, I., Rodriguez-Esteban, R., Mayzus, I., Millen, K.J., & Rzhetsky, A. Looking at cerebellar malformations through text-mined interactomes of mice and humans. (2009) PLoS Comput Biol. 5: e1000559 PubMed | Read the paper

• Rodriguez-Esteban, R. & Iossifov, I. Figure and table mining for biomedical research. (2009) Bioinformatics 25: 2082–4 PubMed | Read the paper

• Liu, J., Ghanim, M., Xue, L., Brown, C. D., Iossifov, I., Angeletti, C., Hua, S., Nègre, 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. Integrated genomic analysis of the Drosophila segmentation network leads to identification of a highly specific biomarker for human kidney cancer. (2009) Science 323: 1218–22 PubMed | Read the paper

• Iossifov, I., Zheng, T., Baron, M., Gilliam, T. C., & Rzhetsky, A. Genetic-linkage Mapping of Complex Hereditary Disorders to a Whole-genome Molecular-interaction Network. (2008) Genome Research 18: 1150–62 PubMed | Read the paper

• Murat Cokol, Ivan Iossifov, Raul Rodriguez-Esteban, and Andrey Rzhetsky How many scientific papers should be retracted? (2007) EMBO reports 8: 422–3 PubMed | Read the paper

• Rodriguez-Esteban, R., Iossifov, I., & Rzhetsky, A. Imitating manual curation of text-mined facts in biomedicine. (2006) PLoS Comput Biol. 2: e118 PubMed | Read the paper

• Rzhetsky, A., Iossifov, I., Loh, J.M., & White, K.P. Microparadigms: chains of collective reasoning in publications about molecular interactions. (2006) PNAS 103: 4940–5 PubMed | Read the paper

• 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. 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. (2006) Mol Psychiatry 11: 252–60 PubMed | Read the paper

• Cokol, M., Iossifov, I., Weinreb, C., & Rzhetsky, A. Emergent behavior of growing knowledge about molecular interactions. (2005) Nat Biotechnol. 23: 1243–7 PubMed | Read the paper

• Rzhetsky, A., Iossifov, I., Koike, T., Krauthammer, M., Kra, P., Morris, M., Yu, H., Duboué, P.A., Weng, W., Wilbur, W.J., Hatzivassiloglou, V., & Friedman, C. GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. (2005) Book chapter in "Databasing the Brain: From Data to Knowledge (Neuroinformatics)", Koslow and Subramaniam (Eds).

• Iossifov, I., Krauthammer, M., Friedman, C., Hatzivassiloglou, V., Bader, J.S., White, K.P., & Rzhetsky, A. Probabilistic pathway inference from noisy data sources. (2004) Bioinformatics 22: 1205–13 PubMed | Read the paper

• Rzhetsky, A., Iossifov, I., Koike, T., Krauthammer, M., Kra, P., Morris, M., Yu, H., Duboué, P.A., Weng, W., Wilbur, W.J., Hatzivassiloglou, V., & Friedman, C. GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. (2004) J Biomed Inform. 37: 43–53 PubMed | Read the paper

• Krauthammer, M., Kra, P., Iossifov, I., Gomez, S., Hripcsak, G., Hatzivassiloglou, V., Friedman, C., & Rzhetsky, A. Of truth and pathways: Chasing bits of information through myriads of articles. (2002) Bioinformatics 18: S249–57 PubMed | Read the paper

• Hong, Y., Hatzivassiloglou, V., Friedman, C., Iossifov, I., & Rzhetsky, A. A rule-based approach for automatically identifying gene and protein names in MEDLINE abstracts. (2002) ISMB, Edmonton Poster 240A Read the poster abstract.

Cold Spring Harbor Laboratory