Additional materials of the author at
CSHL Institutional Repository

Chorbadjiev, Liubomir, Cokol, Murat, Weinstein, Zohar, Shi, Kevin, Fleisch, Chris, Dimitrov, Nikolay, Mladenov, Svetlin, Xu, Simon, Hall, Jake, Ford, Steven, Lee, Yoon-Ha, Yamrom, Boris, Marks, Steven, Munoz, Adriana, Lash, Alex, Volfovsky, Natalia , Iossifov, Ivan (2024) The Genotype and Phenotypes in Families (GPF) platform manages the large and complex data at SFARI. bioRxiv,

Shi, Xi, Lu, Congyi, Corman, Alba, Nikish, Alexandra, Zhou, Yang, Platt, Randy J, Iossifov, Ivan, Zhang, Feng, Pan, Jen Q , Sanjana, Neville E (2023) Heterozygous deletion of the autism-associated gene CHD8 impairs synaptic function through widespread changes in gene expression and chromatin compaction. American Journal of Human Genetics, 110(10) pp. 1750-1768.

Einson, Jonah, Glinos, Dafni, Boerwinkle, Eric, Castaldi, Peter, Darbar, Dawood, de Andrade, Mariza, Ellinor, Patrick, Fornage, Myriam, Gabriel, Stacey, Germer, Soren, Gibbs, Richard, Hersh, Craig P, Johnsen, Jill, Kaplan, Robert, Konkle, Barbara A, Kooperberg, Charles, Nassir, Rami, Loos, Ruth JF, Meyers, Deborah A, Mitchell, Braxton D, Psaty, Bruce, Vasan, Ramachandran S, Rich, Stephen S, Rienstra, Michael, Rotter, Jerome I, Saferali, Aabida, Shoemaker, Moore Benjamin, Silverman, Edwin, Smith, Albert Vernon, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, , Mohammadi, Pejman, Castel, Stephane E, Iossifov, Ivan , Lappalainen, Tuuli (2023) Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants. Zhao, H (Ed.). Genetics: a periodical record of investigations bearing on heredity and variation, 224(4) pp. iyad115.

Wroten, Mathew, Yoon, Seungtai, Andrews, Peter, Yamrom, Boris, Ronemus, Michael, Buja, Andreas, Krieger, Abba M, Levy, Dan, Ye, Kenny, Wigler, Michael , Iossifov, Ivan (2023) Sharing parental genomes by siblings concordant or discordant for autism. Cell Genomics, 3(6) pp. 100319.

Einson, Jonah, Glinos, Dafni, Boerwinkle, Eric, Castaldi, Peter, Darbar, Dawood, de Andrade, Mariza, Ellinor, Patrick, Fornage, Myriam, Gabriel, Stacey, Germer, Soren, Gibbs, Richard, Hersh, Craig P, Johnsen, Jill, Kaplan, Robert, Konkle, Barbara A, Kooperberg, Charles, Nassir, Rami, Loos, Ruth JF, Meyers, Deborah A, Mitchell, Braxton D, Psaty, Bruce, Vasan, Ramachandran S, Rich, Stephen S, Rienstra, Michael, Rotter, Jerome I, Saferali, Aabida, Shoemaker, M Benjamin, Silverman, Edwin, Smith, Albert Vernon, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, , Mohammadi, Pejman, Castel, Stephane E, Iossifov, Ivan , Lappalainen, Tuuli (2023) Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants. bioRxiv,

Yamrom, Boris, Lee, Yoon-ha, Marks, Steven, Chorbadjiev, Lubomir, Meyer, Hannah V , Iossifov, Ivan (2022) Snakeobjects: an object-oriented workflow management system. bioRxiv,

Yoon, Seungtai, Munoz, Adriana, Yamrom, Boris, Lee, Yoon-Ha, Andrews, Peter, Marks, Steven, Wang, Zihua, Reeves, Catherine, Winterkorn, Lara, Krieger, Abba M, Buja, Andreas, Pradhan, Kith, Ronemus, Michael, Baldwin, Kristin K, Levy, Dan, Wigler, Michael , Iossifov, Ivan (2021) Rates of contributory de novo mutation in high and low-risk autism families.. Communications Biology, 4(1) pp. 1026.

Venkatasubramani, J.P., Subramanyam, P., Pal, R., Reddy, B.K., Srinivasan, D.J., Chattarji, S., Iossifov, I., Klann, E. , Bhattacharya, S. (2020) N-terminal Variant Asp14Asn of the Human p70 S6 Kinase 1 Enhances Translational Signaling Causing Different Effects in Developing and Mature Neuronal Cells. Neurobiology of Learning and Memory, 171(107203)

Jansen, S., van der Werf, I. M., Innes, A. M., Afenjar, A., Agrawal, P. B., Anderson, I. J., Atwal, P. S., van Binsbergen, E., van den Boogaard, M. J., Castiglia, L., Coban-Akdemir, Z. H., van Dijck, A., Doummar, D., van Eerde, A. M., van Essen, A. J., van Gassen, K. L., Guillen Sacoto, M. J., van Haelst, M. M., Iossifov, I., Jackson, J. L., Judd, E., Kaiwar, C., Keren, B., Klee, E. W., Klein Wassink-Ruiter, J. S., Meuwissen, M. E., Monaghan, K. G., de Munnik, S. A., Nava, C., Ockeloen, C. W., Pettinato, R., Racher, H., Rinne, T., Romano, C., Sanders, V. R., Schnur, R. E., Smeets, E. J., Stegmann, A. P. A., Stray-Pedersen, A., Sweetser, D. A., Terhal, P. A., Tveten, K., VanNoy, G. E., de Vries, P. F., Waxler, J. L., Willing, M., Pfundt, R., Veltman, J. A., Kooy, R. F., Vissers, Lelm , de Vries, B. B. A. (2019) De novo variants in FBXO11 cause a syndromic form of intellectual disability with behavioral problems and dysmorphisms. Eur J Hum Genet, 27(5) pp. 738-746.

Castel, S. E., Cervera, A., Mohammadi, P., Aguet, F., Reverter, F., Wolman, A., Guigo, R., Iossifov, I., Vasileva, A. , Lappalainen, T. (2018) Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk. Nat Genet, 50(9) pp. 1327-1334.

Buja, A., Volfovsky, N., Krieger, A. M., Lord, C., Lash, A. E., Wigler, M. , Iossifov, I. (2018) Damaging de novo mutations diminish motor skills in children on the autism spectrum. Proc Natl Acad Sci U S A, 115(8) pp. E1859-E1866.

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, 114(27) pp. 7073-7076.

Munoz, Adriana, Yamrom, Boris, Lee, Yoon-ha, Andrews, Peter, Marks, Steven, Lin, Kuan-Ting, Wang, Zihua, Krainer, Adrian R., Darnell, Robert B., Wigler, Michael , Iossifov, Ivan (2017) De novo indels within introns contribute to ASD incidence. bioRxiv, pp. 137471.

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.

Andrews, Peter A., Iossifov, Ivan, Kendall, Jude, Marks, Steven, Muthuswamy, Lakshmi, Wang, Zihua, Levy, Dan , Wigler, Michael (2016) MUMdex: MUM-based structural variation detection. bioRxiv, pp. 78261.

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 pp. 461A-461A.

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.

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.

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,

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.

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.

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.

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.

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) pp. 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.

Iossifov, I., Ronemus, M., Levy, D., Wang, Z. H., Hakker, I., Rosenbaum, J., Yamrom, B., Lee, Y. H., Narzisi, G., Leotta, A., Kendall, J., Grabowska, E., Ma, B. C., 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. (2012) De Novo Gene Disruptions in Children on the Autistic Spectrum. Neuron, 74(2) pp. 285-299.

Kolterman, Brian E, Iossifov, Ivan , Koulakov, Alexei A (2012) A race model for singular olfactory receptor expression.

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) pp. R97.

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.

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.

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) pp. 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.

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.

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

Rodriguez-Esteban, R., Iossifov, I. , Rzhetsky, A. (2006) Imitating manual curation of text-mined facts in biomedicine. PLoS Comput Biol, 2(9) pp. e118.

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.

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.

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

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.

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.

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 pp. S249-57.