Items where Community is "Iossifov lab"

Paper

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 (February 2024) The Genotype and Phenotypes in Families (GPF) platform manages the large and complex data at SFARI. bioRxiv. (Submitted)

Shi, Xi, Lu, Congyi, Corman, Alba, Nikish, Alexandra, Zhou, Yang, Platt, Randy J, Iossifov, Ivan, Zhang, Feng, Pan, Jen Q, Sanjana, Neville E (October 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. ISSN 0002-9297 (Public Dataset)

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 (August 2023) Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants. Genetics, 224 (4). iyad115. ISSN 0016-6731

Wroten, Mathew, Yoon, Seungtai, Andrews, Peter, Yamrom, Boris, Ronemus, Michael, Buja, Andreas, Krieger, Abba M, Levy, Dan, Ye, Kenny, Wigler, Michael, Iossifov, Ivan (June 2023) Sharing parental genomes by siblings concordant or discordant for autism. Cell Genomics, 3 (6). p. 100319. ISSN 2666-979X (Public Dataset)

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 (January 2023) Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants. bioRxiv. (Submitted)

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

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 (September 2021) Rates of contributory de novo mutation in high and low-risk autism families. Communications Biology, 4 (1). p. 1026. ISSN 2399-3642

Abel, Haley J, Larson, David E, Regier, Allison A, Chiang, Colby, Das, Indraniel, Kanchi, Krishna L, Layer, Ryan M, Neale, Benjamin M, Salerno, William J, Reeves, Catherine, Buyske, Steven, NHGRI Centers for Common Disease Genomics, Matise, Tara C, Muzny, Donna M, Zody, Michael C, Lander, Eric S, Dutcher, Susan K, Stitziel, Nathan O, Hall, Ira M (July 2020) Mapping and characterization of structural variation in 17,795 human genomes. Nature, 583 (7814). pp. 83-89. ISSN 0028-0836

Venkatasubramani, J.P., Subramanyam, P., Pal, R., Reddy, B.K., Srinivasan, D.J., Chattarji, S., Iossifov, I., Klann, E., Bhattacharya, S. (March 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). ISSN 1074-7427

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. (January 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. ISSN 1018-4813

Castel, S. E., Cervera, A., Mohammadi, P., Aguet, F., Reverter, F., Wolman, A., Guigo, R., Iossifov, I., Vasileva, A., Lappalainen, T. (August 2018) Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk. Nat Genet, 50 (9). pp. 1327-1334. ISSN 1061-4036

Buja, A., Volfovsky, N., Krieger, A. M., Lord, C., Lash, A. E., Wigler, M., Iossifov, I. (February 2018) Damaging de novo mutations diminish motor skills in children on the autism spectrum. Proc Natl Acad Sci U S A, 115 (8). E1859-E1866. ISSN 0027-8424

Ye, K., Iossifov, I., Levy, D., Yamrom, B., Buja, A., Krieger, A. M., Wigler, M. (July 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. ISSN 0027-8424

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 (May 2017) De novo indels within introns contribute to ASD incidence. bioRxiv. p. 137471. (Unpublished)

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. (December 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)

Andrews, Peter A., Iossifov, Ivan, Kendall, Jude, Marks, Steven, Muthuswamy, Lakshmi, Wang, Zihua, Levy, Dan, Wigler, Michael (September 2016) MUMdex: MUM-based structural variation detection. bioRxiv. 078261.

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. (February 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 (January 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. (December 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. (October 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. (September 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. (November 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. (October 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. (August 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. (August 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. (April 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. (June 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

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

Parla, J. S., Iossifov, I., Grabill, I., Spector, M. S., Kramer, M., McCombie, W. R. (September 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. (June 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. (June 2011) Rare De Novo and Transmitted Copy-Number Variation in Autistic Spectrum Disorders. Neuron, 70 (5). pp. 886-897. ISSN 0896-6273

Lee, Yoon-ha, Ronemus, Michael, Kendall, Jude, Lakshmi, B, Leotta, Anthony, Levy, Dan, Esposito, Diane, Grubor, Vladimir, Ye, Kenny, Wigler, Michael, Yamrom, Boris (May 2011) Removing System Noise from Comparative Genomic Hybridization Data by Self-Self Analysis. (Submitted)

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

Rodriguez-Esteban, R., Iossifov, I. (August 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. (February 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. (July 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. (May 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. (September 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. (March 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. (March 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. (October 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. (May 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. (February 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. (November 2011) Talk from Ivan Iossifov at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)