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Items: 31


Damaging de novo mutations diminish motor skills in children on the autism spectrum.

Buja A, Volfovsky N, Krieger AM, Lord C, Lash AE, Wigler M, Iossifov I.

Proc Natl Acad Sci U S A. 2018 Feb 20;115(8):E1859-E1866. doi: 10.1073/pnas.1715427115. Epub 2018 Feb 6.


Measuring shared variants in cohorts of discordant siblings with applications to autism.

Ye K, Iossifov I, Levy D, Yamrom B, Buja A, Krieger AM, Wigler M.

Proc Natl Acad Sci U S A. 2017 Jul 3;114(27):7073-7076. doi: 10.1073/pnas.1700439114. Epub 2017 Jun 19.


Indel variant analysis of short-read sequencing data with Scalpel.

Fang H, Bergmann EA, Arora K, Vacic V, Zody MC, Iossifov I, O'Rawe JA, Wu Y, Jimenez Barron LT, Rosenbaum J, Ronemus M, Lee YH, Wang Z, Dikoglu E, Jobanputra V, Lyon GJ, Wigler M, Schatz MC, Narzisi G.

Nat Protoc. 2016 Dec;11(12):2529-2548. doi: 10.1038/nprot.2016.150. Epub 2016 Nov 17.


Genome-wide variant analysis of simplex autism families with an integrative clinical-bioinformatics pipeline.

Jiménez-Barrón LT, O'Rawe JA, Wu Y, Yoon M, Fang H, Iossifov I, Lyon GJ.

Cold Spring Harb Mol Case Stud. 2015 Oct;1(1):a000422. doi: 10.1101/mcs.a000422.


De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies.

Homsy J, Zaidi S, Shen Y, Ware JS, Samocha KE, Karczewski KJ, DePalma SR, McKean D, Wakimoto H, Gorham J, Jin SC, Deanfield J, Giardini A, Porter GA Jr, Kim R, Bilguvar K, López-Giráldez F, Tikhonova I, Mane S, Romano-Adesman A, Qi H, Vardarajan B, Ma L, Daly M, Roberts AE, Russell MW, Mital S, Newburger JW, Gaynor JW, Breitbart RE, Iossifov I, Ronemus M, Sanders SJ, Kaltman JR, Seidman JG, Brueckner M, Gelb BD, Goldmuntz E, Lifton RP, Seidman CE, Chung WK.

Science. 2015 Dec 4;350(6265):1262-6. doi: 10.1126/science.aac9396.


Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA.

Turner TN, Hormozdiari F, Duyzend MH, McClymont SA, Hook PW, Iossifov I, Raja A, Baker C, Hoekzema K, Stessman HA, Zody MC, Nelson BJ, Huddleston J, Sandstrom R, Smith JD, Hanna D, Swanson JM, Faustman EM, Bamshad MJ, Stamatoyannopoulos J, Nickerson DA, McCallion AS, Darnell R, Eichler EE.

Am J Hum Genet. 2016 Jan 7;98(1):58-74. doi: 10.1016/j.ajhg.2015.11.023. Epub 2015 Dec 31.


Low load for disruptive mutations in autism genes and their biased transmission.

Iossifov I, Levy D, Allen J, Ye K, Ronemus M, Lee YH, Yamrom B, Wigler M.

Proc Natl Acad Sci U S A. 2015 Oct 13;112(41):E5600-7. doi: 10.1073/pnas.1516376112. Epub 2015 Sep 23.


Reducing INDEL calling errors in whole genome and exome sequencing data.

Fang H, Wu Y, Narzisi G, O'Rawe JA, Barrón LT, Rosenbaum J, Ronemus M, Iossifov I, Schatz MC, Lyon GJ.

Genome Med. 2014 Oct 28;6(10):89. doi: 10.1186/s13073-014-0089-z. eCollection 2014.


The contribution of de novo coding mutations to autism spectrum disorder.

Iossifov I, O'Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE, Smith JD, Paeper B, Nickerson DA, Dea J, Dong S, Gonzalez LE, Mandell JD, Mane SM, Murtha MT, Sullivan CA, Walker MF, Waqar Z, Wei L, Willsey AJ, Yamrom B, Lee YH, 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 MC, Ye K, McCombie WR, Shendure J, Eichler EE, State MW, Wigler M.

Nature. 2014 Nov 13;515(7526):216-21. doi: 10.1038/nature13908. Epub 2014 Oct 29.


Increased frequency of de novo copy number variants in congenital heart disease by integrative analysis of single nucleotide polymorphism array and exome sequence data.

Glessner JT, Bick AG, Ito K, Homsy J, Rodriguez-Murillo L, Fromer M, Mazaika E, Vardarajan B, Italia M, Leipzig J, DePalma SR, Golhar R, Sanders SJ, Yamrom B, Ronemus M, Iossifov I, Willsey AJ, State MW, Kaltman JR, White PS, Shen Y, Warburton D, Brueckner M, Seidman C, Goldmuntz E, Gelb BD, Lifton R, Seidman J, Hakonarson H, Chung WK.

Circ Res. 2014 Oct 24;115(10):884-896. doi: 10.1161/CIRCRESAHA.115.304458. Epub 2014 Sep 9.


Accurate de novo and transmitted indel detection in exome-capture data using microassembly.

Narzisi G, O'Rawe JA, Iossifov I, Fang H, Lee YH, Wang Z, Wu Y, Lyon GJ, Wigler M, Schatz MC.

Nat Methods. 2014 Oct;11(10):1033-6. doi: 10.1038/nmeth.3069. Epub 2014 Aug 17.


Target-independent prediction of drug synergies using only drug lipophilicity.

Yilancioglu K, Weinstein ZB, Meydan C, Akhmetov A, Toprak I, Durmaz A, Iossifov I, Kazan H, Roth FP, Cokol M.

J Chem Inf Model. 2014 Aug 25;54(8):2286-93. doi: 10.1021/ci500276x. Epub 2014 Aug 1.


Large-scale identification and analysis of suppressive drug interactions.

Cokol M, Weinstein ZB, 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 FP.

Chem Biol. 2014 Apr 24;21(4):541-551. doi: 10.1016/j.chembiol.2014.02.012. Epub 2014 Apr 3.


The role of de novo mutations in the genetics of autism spectrum disorders.

Ronemus M, Iossifov I, Levy D, Wigler M.

Nat Rev Genet. 2014 Feb;15(2):133-41. doi: 10.1038/nrg3585. Epub 2014 Jan 16. Review.


De novo gene disruptions in children on the autistic spectrum.

Iossifov I, Ronemus M, Levy D, Wang Z, Hakker I, Rosenbaum J, Yamrom B, Lee YH, 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 LL, Fulton RS, Magrini VJ, Ye K, Darnell JC, Darnell RB, Mardis ER, Wilson RK, Schatz MC, McCombie WR, Wigler M.

Neuron. 2012 Apr 26;74(2):285-99. doi: 10.1016/j.neuron.2012.04.009.


Mast-cell leukemia exome sequencing reveals a mutation in the IgE mast-cell receptor β chain and KIT V654A.

Spector MS, Iossifov I, Kritharis A, He C, Kolitz JE, Lowe SW, Allen SL.

Leukemia. 2012 Jun;26(6):1422-5. doi: 10.1038/leu.2011.354. Epub 2011 Dec 16. No abstract available.


A comparative analysis of exome capture.

Parla JS, Iossifov I, Grabill I, Spector MS, Kramer M, McCombie WR.

Genome Biol. 2011 Sep 29;12(9):R97. doi: 10.1186/gb-2011-12-9-r97.


Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses.

Gilman SR, Iossifov I, Levy D, Ronemus M, Wigler M, Vitkup D.

Neuron. 2011 Jun 9;70(5):898-907. doi: 10.1016/j.neuron.2011.05.021.


Rare de novo and transmitted copy-number variation in autistic spectrum disorders.

Levy D, Ronemus M, Yamrom B, Lee YH, 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.

Neuron. 2011 Jun 9;70(5):886-97. doi: 10.1016/j.neuron.2011.05.015.


Looking at cerebellar malformations through text-mined interactomes of mice and humans.

Iossifov I, Rodriguez-Esteban R, Mayzus I, Millen KJ, Rzhetsky A.

PLoS Comput Biol. 2009 Nov;5(11):e1000559. doi: 10.1371/journal.pcbi.1000559. Epub 2009 Nov 6.


Figure mining for biomedical research.

Rodriguez-Esteban R, Iossifov I.

Bioinformatics. 2009 Aug 15;25(16):2082-4. doi: 10.1093/bioinformatics/btp318. Epub 2009 May 13.


Analysis of Drosophila segmentation network identifies a JNK pathway factor overexpressed in kidney cancer.

Liu J, Ghanim M, Xue L, Brown CD, Iossifov I, Angeletti C, Hua S, Nègre N, Ludwig M, Stricker T, Al-Ahmadie HA, Tretiakova M, Camp RL, Perera-Alberto M, Rimm DL, Xu T, Rzhetsky A, White KP.

Science. 2009 Feb 27;323(5918):1218-22. doi: 10.1126/science.1157669. Epub 2009 Jan 22.


Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network.

Iossifov I, Zheng T, Baron M, Gilliam TC, Rzhetsky A.

Genome Res. 2008 Jul;18(7):1150-62. doi: 10.1101/gr.075622.107. Epub 2008 Apr 16.


How many scientific papers should be retracted?

Cokol M, Iossifov I, Rodriguez-Esteban R, Rzhetsky A.

EMBO Rep. 2007 May;8(5):422-3. No abstract available.


Imitating manual curation of text-mined facts in biomedicine.

Rodriguez-Esteban R, Iossifov I, Rzhetsky A.

PLoS Comput Biol. 2006 Sep 8;2(9):e118. Epub 2006 Jul 27.


Microparadigms: chains of collective reasoning in publications about molecular interactions.

Rzhetsky A, Iossifov I, Loh JM, White KP.

Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):4940-5. Epub 2006 Mar 16.


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.

Cheng R, Juo SH, Loth JE, Nee J, Iossifov I, Blumenthal R, Sharpe L, Kanyas K, Lerer B, Lilliston B, Smith M, Trautman K, Gilliam TC, Endicott J, Baron M.

Mol Psychiatry. 2006 Mar;11(3):252-60.


Emergent behavior of growing knowledge about molecular interactions.

Cokol M, Iossifov I, Weinreb C, Rzhetsky A.

Nat Biotechnol. 2005 Oct;23(10):1243-7. No abstract available.


GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data.

Rzhetsky A, Iossifov I, Koike T, Krauthammer M, Kra P, Morris M, Yu H, Duboué PA, Weng W, Wilbur WJ, Hatzivassiloglou V, Friedman C.

J Biomed Inform. 2004 Feb;37(1):43-53.


Probabilistic inference of molecular networks from noisy data sources.

Iossifov I, Krauthammer M, Friedman C, Hatzivassiloglou V, Bader JS, White KP, Rzhetsky A.

Bioinformatics. 2004 May 22;20(8):1205-13. Epub 2004 Feb 10.


Of truth and pathways: chasing bits of information through myriads of articles.

Krauthammer M, Kra P, Iossifov I, Gomez SM, Hripcsak G, Hatzivassiloglou V, Friedman C, Rzhetsky A.

Bioinformatics. 2002;18 Suppl 1:S249-57.


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