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Dr.Nod: computational framework for discovery of regulatory non-coding drivers in tissue-matched distal regulatory elements. Nucleic Acids Res. 2023 02 28; 51(4):e23.
Tomkova M, Tomek J, Chow J, McPherson JD, Segal DJ, Hormozdiari F. PMID: 36625266; PMCID: PMC9976879.
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PubMed Mentions: Fields:
Translation:
HumansCells
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SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads. Nat Methods. 2023 04; 20(4):550-558.
Denti L, Khorsand P, Bonizzoni P, Hormozdiari F, Chikhi R. PMID: 36550274.
View in:
PubMed Mentions:
6 Fields:
Translation:
HumansCells
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Prediction of Neurodevelopmental Disorders Based on De Novo Coding Variation. J Autism Dev Disord. 2023 Mar; 53(3):963-976.
Chow JC, Hormozdiari F. PMID: 35596027; PMCID: PMC9986216.
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PubMed Mentions:
1 Fields:
Translation:
Humans
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MAGI-MS: multiple seed-centric module discovery. Bioinform Adv. 2022; 2(1):vbac025.
Chow JC, Zhou R, Hormozdiari F. PMID: 36699383; PMCID: PMC9710684.
View in:
PubMed Mentions:
-
Comparative genome analysis using sample-specific string detection in accurate long reads. Bioinform Adv. 2021; 1(1):vbab005.
Khorsand P, Denti L, Human Genome Structural Variant Consortium, Bonizzoni P, Chikhi R, Hormozdiari F. PMID: 36700094; PMCID: PMC9710709.
View in:
PubMed Mentions:
2
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Nebula: ultra-efficient mapping-free structural variant genotyper. Nucleic Acids Res. 2021 05 07; 49(8):e47.
Khorsand P, Hormozdiari F. PMID: 33503255; PMCID: PMC8096284.
View in:
PubMed Mentions:
9 Fields:
-
Meltos: multi-sample tumor phylogeny reconstruction for structural variants. Bioinformatics. 2020 02 15; 36(4):1082-1090.
Ricketts C, Seidman D, Popic V, Hormozdiari F, Batzoglou S, Hajirasouliha I. PMID: 31584621; PMCID: PMC8215921.
View in:
PubMed Mentions:
6 Fields:
Translation:
Humans
-
Dissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders. Genome Med. 2019 10 25; 11(1):65.
Chow J, Jensen M, Amini H, Hormozdiari F, Penn O, Shifman S, Girirajan S, Hormozdiari F. PMID: 31653223; PMCID: PMC6815046.
View in:
PubMed Mentions:
14 Fields:
Translation:
Humans
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Discovery of tandem and interspersed segmental duplications using high-throughput sequencing. Bioinformatics. 2019 10 15; 35(20):3923-3930.
Soylev A, Le TM, Amini H, Alkan C, Hormozdiari F. PMID: 30937433; PMCID: PMC6792081.
View in:
PubMed Mentions:
16 Fields:
Translation:
HumansCells
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Functional disease architectures reveal unique biological role of transposable elements. Nat Commun. 2019 09 06; 10(1):4054.
Hormozdiari F, van de Geijn B, Nasser J, Weissbrod O, Gazal S, Ju CJ, Connor LO, Hujoel MLA, Engreitz J, Hormozdiari F, Price AL. PMID: 31492842; PMCID: PMC6731302.
View in:
PubMed Mentions:
7 Fields:
Translation:
HumansCells
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Kevlar: A Mapping-Free Framework for Accurate Discovery of De Novo Variants. iScience. 2019 Aug 30; 18:28-36.
Standage DS, Brown CT, Hormozdiari F. PMID: 31377530; PMCID: PMC6682328.
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PubMed Mentions:
12
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Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat Commun. 2019 04 16; 10(1):1784.
Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C. PMID: 30992455; PMCID: PMC6467913.
View in:
PubMed Mentions:
390 Fields:
Translation:
Humans
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TAD fusion score: discovery and ranking the contribution of deletions to genome structure. Genome Biol. 2019 03 21; 20(1):60.
Huynh L, Hormozdiari F. PMID: 30898144; PMCID: PMC6427865.
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PubMed Mentions:
19 Fields:
Translation:
HumansCells
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How bioinformatics and open data can boost basic science in countries and universities with limited resources. Nat Biotechnol. 2019 03; 37(3):324-326.
Mangul S, Martin LS, Langmead B, Sanchez-Galan JE, Toma I, Hormozdiari F, Pevzner P, Eskin E. PMID: 30833765.
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PubMed Mentions:
11 Fields:
Translation:
Humans
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Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity. Nat Genet. 2019 01; 51(1):106-116.
Coe BP, Stessman HAF, Sulovari A, Geisheker MR, Bakken TE, Lake AM, Dougherty JD, Lein ES, Hormozdiari F, Bernier RA, Eichler EE. PMID: 30559488; PMCID: PMC6309590.
View in:
PubMed Mentions:
133 Fields:
Translation:
HumansAnimals
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Skewed X-inactivation is common in the general female population. Eur J Hum Genet. 2019 03; 27(3):455-465.
Shvetsova E, Sofronova A, Monajemi R, Gagalova K, Draisma HHM, White SJ, Santen GWE, Chuva de Sousa Lopes SM, Heijmans BT, van Meurs J, Jansen R, Franke L, Kielbasa SM, den Dunnen JT, 't Hoen PAC, BIOS consortium, GoNL consortium. PMID: 30552425; PMCID: PMC6460563.
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PubMed Mentions:
65 Fields:
Translation:
Humans
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Combinatorial Approach for Complex Disorder Prediction: Case Study of Neurodevelopmental Disorders. Genetics. 2018 12; 210(4):1483-1495.
Huynh L, Hormozdiari F. PMID: 30297454; PMCID: PMC6283174.
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PubMed Mentions:
1 Fields:
Translation:
Humans
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High-resolution comparative analysis of great ape genomes. Science. 2018 06 08; 360(6393).
Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, Underwood JG, Nelson BJ, Chaisson MJP, Dougherty ML, Munson KM, Hastie AR, Diekhans M, Hormozdiari F, Lorusso N, Hoekzema K, Qiu R, Clark K, Raja A, Welch AE, Sorensen M, Baker C, Fulton RS, Armstrong J, Graves-Lindsay TA, Denli AM, Hoppe ER, Hsieh P, Hill CM, Pang AWC, Lee J, Lam ET, Dutcher SK, Gage FH, Warren WC, Shendure J, Haussler D, Schneider VA, Cao H, Ventura M, Wilson RK, Paten B, Pollen A, Eichler EE. PMID: 29880660; PMCID: PMC6178954.
View in:
PubMed Mentions:
162 Fields:
Translation:
HumansAnimals
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Genetic variation associated with increased insecticide resistance in the malaria mosquito, Anopheles coluzzii. Parasit Vectors. 2018 04 04; 11(1):225.
Main BJ, Everitt A, Cornel AJ, Hormozdiari F, Lanzaro GC. PMID: 29618373; PMCID: PMC5885317.
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PubMed Mentions:
14 Fields:
Translation:
AnimalsPHPublic Health
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Genomic Patterns of De Novo Mutation in Simplex Autism. Cell. 2017 Oct 19; 171(3):710-722.e12.
Turner TN, Coe BP, Dickel DE, Hoekzema K, Nelson BJ, Zody MC, Kronenberg ZN, Hormozdiari F, Raja A, Pennacchio LA, Darnell RB, Eichler EE. PMID: 28965761; PMCID: PMC5679715.
View in:
PubMed Mentions:
173 Fields:
Translation:
HumansAnimals
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Toolkit for automated and rapid discovery of structural variants. Methods. 2017 10 01; 129:3-7.
Soylev A, Kockan C, Hormozdiari F, Alkan C. PMID: 28583483.
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PubMed Mentions:
14 Fields:
Translation:
Humans
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Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases. Nat Genet. 2017 Apr; 49(4):515-526.
Stessman HA, Xiong B, Coe BP, Wang T, Hoekzema K, Fenckova M, Kvarnung M, Gerdts J, Trinh S, Cosemans N, Vives L, Lin J, Turner TN, Santen G, Ruivenkamp C, Kriek M, van Haeringen A, Aten E, Friend K, Liebelt J, Barnett C, Haan E, Shaw M, Gecz J, Anderlid BM, Nordgren A, Lindstrand A, Schwartz C, Kooy RF, Vandeweyer G, Helsmoortel C, Romano C, Alberti A, Vinci M, Avola E, Giusto S, Courchesne E, Pramparo T, Pierce K, Nalabolu S, Amaral DG, Scheffer IE, Delatycki MB, Lockhart PJ, Hormozdiari F, Harich B, Castells-Nobau A, Xia K, Peeters H, Nordenskjöld M, Schenck A, Bernier RA, Eichler EE. PMID: 28191889; PMCID: PMC5374041.
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PubMed Mentions:
264 Fields:
Translation:
Humans
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A high-quality human reference panel reveals the complexity and distribution of genomic structural variants. Nat Commun. 2016 10 06; 7:12989.
Hehir-Kwa JY, Marschall T, Kloosterman WP, Francioli LC, Baaijens JA, Dijkstra LJ, Abdellaoui A, Koval V, Thung DT, Wardenaar R, Renkens I, Coe BP, Deelen P, de Ligt J, Lameijer EW, van Dijk F, Hormozdiari F, Genome of the Netherlands Consortium, Uitterlinden AG, van Duijn CM, Eichler EE, de Bakker PI, Swertz MA, Wijmenga C, van Ommen GB, Slagboom PE, Boomsma DI, Schönhuth A, Ye K, Guryev V. PMID: 27708267; PMCID: PMC5059695.
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PubMed Mentions:
52 Fields:
Translation:
HumansCells
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The Second Decade of the International Conference on Research in Computational Molecular Biology (RECOMB). . 2016 Jan 1; 9649:3-16.
Hormozdiari HF, Hormozdiari HF, Kingsford KC, Medvedev MP, Vandin VF. .
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Publisher Site Mentions:
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Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA. Am J Hum Genet. 2016 Jan 07; 98(1):58-74.
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. PMID: 26749308; PMCID: PMC4716689.
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PubMed Mentions:
147 Fields:
Translation:
Humans
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The Time Scale of Recombination Rate Evolution in Great Apes. Mol Biol Evol. 2016 Apr; 33(4):928-45.
Stevison LS, Woerner AE, Kidd JM, Kelley JL, Veeramah KR, McManus KF, Great Ape Genome Project, Bustamante CD, Hammer MF, Wall JD. PMID: 26671457; PMCID: PMC5870646.
View in:
PubMed Mentions:
55 Fields:
Translation:
HumansAnimalsCells
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A global reference for human genetic variation. Nature. 2015 Oct 01; 526(7571):68-74.
1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. PMID: 26432245; PMCID: PMC4750478.
View in:
PubMed Mentions:
6974 Fields:
Translation:
Humans
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An integrated map of structural variation in 2,504 human genomes. Nature. 2015 Oct 01; 526(7571):75-81.
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. PMID: 26432246; PMCID: PMC4617611.
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PubMed Mentions:
1038 Fields:
Translation:
HumansCells
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Global diversity, population stratification, and selection of human copy-number variation. Science. 2015 09 11; 349(6253):aab3761.
Sudmant PH, Mallick S, Nelson BJ, Hormozdiari F, Krumm N, Huddleston J, Coe BP, Baker C, Nordenfelt S, Bamshad M, Jorde LB, Posukh OL, Sahakyan H, Watkins WS, Yepiskoposyan L, Abdullah MS, Bravi CM, Capelli C, Hervig T, Wee JT, Tyler-Smith C, van Driem G, Romero IG, Jha AR, Karachanak-Yankova S, Toncheva D, Comas D, Henn B, Kivisild T, Ruiz-Linares A, Sajantila A, Metspalu E, Parik J, Villems R, Starikovskaya EB, Ayodo G, Beall CM, Di Rienzo A, Hammer MF, Khusainova R, Khusnutdinova E, Klitz W, Winkler C, Labuda D, Metspalu M, Tishkoff SA, Dryomov S, Sukernik R, Patterson N, Reich D, Eichler EE. PMID: 26249230; PMCID: PMC4568308.
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PubMed Mentions:
174 Fields:
Translation:
HumansAnimals
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Extreme selective sweeps independently targeted the X chromosomes of the great apes. Proc Natl Acad Sci U S A. 2015 May 19; 112(20):6413-8.
Nam K, Munch K, Hobolth A, Dutheil JY, Veeramah KR, Woerner AE, Hammer MF, Great Ape Genome Diversity Project, Mailund T, Schierup MH. PMID: 25941379; PMCID: PMC4443357.
View in:
PubMed Mentions:
42 Fields:
Translation:
AnimalsCells
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Characteristics of de novo structural changes in the human genome. Genome Res. 2015 Jun; 25(6):792-801.
Kloosterman WP, Francioli LC, Hormozdiari F, Marschall T, Hehir-Kwa JY, Abdellaoui A, Lameijer EW, Moed MH, Koval V, Renkens I, van Roosmalen MJ, Arp P, Karssen LC, Coe BP, Handsaker RE, Suchiman ED, Cuppen E, Thung DT, McVey M, Wendl MC, Genome of Netherlands Consortium, Uitterlinden A, van Duijn CM, Swertz MA, Wijmenga C, van Ommen GB, Slagboom PE, Boomsma DI, Schönhuth A, Eichler EE, de Bakker PI, Ye K, Guryev V. PMID: 25883321; PMCID: PMC4448676.
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PubMed Mentions:
68 Fields:
Translation:
HumansCells
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Genome of The Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels. Nat Commun. 2015 Mar 09; 6:6065.
van Leeuwen EM, Karssen LC, Deelen J, Isaacs A, Medina-Gomez C, Mbarek H, Kanterakis A, Trompet S, Postmus I, Verweij N, van Enckevort DJ, Huffman JE, White CC, Feitosa MF, Bartz TM, Manichaikul A, Joshi PK, Peloso GM, Deelen P, van Dijk F, Willemsen G, de Geus EJ, Milaneschi Y, Penninx BW, Francioli LC, Menelaou A, Pulit SL, Rivadeneira F, Hofman A, Oostra BA, Franco OH, Mateo Leach I, Beekman M, de Craen AJ, Uh HW, Trochet H, Hocking LJ, Porteous DJ, Sattar N, Packard CJ, Buckley BM, Brody JA, Bis JC, Rotter JI, Mychaleckyj JC, Campbell H, Duan Q, Lange LA, Wilson JF, Hayward C, Polasek O, Vitart V, Rudan I, Wright AF, Rich SS, Psaty BM, Borecki IB, Kearney PM, Stott DJ, Adrienne Cupples L, Genome of The Netherlands Consortium, Jukema JW, van der Harst P, Sijbrands EJ, Hottenga JJ, Uitterlinden AG, Swertz MA, van Ommen GJ, de Bakker PI, Eline Slagboom P, Boomsma DI, Wijmenga C, van Duijn CM. PMID: 25751400; PMCID: PMC4366498.
View in:
PubMed Mentions:
24 Fields:
Translation:
Humans
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Resolving the complexity of the human genome using single-molecule sequencing. Nature. 2015 Jan 29; 517(7536):608-11.
Chaisson MJ, Huddleston J, Dennis MY, Sudmant PH, Malig M, Hormozdiari F, Antonacci F, Surti U, Sandstrom R, Boitano M, Landolin JM, Stamatoyannopoulos JA, Hunkapiller MW, Korlach J, Eichler EE. PMID: 25383537; PMCID: PMC4317254.
View in:
PubMed Mentions:
376 Fields:
Translation:
HumansCells
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The discovery of integrated gene networks for autism and related disorders. Genome Res. 2015 Jan; 25(1):142-54.
Hormozdiari F, Penn O, Borenstein E, Eichler EE. PMID: 25378250; PMCID: PMC4317170.
View in:
PubMed Mentions:
128 Fields:
Translation:
Humans
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Whole-genome sequencing of individuals from a founder population identifies candidate genes for asthma. PLoS One. 2014; 9(8):e104396.
Campbell CD, Mohajeri K, Malig M, Hormozdiari F, Nelson B, Du G, Patterson KM, Eng C, Torgerson DG, Hu D, Herman C, Chong JX, Ko A, O'Roak BJ, Krumm N, Vives L, Lee C, Roth LA, Rodriguez-Cintron W, Rodriguez-Santana J, Brigino-Buenaventura E, Davis A, Meade K, LeNoir MA, Thyne S, Jackson DJ, Gern JE, Lemanske RF, Shendure J, Abney M, Burchard EG, Ober C, Eichler EE. PMID: 25116239; PMCID: PMC4130548.
View in:
PubMed Mentions:
20 Fields:
Translation:
Humans
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Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome Biol. 2014 Jun 30; 15(6):R88.
Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C, 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. PMID: 24980144; PMCID: PMC4197830.
View in:
PubMed Mentions:
39 Fields:
Translation:
Humans
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Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat Genet. 2014 Aug; 46(8):818-25.
Genome of the Netherlands Consortium. PMID: 24974849.
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PubMed Mentions:
339 Fields:
Translation:
Humans
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Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nat Commun. 2014 Jun 13; 5:3934.
Delaneau O, Marchini J, 1000 Genomes Project Consortium, 1000 Genomes Project Consortium. PMID: 25653097; PMCID: PMC4338501.
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PubMed Mentions:
216 Fields:
Translation:
Humans
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Integrative annotation of variants from 1092 humans: application to cancer genomics. Science. 2013 Oct 04; 342(6154):1235587.
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüs ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. PMID: 24092746; PMCID: PMC3947637.
View in:
PubMed Mentions:
220 Fields:
Translation:
HumansCells
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Rates and patterns of great ape retrotransposition. Proc Natl Acad Sci U S A. 2013 Aug 13; 110(33):13457-62.
Hormozdiari F, Konkel MK, Prado-Martinez J, Chiatante G, Herraez IH, Walker JA, Nelson B, Alkan C, Sudmant PH, Huddleston J, Catacchio CR, Ko A, Malig M, Baker C, Great Ape Genome Project, Marques-Bonet T, Ventura M, Batzer MA, Eichler EE. PMID: 23884656; PMCID: PMC3746892.
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PubMed Mentions:
35 Fields:
Translation:
HumansAnimalsCells
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Great ape genetic diversity and population history. Nature. 2013 Jul 25; 499(7459):471-5.
Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prüfer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubí C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers S, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH, Hvilsom C, Andrés AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T. PMID: 23823723; PMCID: PMC3822165.
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PubMed Mentions:
365 Fields:
Translation:
HumansAnimals
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The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild. BMC Genomics. 2013 May 31; 14:363.
Prado-Martinez J, Hernando-Herraez I, Lorente-Galdos B, Dabad M, Ramirez O, Baeza-Delgado C, Morcillo-Suarez C, Alkan C, Hormozdiari F, Raineri E, Estellé J, Fernandez-Callejo M, Valles M, Ritscher L, Schöneberg T, de la Calle-Mustienes E, Casillas S, Rubio-Acero R, Melé M, Engelken J, Caceres M, Gomez-Skarmeta JL, Gut M, Bertranpetit J, Gut IG, Abello T, Eichler EE, Mingarro I, Lalueza-Fox C, Navarro A, Marques-Bonet T. PMID: 23721540; PMCID: PMC3673836.
View in:
PubMed Mentions:
18 Fields:
Translation:
AnimalsCells
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An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Nov 01; 491(7422):56-65.
1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. PMID: 23128226; PMCID: PMC3498066.
View in:
PubMed Mentions:
4311 Fields:
Translation:
HumansCells
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From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer. J Pathol. 2012 Jul; 227(3):286-97.
Lapuk AV, Wu C, Wyatt AW, McPherson A, McConeghy BJ, Brahmbhatt S, Mo F, Zoubeidi A, Anderson S, Bell RH, Haegert A, Shukin R, Wang Y, Fazli L, Hurtado-Coll A, Jones EC, Hach F, Hormozdiari F, Hajirasouliha I, Boutros PC, Bristow RG, Zhao Y, Marra MA, Fanjul A, Maher CA, Chinnaiyan AM, Rubin MA, Beltran H, Sahinalp SC, Gleave ME, Volik SV, Collins CC. PMID: 22553170; PMCID: PMC3659819.
View in:
PubMed Mentions:
101 Fields:
Translation:
HumansCells
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Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer. J Pathol. 2012 May; 227(1):53-61.
Wu C, Wyatt AW, Lapuk AV, McPherson A, McConeghy BJ, Bell RH, Anderson S, Haegert A, Brahmbhatt S, Shukin R, Mo F, Li E, Fazli L, Hurtado-Coll A, Jones EC, Butterfield YS, Hach F, Hormozdiari F, Hajirasouliha I, Boutros PC, Bristow RG, Jones SJ, Hirst M, Marra MA, Maher CA, Chinnaiyan AM, Sahinalp SC, Gleave ME, Volik SV, Collins CC. PMID: 22294438; PMCID: PMC3768138.
View in:
PubMed Mentions:
34 Fields:
Translation:
HumansCells
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Proteome Network Emulating Models. . 2012 Jan 1; 69-95.
Dao DP, Hormozdiari HF, Hajirasouliha HI, Ester EM, Sahinalp SS. .
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Simultaneous structural variation discovery among multiple paired-end sequenced genomes. Genome Res. 2011 Dec; 21(12):2203-12.
Hormozdiari F, Hajirasouliha I, McPherson A, Eichler EE, Sahinalp SC. PMID: 22048523; PMCID: PMC3227108.
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PubMed Mentions:
38 Fields:
Translation:
Humans
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Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee. Genome Res. 2011 Oct; 21(10):1640-9.
Ventura M, Catacchio CR, Alkan C, Marques-Bonet T, Sajjadian S, Graves TA, Hormozdiari F, Navarro A, Malig M, Baker C, Lee C, Turner EH, Chen L, Kidd JM, Archidiacono N, Shendure J, Wilson RK, Eichler EE. PMID: 21685127; PMCID: PMC3202281.
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PubMed Mentions:
41 Fields:
Translation:
HumansAnimalsCells
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deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol. 2011 May; 7(5):e1001138.
McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MG, Griffith M, Heravi Moussavi A, Senz J, Melnyk N, Pacheco M, Marra MA, Hirst M, Nielsen TO, Sahinalp SC, Huntsman D, Shah SP. PMID: 21625565; PMCID: PMC3098195.
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PubMed Mentions:
294 Fields:
Translation:
HumansCells
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Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data. Bioinformatics. 2011 Jun 01; 27(11):1481-8.
McPherson A, Wu C, Hajirasouliha I, Hormozdiari F, Hach F, Lapuk A, Volik S, Shah S, Collins C, Sahinalp SC. PMID: 21478487.
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PubMed Mentions:
27 Fields:
Translation:
HumansCells
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Mapping copy number variation by population-scale genome sequencing. Nature. 2011 Feb 03; 470(7332):59-65.
Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO, 1000 Genomes Project. PMID: 21293372; PMCID: PMC3077050.
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PubMed Mentions:
613 Fields:
Translation:
Humans
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Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes. . 2011 Jan 1; 6577:104-105.
Hormozdiari HF, Hajirasouliha HI, McPherson MA, Eichler EE, Sahinalp SS. .
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Alu repeat discovery and characterization within human genomes. Genome Res. 2011 Jun; 21(6):840-9.
Hormozdiari F, Alkan C, Ventura M, Hajirasouliha I, Malig M, Hach F, Yorukoglu D, Dao P, Bakhshi M, Sahinalp SC, Eichler EE. PMID: 21131385; PMCID: PMC3106317.
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PubMed Mentions:
61 Fields:
Translation:
HumansCells
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Diversity of human copy number variation and multicopy genes. Science. 2010 Oct 29; 330(6004):641-6.
Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, 1000 Genomes Project, Eichler EE. PMID: 21030649; PMCID: PMC3020103.
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PubMed Mentions:
375 Fields:
Translation:
Humans
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A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28; 467(7319):1061-73.
1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. PMID: 20981092; PMCID: PMC3042601.
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PubMed Mentions:
4010 Fields:
Translation:
HumansCells
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mrsFAST: a cache-oblivious algorithm for short-read mapping. Nat Methods. 2010 Aug; 7(8):576-7.
Hach F, Hormozdiari F, Alkan C, Hormozdiari F, Birol I, Eichler EE, Sahinalp SC. PMID: 20676076; PMCID: PMC3115707.
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PubMed Mentions:
139 Fields:
Translation:
Humans
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Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics. 2010 Jun 15; 26(12):i350-7.
Hormozdiari F, Hajirasouliha I, Dao P, Hach F, Yorukoglu D, Alkan C, Eichler EE, Sahinalp SC. PMID: 20529927; PMCID: PMC2881400.
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PubMed Mentions:
119 Fields:
Translation:
Cells
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Protein-protein interaction network evaluation for identifying potential drug targets. J Comput Biol. 2010 May; 17(5):669-84.
Hormozdiari F, Salari R, Bafna V, Sahinalp SC. PMID: 20500021.
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PubMed Mentions:
10 Fields:
Translation:
HumansCells
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Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinformatics. 2010 May 15; 26(10):1277-83.
Hajirasouliha I, Hormozdiari F, Alkan C, Kidd JM, Birol I, Eichler EE, Sahinalp SC. PMID: 20385726; PMCID: PMC2865866.
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PubMed Mentions:
55 Fields:
Translation:
Humans
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Towards improved assessment of functional similarity in large-scale screens: a study on indel length. J Comput Biol. 2010 Jan; 17(1):1-20.
Schönhuth A, Salari R, Hormozdiari F, Cherkasov A, Sahinalp SC. PMID: 20078394.
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PubMed Mentions:
1 Fields:
Translation:
Cells
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Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet. 2009 Oct; 41(10):1061-7.
Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C, Malig M, Mutlu O, Sahinalp SC, Gibbs RA, Eichler EE. PMID: 19718026; PMCID: PMC2875196.
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PubMed Mentions:
345 Fields:
Translation:
Humans
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MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Nat Methods. 2009 Jul; 6(7):473-4.
Lee S, Hormozdiari F, Alkan C, Brudno M. PMID: 19483690.
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PubMed Mentions:
62 Fields:
Translation:
Humans
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Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res. 2009 Jul; 19(7):1270-8.
Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC. PMID: 19447966; PMCID: PMC2704429.
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PubMed Mentions:
150 Fields:
Translation:
Humans
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The effect of insertions and deletions on wirings in protein-protein interaction networks: a large-scale study. J Comput Biol. 2009 Feb; 16(2):159-67.
Hormozdiari F, Salari R, Hsing M, Schönhuth A, Chan SK, Sahinalp SC, Cherkasov A. PMID: 19193143.
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PubMed Mentions:
15 Fields:
Translation:
HumansAnimals
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Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks. . 2009 Jan 1; 5724:37-48.
Dao DP, Schönhuth SA, Hormozdiari HF, Hajirasouliha HI, Sahinalp SS, Ester EM. .
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Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes. . 2009 Jan 1; 5541:218-219.
Hormozdiari HF, Alkan AC, Eichler EE, Sahinalp SS. .
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Dense graphlet statistics of protein interaction and random networks. Pac Symp Biocomput. 2009; 178-89.
Colak R, Hormozdiari F, Moser F, Schönhuth A, Holman J, Ester M, Sahinalp SC. PMID: 19213135.
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PubMed Mentions:
9 Fields:
Translation:
Cells
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Biomolecular network motif counting and discovery by color coding. Bioinformatics. 2008 Jul 01; 24(13):i241-9.
Alon N, Dao P, Hajirasouliha I, Hormozdiari F, Sahinalp SC. PMID: 18586721; PMCID: PMC2718641.
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PubMed Mentions:
18 Fields:
Translation:
Cells
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Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. Bioinformatics. 2008 Jul 01; 24(13):i32-40.
Hajirasouliha I, Hormozdiari F, Sahinalp SC, Birol I. PMID: 18586730; PMCID: PMC2718651.
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PubMed Mentions:
8 Fields:
Translation:
Cells
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The Relation between Indel Length and Functional Divergence: A Formal Study. . 2008 Jan 1; 5251:330-341.
Salari SR, Schönhuth SA, Hormozdiari HF, Cherkasov CA, Sahinalp SS. .
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Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution. PLoS Comput Biol. 2007 Jul; 3(7):e118.
Hormozdiari F, Berenbrink P, Przulj N, Sahinalp SC. PMID: 17616981; PMCID: PMC1913096.
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PubMed Mentions:
22 Fields:
Translation:
AnimalsCells
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Relationship between insertion/deletion (indel) frequency of proteins and essentiality. BMC Bioinformatics. 2007 Jun 28; 8:227.
Chan SK, Hsing M, Hormozdiari F, Cherkasov A. PMID: 17598914; PMCID: PMC1925122.
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PubMed Mentions:
19 Fields:
Translation:
Cells