Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data (2009)
Can Alkan, Mario Ventura, Nicoletta Archidiacono, Mariano Rocchi, S. Cenk Sahinalp, Evan E. Eichler
The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%–5 % of sequence generated as part of primate genome sequencing projects consists of this material, which is...
A burst of segmental duplications in the genome of the African great ape ancestor (2009)
Marqués-Bonet, Tomàs, Kidd, Jeffrey M., Ventura, Mario, Graves, Tina A., Cheng, Ze, Hillier, LaDeana W., ...
5 pages, 4 figures.-- Supplementary information (3 files) available at: http://www.nature.com/nature/journal/v457/n7231/suppinfo/nature07744.html
Girirajan, Santhosh, Chen, Lin, Graves, Tina, Marques-Bonet, Tomas, Ventura, Mario, Fronick, Catrina, ...
The gibbon genome exhibits extensive karyotypic diversity with an increased rate of chromosomal rearrangements during evolution. In an effort to understand the mechanistic origin and implications of...
Characterization of six human disease-associated inversion polymorphisms (2009)
Antonacci, Francesca, Kidd, Jeffrey M., Marques-Bonet, Tomas, Ventura, Mario, Siswara, Priscillia, Jiang, Zhaoshi, ...
The human genome is a highly dynamic structure that shows a wide range of genetic polymorphic variation. Unlike other types of structural variation, little is known about inversion variants within...
Nicholas, Thomas J., Cheng, Ze, Ventura, Mario, Mealey, Katrina, Eichler, Evan E., Akey, Joshua M.
Structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of segmental duplications and associated...
Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication (2008)
Cardone, Maria, Jiang, Zhaoshi, D'Addabbo, Pietro, Archidiacono, Nicoletta, Rocchi, Mariano, Eichler, Evan E, ...
Abstract Background Chromosomal rearrangements, such as translocations and inversions, are recurrent phenomena during evolution, and both of them are involved in reproductive isolation and...
Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data (2007)
Can Alkan, Mario Ventura, Nicoletta Archidiacono, Mariano Rocchi, S. Cenk Sahinalp, Evan E. Eichler
The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%–5% of sequence generated as part of primate genome sequencing projects consists of this material, which is...
Mefford, Heather C., Clauin, Séverine, Sharp, Andrew J., Moller, Rikke S., Ullmann, Reinhard, Kapur, Raj, ...
Most studies of genomic disorders have focused on patients with cognitive disability and/or peripheral nervous system defects. In an effort to broaden the phenotypic spectrum of this disease model,...
Cardone, Maria, Alonso, Alicia, Pazienza, Michele, Ventura, Mario, Montemurro, Gabriella, Carbone, Lucia, ...
Abstract Background Evolutionary centromere repositioning and human analphoid neocentromeres occurring in clinical cases are, very likely, two stages of the same phenomenon whose properties still...
Recurrent duplication-driven transposition of DNA during hominoid evolution. (2006)
Johnson, Matthew E., Cheng, Ze, Morrison, V. Anne, Scherer, Steven, Ventura, Mario, Gibbs, Richard A., ...
The underlying mechanism by which the interspersed pattern of human segmental duplications has evolved is unknown. Based on a comparative analysis of primate genomes, we show that a particular...
She, Xinwei, Liu, Ge, Ventura, Mario, Zhao, Shaying, Misceo, Doriana, Roberto, Roberta, ...
Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence...
She, Xinwei, Liu, Ge, Ventura, Mario, Zhao, Shaying, Misceo, Doriana, Roberto, Roberta, ...
Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence...
She, Xinwei, Liu, Ge, Ventura, Mario, Zhao, Shaying, Misceo, Doriana, Roberto, Roberta, ...
Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence...
Vives, Ingrid, Grimalt, Joan O., Ventura, Mario, Catalán, Jordi, Rosseland, B. O.
8 pages, 3 figures.-- PMID: 15519465 [PubMed].-- Available online Jul 31, 2004.
Initial sequence of the chimpanzee genome and comparison with the human genome (2005)
Mikkelsen, Tarjei S., Hillier, LaDeana W., Eichler, Evan E., Zody, Michael C., Jaffe, David B., Yang, Shiaw-Pyng, ...
Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences...
Punctuated duplication seeding events during the evolution of human chromosome 2p11. (2005)
Horvath, Julie E., Gulden, Cassandra L., Vallente, Rhea U., Eichler, Marla Y., Ventura, Mario, McPherson, John D., ...
Primate genomic sequence comparisons are becoming increasingly useful for elucidating the evolutionary history and organization of our own genome. Such studies are particularly informative within...
A genome-wide survey of structural variation between human and chimpanzee. (2005)
Newman, Tera L., Tuzun, Eray, Morrison, V. Anne, Hayden, Karen E., Ventura, Mario, McGrath, Sean D., ...
Structural changes (deletions, insertions, and inversions) between human and chimpanzee genomes have likely had a significant impact on lineage-specific evolution because of their potential for...
Punctuated duplication seeding events during the evolution of human chromosome 2p11 (2005)
Horvath, Julie E., Gulden, Cassandra L., Vallente, Rhea U., Eichler, Marla Y., Ventura, Mario, McPherson, John D., ...
Primate genomic sequence comparisons are becoming increasingly useful for elucidating the evolutionary history and organization of our own genome. Such studies are particularly informative within...
Punctuated duplication seeding events during the evolution of human chromosome 2p11 (2005)
Horvath, Julie E., Gulden, Cassandra L., Vallente, Rhea U., Eichler, Marla Y., Ventura, Mario, McPherson, John D., ...
Primate genomic sequence comparisons are becoming increasingly useful for elucidating the evolutionary history and organization of our own genome. Such studies are particularly informative within...
A genome-wide survey of structural variation between human and chimpanzee (2005)
Newman, Tera L., Tuzun, Eray, Morrison, V. Anne, Hayden, Karen E., Ventura, Mario, McGrath, Sean D., ...
Structural changes (deletions, insertions, and inversions) between human and chimpanzee genomes have likely had a significant impact on lineage-specific evolution because of their potential for...
A genome-wide survey of structural variation between human and chimpanzee (2005)
Newman, Tera L., Tuzun, Eray, Morrison, V. Anne, Hayden, Karen E., Ventura, Mario, McGrath, Sean D., ...
Structural changes (deletions, insertions, and inversions) between human and chimpanzee genomes have likely had a significant impact on lineage-specific evolution because of their potential for...
Analysis of segmental duplications and genome assembly in the mouse. (2004)
Bailey, Jeffrey A., Church, Deanna M., Ventura, Mario, Rocchi, Mariano, Eichler, Evan E.
Limited comparative studies suggest that the human genome is particularly enriched for recent segmental duplications. The extent of segmental duplications in other mammalian genomes is unknown and...
Recurrent sites for new centromere seeding. (2004)
Ventura, Mario, Weigl, Stefania, Carbone, Lucia, Cardone, Maria Francesca, Misceo, Doriana, Teti, Mariagrazia, ...
Using comparative FISH and genomics, we have studied and compared the evolution of chromosome 3 in primates and two human neocentromere cases on the long arm of this chromosome. Our results show that...
Neocentromeres in 15q24-26 Map to Duplicons Which Flanked an Ancestral Centromere in 15q25 (2003)
Ventura, Mario, Mudge, Jonathan M., Palumbo, Valeria, Burn, Sally, Blennow, Elisabeth, Pierluigi, Mauro, ...
The existence of latent centromeres has been proposed as a possible explanation for the ectopic emergence of neocentromeres in humans. This hypothesis predicts an association between the position of...
Neocentromeres in 15q24-26 Map to Duplicons Which Flanked an Ancestral Centromere in 15q25 (2003)
Ventura, Mario, Mudge, Jonathan M., Palumbo, Valeria, Burn, Sally, Blennow, Elisabeth, Pierluigi, Mauro, ...
The existence of latent centromeres has been proposed as a possible explanation for the ectopic emergence of neocentromeres in humans. This hypothesis predicts an association between the position of...
Complex Events in the Evolution of the Human Pseudoautosomal Region 2 (PAR2) (2003)
Charchar, Fadi J., Svartman, Marta, El-Mogharbel, Nisrine, Ventura, Mario, Kirby, Patrick, Matarazzo, Maria R., ...
Chromosome 6 Phylogeny in Primates and Centromere Repositioning (2003)
Eder, Verena, Ventura, Mario, Ianigro, Massimo, Teti, Mariagrazia, Rocchi, Mariano, Archidiacono, Nicoletta
A panel of 15 human BAC/PAC probes, covering the entire chromosome 6, was used in FISH experiments on great apes and on representatives of Old World monkeys, New World monkeys, and lemurs to...
Complex Events in the Evolution of the Human Pseudoautosomal Region 2 (PAR2) (2003)
Charchar, Fadi J., Svartman, Marta, El-Mogharbel, Nisrine, Ventura, Mario, Kirby, Patrick, Matarazzo, Maria R., ...
The 320-kb human pseudoautosomal region 2 (PAR2) at the tips of the long arms of the X and Y chromosomes is thought to have been duplicated onto the Y chromosome recently in primate evolution. The...
Crosier, Moira, Viggiano, Luigi, Guy, Jane, Misceo, Doriana, Stones, Robert, Wei, Wenbin, ...
KIAA0187 is a gene of unknown function that maps to 10q11 and has been subject to recent duplication events. Here we analyze 18 human paralogs of this gene and show that paralogs of exons 14-23 were...
Giglio, Sabrina, Calvari, Vladimiro, Gregato, Giuliana, Gimelli, Giorgio, Camanini, Silvia, Giorda, Roberto, ...
The t(4;8)(p16;p23) translocation, in either the balanced form or the unbalanced form, has been reported several times. Taking into consideration the fact that this translocation may be undetected in...
Centromere Emergence in Evolution
Ventura, Mario, Archidiacono, Nicoletta, Rocchi, Mariano
Evolutionary centromere repositioning is a paradox we have recently discovered while studying the conservation of the phylogenetic chromosome IX in primates. Two explanations were proposed: a...
Neocentromeres in 15q24-26 Map to Duplicons Which Flanked an Ancestral Centromere in 15q25
Ventura, Mario, Mudge, Jonathan M., Palumbo, Valeria, Burn, Sally, Blennow, Elisabeth, Pierluigi, Mauro, ...
The existence of latent centromeres has been proposed as a possible explanation for the ectopic emergence of neocentromeres in humans. This hypothesis predicts an association between the position of...
Complex Events in the Evolution of the Human Pseudoautosomal Region 2 (PAR2)
Charchar, Fadi J., Svartman, Marta, El-Mogharbel, Nisrine, Ventura, Mario, Kirby, Patrick, Matarazzo, Maria R., ...
The 320-kb human pseudoautosomal region 2 (PAR2) at the tips of the long arms of the X and Y chromosomes is thought to have been duplicated onto the Y chromosome recently in primate evolution. The...
Analysis of Segmental Duplications and Genome Assembly in the Mouse
Bailey, Jeffrey A., Church, Deanna M., Ventura, Mario, Rocchi, Mariano, Eichler, Evan E.
Limited comparative studies suggest that the human genome is particularly enriched for recent segmental duplications. The extent of segmental duplications in other mammalian genomes is unknown and...
Recurrent Sites for New Centromere Seeding
Ventura, Mario, Weigl, Stefania, Carbone, Lucia, Cardone, Maria Francesca, Misceo, Doriana, Teti, Mariagrazia, ...
Using comparative FISH and genomics, we have studied and compared the evolution of chromosome 3 in primates and two human neocentromere cases on the long arm of this chromosome. Our results show that...
Punctuated duplication seeding events during the evolution of human chromosome 2p11
Horvath, Julie E., Gulden, Cassandra L., Vallente, Rhea U., Eichler, Marla Y., Ventura, Mario, McPherson, John D., ...
Primate genomic sequence comparisons are becoming increasingly useful for elucidating the evolutionary history and organization of our own genome. Such studies are particularly informative within...
Crosier, Moira, Viggiano, Luigi, Guy, Jane, Misceo, Doriana, Stones, Robert, Wei, Wenbin, ...
KIAA0187 is a gene of unknown function that maps to 10q11 and has been subject to recent duplication events. Here we analyze 18 human paralogs of this gene and show that paralogs of exons 14–23...
A genome-wide survey of structural variation between human and chimpanzee
Newman, Tera L., Tuzun, Eray, Morrison, V. Anne, Hayden, Karen E., Ventura, Mario, McGrath, Sean D., ...
Structural changes (deletions, insertions, and inversions) between human and chimpanzee genomes have likely had a significant impact on lineage-specific evolution because of their potential for...
She, Xinwei, Liu, Ge, Ventura, Mario, Zhao, Shaying, Misceo, Doriana, Roberto, Roberta, ...
Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence...
Crosier, Moira, Viggiano, Luigi, Guy, Jane, Misceo, Doriana, Stones, Robert, Wei, Wenbin, ...
KIAA0187 is a gene of unknown function that maps to 10q11 and has been subject to recent duplication events. Here we analyze 18 human paralogs of this gene and show that paralogs of exons 14–23...
Centromere Emergence in Evolution
Ventura, Mario, Archidiacono, Nicoletta, Rocchi, Mariano
Evolutionary centromere repositioning is a paradox we have recently discovered while studying the conservation of the phylogenetic chromosome IX in primates. Two explanations were proposed: a...
Giglio, Sabrina, Calvari, Vladimiro, Gregato, Giuliana, Gimelli, Giorgio, Camanini, Silvia, Giorda, Roberto, ...
The t(4;8)(p16;p23) translocation, in either the balanced form or the unbalanced form, has been reported several times. Taking into consideration the fact that this translocation may be undetected in...
Neocentromeres in 15q24-26 Map to Duplicons Which Flanked an Ancestral Centromere in 15q25
Ventura, Mario, Mudge, Jonathan M., Palumbo, Valeria, Burn, Sally, Blennow, Elisabeth, Pierluigi, Mauro, ...
The existence of latent centromeres has been proposed as a possible explanation for the ectopic emergence of neocentromeres in humans. This hypothesis predicts an association between the position of...
Complex Events in the Evolution of the Human Pseudoautosomal Region 2 (PAR2)
Charchar, Fadi J., Svartman, Marta, El-Mogharbel, Nisrine, Ventura, Mario, Kirby, Patrick, Matarazzo, Maria R., ...
The 320-kb human pseudoautosomal region 2 (PAR2) at the tips of the long arms of the X and Y chromosomes is thought to have been duplicated onto the Y chromosome recently in primate evolution. The...
Analysis of Segmental Duplications and Genome Assembly in the Mouse
Bailey, Jeffrey A., Church, Deanna M., Ventura, Mario, Rocchi, Mariano, Eichler, Evan E.
Limited comparative studies suggest that the human genome is particularly enriched for recent segmental duplications. The extent of segmental duplications in other mammalian genomes is unknown and...
Recurrent Sites for New Centromere Seeding
Ventura, Mario, Weigl, Stefania, Carbone, Lucia, Cardone, Maria Francesca, Misceo, Doriana, Teti, Mariagrazia, ...
Using comparative FISH and genomics, we have studied and compared the evolution of chromosome 3 in primates and two human neocentromere cases on the long arm of this chromosome. Our results show that...
Punctuated duplication seeding events during the evolution of human chromosome 2p11
Horvath, Julie E., Gulden, Cassandra L., Vallente, Rhea U., Eichler, Marla Y., Ventura, Mario, McPherson, John D., ...
Primate genomic sequence comparisons are becoming increasingly useful for elucidating the evolutionary history and organization of our own genome. Such studies are particularly informative within...
A genome-wide survey of structural variation between human and chimpanzee
Newman, Tera L., Tuzun, Eray, Morrison, V. Anne, Hayden, Karen E., Ventura, Mario, McGrath, Sean D., ...
Structural changes (deletions, insertions, and inversions) between human and chimpanzee genomes have likely had a significant impact on lineage-specific evolution because of their potential for...
She, Xinwei, Liu, Ge, Ventura, Mario, Zhao, Shaying, Misceo, Doriana, Roberto, Roberta, ...
Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence...
Cardone, Maria Francesca, Alonso, Alicia, Pazienza, Michele, Ventura, Mario, Montemurro, Gabriella, Carbone, Lucia, ...
The mammalian evolutionary history of chromosome 13 was characterized and evolutionary-new centromeres compared to two human neocentromeres at 13q21 using chromatin immunoprecipitation and genomic...
Recurrent duplication-driven transposition of DNA during hominoid evolution
Johnson, Matthew E., Cheng, Ze, Morrison, V. Anne, Scherer, Steven, Ventura, Mario, Gibbs, Richard A., ...
The underlying mechanism by which the interspersed pattern of human segmental duplications has evolved is unknown. Based on a comparative analysis of primate genomes, we show that a particular...
Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data
Alkan, Can, Ventura, Mario, Archidiacono, Nicoletta, Rocchi, Mariano, Sahinalp, S. Cenk, Eichler, Evan E
The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%–5% of sequence generated as part of primate genome sequencing projects consists of this material, which is...
Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication
Cardone, Maria Francesca, Jiang, Zhaoshi, D'Addabbo, Pietro, Archidiacono, Nicoletta, Rocchi, Mariano, Eichler, Evan E, ...
A FISH analysis of chromosome 17 homologs in primates suggests that genomic architecture has a direct role in karyotype evolution and in the genomic instability associated with human disease.
Degenhardt, Jeremiah D., De Candia, Paola, Chabot, Adrien, Schwartz, Stuart, Henderson, Les, Ling, Binhua, ...
Variation in genes underlying host immunity can lead to marked differences in susceptibility to HIV infection among humans. Despite heavy reliance on non-human primates as models for HIV/AIDS, little...
Death and Resurrection of the Human IRGM Gene
Bekpen, Cemalettin, Marques-Bonet, Tomas, Alkan, Can, Antonacci, Francesca, Leogrande, Maria Bruna, Ventura, Mario, ...
Immunity-related GTPases (IRG) play an important role in defense against intracellular pathogens. One member of this gene family in humans, IRGM, has been recently implicated as a risk factor for...
Characterization of six human disease-associated inversion polymorphisms
Antonacci, Francesca, Kidd, Jeffrey M., Marques-Bonet, Tomas, Ventura, Mario, Siswara, Priscillia, Jiang, Zhaoshi, ...
The human genome is a highly dynamic structure that shows a wide range of genetic polymorphic variation. Unlike other types of structural variation, little is known about inversion variants within...
Sequencing human–gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites
Girirajan, Santhosh, Chen, Lin, Graves, Tina, Marques-Bonet, Tomas, Ventura, Mario, Fronick, Catrina, ...
The gibbon genome exhibits extensive karyotypic diversity with an increased rate of chromosomal rearrangements during evolution. In an effort to understand the mechanistic origin and implications of...
The genomic architecture of segmental duplications and associated copy number variants in dogs
Nicholas, Thomas J., Cheng, Ze, Ventura, Mario, Mealey, Katrina, Eichler, Evan E., Akey, Joshua M.
Structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of segmental duplications and associated...