1. Genomic characterization of large heterochromatic gaps in the human genome assembly.

    PLoS computational biology 10(5):e1003628 (2014) PMID 24831296 PMCID PMC4022460

    The largest gaps in the human genome assembly correspond to multi-megabase heterochromatic regions composed primarily of two related families of tandem repeats, Human Satellites 2 and 3 (HSat2,3). The abundance of repetitive DNA in these regions challenges standard mapping and assembly algorithm...
  2. Genomic characterization of large heterochromatic gaps in the human genome assembly.

    PLoS computational biology 10(5):e1003628 (2014) PMID 24831296 PMCID PMC4022460

    The largest gaps in the human genome assembly correspond to multi-megabase heterochromatic regions composed primarily of two related families of tandem repeats, Human Satellites 2 and 3 (HSat2,3). The abundance of repetitive DNA in these regions challenges standard mapping and assembly algorithm...
  3. Centromere reference models for human chromosomes X and Y satellite arrays.

    Genome Research 24(4):697 (2014) PMID 24501022 PMCID PMC3975068

    The human genome sequence remains incomplete, with multimegabase-sized gaps representing the endogenous centromeres and other heterochromatic regions. Available sequence-based studies within these sites in the genome have demonstrated a role in centromere function and chromosome pairing, necessa...
  4. Centromere reference models for human chromosomes X and Y satellite arrays.

    Genome Research 24(4):697 (2014) PMID 24501022 PMCID PMC3975068

    The human genome sequence remains incomplete, with multimegabase-sized gaps representing the endogenous centromeres and other heterochromatic regions. Available sequence-based studies within these sites in the genome have demonstrated a role in centromere function and chromosome pairing, necessa...
  5. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.
    Catherine A Brownstein, Alan H Beggs, Nils Homer, Barry Merriman, Timothy W Yu, Katherine C Flannery, Elizabeth T DeChene, Meghan C Towne, Sarah K Savage, Emily N Price, Ingrid A Holm, Lovelace J Luquette, Elaine Lyon, Joseph Majzoub, Peter Neupert, David McCallie, Peter Szolovits, Huntington F Willard, Nancy J Mendelsohn, Renee Temme, Richard S Finkel, Sabrina W Yum, Livija Medne, Shamil R Sunyaev, Ivan Adzhubey, Christopher A Cassa, Paul I W de Bakker, Hatice Duzkale, Piotr Dworzyński, William Fairbrother, Laurent Francioli, Birgit H Funke, Monica A Giovanni, Robert E Handsaker, Kasper Lage, Matthew S Lebo, Monkol Lek, Ignaty Leshchiner, Daniel G MacArthur, Heather McLaughlin, Michael F Murray, Tune H Pers, Paz Polak, Soumya Raychaudhuri, Heidi L Rehm, Rachel Soemedi, Nathan O Stitziel, Sara Vestecka, Jochen Supper, Claudia Gugenmus, Bernward Klocke, Alexander Hahn, Max Schubach, Mortiz Menzel, Saskia Biskup, Peter Freisinger, Mario Deng, Martin Braun, Sven Perner, Richard J H Smith, Janeen L Andorf, Jian Huang, Kelli Ryckman, Val C Sheffield, Edwin M Stone, Thomas Bair, E Ann Black-Ziegelbein, Terry A Braun, Benjamin Darbro, Adam P DeLuca, Diana L Kolbe, Todd E Scheetz, Aiden E Shearer, Rama Sompallae, Kai Wang, Alexander G Bassuk, Erik Edens, Katherine Mathews, Steven A Moore, Oleg A Shchelochkov, Pamela Trapane, Aaron Bossler, Colleen A Campbell, Jonathan W Heusel, Anne Kwitek, Tara Maga, Karin Panzer, Thomas Wassink, Douglas Van Daele, Hela Azaiez, Kevin Booth, Nic Meyer, Michael Segal, Marc S Williams, Gerard Tromp, Peter White, Donald Corsmeier, Sara Fitzgerald-Butt, Gail Herman, Devon Lamb-Thrush, Kim L McBride, David Newsom, Christopher R Pierson, Alexander T Rakowsky, Aleš Maver, Luca Lovrečić, Anja Palandačić, Borut Peterlin, Ali Torkamani, Anna Wedell, Mikael Huss, Andrey Alexeyenko, Jessica M Lindvall, Måns Magnusson, Daniel Nilsson, Henrik Stranneheim, Fulya Taylan, Christian Gilissen, Alexander Hoischen, Bregje van Bon, Helger Yntema, Marcel Nelen, Weidong Zhang, Jason Sager, Lu Zhang, Kathryn Blair, Deniz Kural, Michael Cariaso, Greg Lennon, Asif Javed, Saloni Agrawal, Pauline C Ng, Komal Sandhu, Shuba Krishna, Vamsi Veeramachaneni, Ofer Isakov, Eran Halperin, Eitan Friedman, Noam Shomron, Gustavo Glusman, Jared C Roach, Juan Caballero, Hannah Cox, Denise Mauldin, Seth Ament, Lee Rowen, Daniel Richards, F Anthony San Lucas, Manuel L, Thomas Caskey, Yu Bai, Ying Huang, Fang, Yan Zhang, Zhengyuan Wang, Jorge Barrera, Juan M Garcia-Lobo, Domingo González-Lamuño, Javier Llorca, Maria C Rodriguez, Ignacio Varela, Martin G Reese, Francisco M De La Vega, Edward Kiruluta, Michele Cargill, Reece K Hart, Jon M Sorenson, Gholson J Lyon, David A Stevenson, Bruce E Bray, Barry Moore, Karen Eilbeck, Mark Yandell, Hongyu Zhao, Lin Hou, Xiaowei Chen, Xiting Yan, Mengjie Chen, Cong Li, Can Yang, Murat Gunel, Peining Li, Yong Kong, Austin C Alexander, Zayed I Albertyn, Kym M Boycott, Dennis E Bulman, Paul M K Gordon, A Micheil Innes, Bartha M Knoppers, Jacek Majewski, Christian R Marshall, Jillian S Parboosingh, Sarah L Sawyer, Mark E Samuels, Jeremy Schwartzentruber, Isaac S Kohane, and David Margulies

    Genome biology 15(3):R53 (2014) PMID 24667040 PMCID PMC4073084

    There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The C...
  6. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.
    Catherine A Brownstein, Alan H Beggs, Nils Homer, Barry Merriman, Timothy W Yu, Katherine C Flannery, Elizabeth T DeChene, Meghan C Towne, Sarah K Savage, Emily N Price, Ingrid A Holm, Lovelace J Luquette, Elaine Lyon, Joseph Majzoub, Peter Neupert, David McCallie, Peter Szolovits, Huntington F Willard, Nancy J Mendelsohn, Renee Temme, Richard S Finkel, Sabrina W Yum, Livija Medne, Shamil R Sunyaev, Ivan Adzhubey, Christopher A Cassa, Paul I W de Bakker, Hatice Duzkale, Piotr Dworzyński, William Fairbrother, Laurent Francioli, Birgit H Funke, Monica A Giovanni, Robert E Handsaker, Kasper Lage, Matthew S Lebo, Monkol Lek, Ignaty Leshchiner, Daniel G MacArthur, Heather McLaughlin, Michael F Murray, Tune H Pers, Paz Polak, Soumya Raychaudhuri, Heidi L Rehm, Rachel Soemedi, Nathan O Stitziel, Sara Vestecka, Jochen Supper, Claudia Gugenmus, Bernward Klocke, Alexander Hahn, Max Schubach, Mortiz Menzel, Saskia Biskup, Peter Freisinger, Mario Deng, Martin Braun, Sven Perner, Richard J H Smith, Janeen L Andorf, Jian Huang, Kelli Ryckman, Val C Sheffield, Edwin M Stone, Thomas Bair, E Ann Black-Ziegelbein, Terry A Braun, Benjamin Darbro, Adam P DeLuca, Diana L Kolbe, Todd E Scheetz, Aiden E Shearer, Rama Sompallae, Kai Wang, Alexander G Bassuk, Erik Edens, Katherine Mathews, Steven A Moore, Oleg A Shchelochkov, Pamela Trapane, Aaron Bossler, Colleen A Campbell, Jonathan W Heusel, Anne Kwitek, Tara Maga, Karin Panzer, Thomas Wassink, Douglas Van Daele, Hela Azaiez, Kevin Booth, Nic Meyer, Michael Segal, Marc S Williams, Gerard Tromp, Peter White, Donald Corsmeier, Sara Fitzgerald-Butt, Gail Herman, Devon Lamb-Thrush, Kim L McBride, David Newsom, Christopher R Pierson, Alexander T Rakowsky, Aleš Maver, Luca Lovrečić, Anja Palandačić, Borut Peterlin, Ali Torkamani, Anna Wedell, Mikael Huss, Andrey Alexeyenko, Jessica M Lindvall, Måns Magnusson, Daniel Nilsson, Henrik Stranneheim, Fulya Taylan, Christian Gilissen, Alexander Hoischen, Bregje van Bon, Helger Yntema, Marcel Nelen, Weidong Zhang, Jason Sager, Lu Zhang, Kathryn Blair, Deniz Kural, Michael Cariaso, Greg Lennon, Asif Javed, Saloni Agrawal, Pauline C Ng, Komal Sandhu, Shuba Krishna, Vamsi Veeramachaneni, Ofer Isakov, Eran Halperin, Eitan Friedman, Noam Shomron, Gustavo Glusman, Jared C Roach, Juan Caballero, Hannah Cox, Denise Mauldin, Seth Ament, Lee Rowen, Daniel Richards, F Anthony San Lucas, Manuel L, Thomas Caskey, Yu Bai, Ying Huang, Fang, Yan Zhang, Zhengyuan Wang, Jorge Barrera, Juan M Garcia-Lobo, Domingo González-Lamuño, Javier Llorca, Maria C Rodriguez, Ignacio Varela, Martin G Reese, Francisco M De La Vega, Edward Kiruluta, Michele Cargill, Reece K Hart, Jon M Sorenson, Gholson J Lyon, David A Stevenson, Bruce E Bray, Barry Moore, Karen Eilbeck, Mark Yandell, Hongyu Zhao, Lin Hou, Xiaowei Chen, Xiting Yan, Mengjie Chen, Cong Li, Can Yang, Murat Gunel, Peining Li, Yong Kong, Austin C Alexander, Zayed I Albertyn, Kym M Boycott, Dennis E Bulman, Paul M K Gordon, A Micheil Innes, Bartha M Knoppers, Jacek Majewski, Christian R Marshall, Jillian S Parboosingh, Sarah L Sawyer, Mark E Samuels, Jeremy Schwartzentruber, Isaac S Kohane, and David Margulies

    Genome biology 15(3):R53 (2014) PMID 24667040 PMCID PMC4073084

    There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The C...
  7. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.
    Catherine A Brownstein, Alan H Beggs, Nils Homer, Barry Merriman, Timothy W Yu, Katherine C Flannery, Elizabeth T DeChene, Meghan C Towne, Sarah K Savage, Emily N Price, Ingrid A Holm, Lovelace J Luquette, Elaine Lyon, Joseph Majzoub, Peter Neupert, David McCallie, Peter Szolovits, Huntington F Willard, Nancy J Mendelsohn, Renee Temme, Richard S Finkel, Sabrina W Yum, Livija Medne, Shamil R Sunyaev, Ivan Adzhubey, Christopher A Cassa, Paul I W de Bakker, Hatice Duzkale, Piotr Dworzyński, William Fairbrother, Laurent Francioli, Birgit H Funke, Monica A Giovanni, Robert E Handsaker, Kasper Lage, Matthew S Lebo, Monkol Lek, Ignaty Leshchiner, Daniel G MacArthur, Heather McLaughlin, Michael F Murray, Tune H Pers, Paz Polak, Soumya Raychaudhuri, Heidi L Rehm, Rachel Soemedi, Nathan O Stitziel, Sara Vestecka, Jochen Supper, Claudia Gugenmus, Bernward Klocke, Alexander Hahn, Max Schubach, Mortiz Menzel, Saskia Biskup, Peter Freisinger, Mario Deng, Martin Braun, Sven Perner, Richard J H Smith, Janeen L Andorf, Jian Huang, Kelli Ryckman, Val C Sheffield, Edwin M Stone, Thomas Bair, E Ann Black-Ziegelbein, Terry A Braun, Benjamin Darbro, Adam P DeLuca, Diana L Kolbe, Todd E Scheetz, Aiden E Shearer, Rama Sompallae, Kai Wang, Alexander G Bassuk, Erik Edens, Katherine Mathews, Steven A Moore, Oleg A Shchelochkov, Pamela Trapane, Aaron Bossler, Colleen A Campbell, Jonathan W Heusel, Anne Kwitek, Tara Maga, Karin Panzer, Thomas Wassink, Douglas Van Daele, Hela Azaiez, Kevin Booth, Nic Meyer, Michael Segal, Marc S Williams, Gerard Tromp, Peter White, Donald Corsmeier, Sara Fitzgerald-Butt, Gail Herman, Devon Lamb-Thrush, Kim L McBride, David Newsom, Christopher R Pierson, Alexander T Rakowsky, Aleš Maver, Luca Lovrečić, Anja Palandačić, Borut Peterlin, Ali Torkamani, Anna Wedell, Mikael Huss, Andrey Alexeyenko, Jessica M Lindvall, Måns Magnusson, Daniel Nilsson, Henrik Stranneheim, Fulya Taylan, Christian Gilissen, Alexander Hoischen, Bregje van Bon, Helger Yntema, Marcel Nelen, Weidong Zhang, Jason Sager, Lu Zhang, Kathryn Blair, Deniz Kural, Michael Cariaso, Greg Lennon, Asif Javed, Saloni Agrawal, Pauline C Ng, Komal Sandhu, Shuba Krishna, Vamsi Veeramachaneni, Ofer Isakov, Eran Halperin, Eitan Friedman, Noam Shomron, Gustavo Glusman, Jared C Roach, Juan Caballero, Hannah Cox, Denise Mauldin, Seth Ament, Lee Rowen, Daniel Richards, F Anthony San Lucas, Manuel L, Thomas Caskey, Yu Bai, Ying Huang, Fang, Yan Zhang, Zhengyuan Wang, Jorge Barrera, Juan M Garcia-Lobo, Domingo González-Lamuño, Javier Llorca, Maria C Rodriguez, Ignacio Varela, Martin G Reese, Francisco M De La Vega, Edward Kiruluta, Michele Cargill, Reece K Hart, Jon M Sorenson, Gholson J Lyon, David A Stevenson, Bruce E Bray, Barry Moore, Karen Eilbeck, Mark Yandell, Hongyu Zhao, Lin Hou, Xiaowei Chen, Xiting Yan, Mengjie Chen, Cong Li, Can Yang, Murat Gunel, Peining Li, Yong Kong, Austin C Alexander, Zayed I Albertyn, Kym M Boycott, Dennis E Bulman, Paul M K Gordon, A Micheil Innes, Bartha M Knoppers, Jacek Majewski, Christian R Marshall, Jillian S Parboosingh, Sarah L Sawyer, Mark E Samuels, Jeremy Schwartzentruber, Isaac S Kohane, and David Margulies

    Genome biology 15(3):R53 (2014) PMID 24667040 PMCID PMC4073084

    There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The C...
  8. Public knowledge of and attitudes toward genetics and genetic testing.

    Genetic Testing and Molecular Biomarkers 17(4):327 (2013) PMID 23406207 PMCID PMC3609633

    Variable health literacy and genetic knowledge may pose significant challenges to engaging the general public in personal genomics, specifically with respect to promoting risk comprehension and healthy behaviors. We are conducting a multistage study of individual responses to genomic risk inform...
  9. Public knowledge of and attitudes toward genetics and genetic testing.

    Genetic Testing and Molecular Biomarkers 17(4):327 (2013) PMID 23406207 PMCID PMC3609633

    Variable health literacy and genetic knowledge may pose significant challenges to engaging the general public in personal genomics, specifically with respect to promoting risk comprehension and healthy behaviors. We are conducting a multistage study of individual responses to genomic risk inform...
  10. Sequences associated with centromere competency in the human genome.

    Molecular and Cellular Biology 33(4):763 (2013) PMID 23230266 PMCID PMC3571344

    Centromeres, the sites of spindle attachment during mitosis and meiosis, are located in specific positions in the human genome, normally coincident with diverse subsets of alpha satellite DNA. While there is strong evidence supporting the association of some subfamilies of alpha satellite with c...
  11. Sequences associated with centromere competency in the human genome.

    Molecular and Cellular Biology 33(4):763 (2013) PMID 23230266 PMCID PMC3571344

    Centromeres, the sites of spindle attachment during mitosis and meiosis, are located in specific positions in the human genome, normally coincident with diverse subsets of alpha satellite DNA. While there is strong evidence supporting the association of some subfamilies of alpha satellite with c...
  12. Nonrandom X chromosome inactivation is influenced by multiple regions on the murine X chromosome.

    Genetics 192(3):1095 (2012) PMID 22887817 PMCID PMC3522153

    During the development of female mammals, one of the two X chromosomes is inactivated, serving as a dosage-compensation mechanism to equalize the expression of X-linked genes in females and males. While the choice of which X chromosome to inactivate is normally random, X chromosome inactivation ...
  13. Nonrandom X chromosome inactivation is influenced by multiple regions on the murine X chromosome.

    Genetics 192(3):1095 (2012) PMID 22887817 PMCID PMC3522153

    During the development of female mammals, one of the two X chromosomes is inactivated, serving as a dosage-compensation mechanism to equalize the expression of X-linked genes in females and males. While the choice of which X chromosome to inactivate is normally random, X chromosome inactivation ...
  14. Effects of sequence variation on differential allelic transcription factor occupancy and gene expression.

    Genome Research 22(5):860 (2012) PMID 22300769 PMCID PMC3337432

    A complex interplay between transcription factors (TFs) and the genome regulates transcription. However, connecting variation in genome sequence with variation in TF binding and gene expression is challenging due to environmental differences between individuals and cell types. To address this pr...
  15. Effects of sequence variation on differential allelic transcription factor occupancy and gene expression.

    Genome Research 22(5):860 (2012) PMID 22300769 PMCID PMC3337432

    A complex interplay between transcription factors (TFs) and the genome regulates transcription. However, connecting variation in genome sequence with variation in TF binding and gene expression is challenging due to environmental differences between individuals and cell types. To address this pr...
  16. Uncoupling of genomic and epigenetic signals in the maintenance and inheritance of heterochromatin domains in fission yeast.

    Genetics 190(2):549 (2012) PMID 22143918 PMCID PMC3276613

    Many essential aspects of genome function, including gene expression and chromosome segregation, are mediated throughout development and differentiation by changes in the chromatin state. Along with genomic signals encoded in the DNA, epigenetic processes regulate heritable gene expression patte...
  17. Uncoupling of genomic and epigenetic signals in the maintenance and inheritance of heterochromatin domains in fission yeast.

    Genetics 190(2):549 (2012) PMID 22143918 PMCID PMC3276613

    Many essential aspects of genome function, including gene expression and chromosome segregation, are mediated throughout development and differentiation by changes in the chromatin state. Along with genomic signals encoded in the DNA, epigenetic processes regulate heritable gene expression patte...
  18. Evidence for sequence biases associated with patterns of histone methylation.

    BMC Genomics 13:367 (2012) PMID 22857523 PMCID PMC3532361

    Combinations of histone variants and modifications, conceptually representing a histone code, have been proposed to play a significant role in gene regulation and developmental processes in complex organisms. While various mechanisms have been implicated in establishing and maintaining epigeneti...
  19. Composition and organization of active centromere sequences in complex genomes.

    BMC Genomics 13:324 (2012) PMID 22817545 PMCID PMC3422206

    Centromeres are sites of chromosomal spindle attachment during mitosis and meiosis. While the sequence basis for centromere identity remains a subject of considerable debate, one approach is to examine the genomic organization at these active sites that are correlated with epigenetic marks of ce...
  20. Composition and organization of active centromere sequences in complex genomes.

    BMC Genomics 13:324 (2012) PMID 22817545 PMCID PMC3422206

    Centromeres are sites of chromosomal spindle attachment during mitosis and meiosis. While the sequence basis for centromere identity remains a subject of considerable debate, one approach is to examine the genomic organization at these active sites that are correlated with epigenetic marks of ce...