1. Opsin Repertoire and Expression Patterns in Horseshoe Crabs: Evidence from the Genome of Limulus polyphemus (Arthropoda: Chelicerata).

    Genome Biology and Evolution 8(5):1571 (2016) PMID 27189985 PMCID PMC4898813

    Horseshoe crabs are xiphosuran chelicerates, the sister group to arachnids. As such, they are important for understanding the most recent common ancestor of Euchelicerata and the evolution and diversification of Arthropoda. Limulus polyphemus is the most investigated of the four extant species o...
  2. Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes.

    Cell 159(4):800 (2014) PMID 25417157 PMCID PMC4260969

    We sequenced the MSY (male-specific region of the Y chromosome) of the C57BL/6J strain of the laboratory mouse Mus musculus. In contrast to theories that Y chromosomes are heterochromatic and gene poor, the mouse MSY is 99.9% euchromatic and contains about 700 protein-coding genes. Only 2% of th...
  3. Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes.

    Nucleic Acids Research 39(17):7529 (2011) PMID 21715380 PMCID PMC3177221

    We took advantage of the unusual genomic organization of the ciliate Oxytricha trifallax to screen for eukaryotic non-coding RNA (ncRNA) genes. Ciliates have two types of nuclei: a germ line micronucleus that is usually transcriptionally inactive, and a somatic macronucleus that contains a reduc...
  4. Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content.

    Nature 463(7280):536 (2010) PMID 20072128 PMCID PMC3653425

    The human Y chromosome began to evolve from an autosome hundreds of millions of years ago, acquiring a sex-determining function and undergoing a series of inversions that suppressed crossing over with the X chromosome. Little is known about the recent evolution of the Y chromosome because only t...
  5. Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee.

    Nature 437(7055):100 (2005) PMID 16136134

    The human Y chromosome, transmitted clonally through males, contains far fewer genes than the sexually recombining autosome from which it evolved. The enormity of this evolutionary decline has led to predictions that the Y chromosome will be completely bereft of functional genes within ten milli...
  6. The DNA sequence of the human X chromosome.
    Mark T Ross, Darren V Grafham, Alison J Coffey, Steven Scherer, Kirsten McLay, Donna Muzny, Matthias Platzer, Gareth R Howell, Christine Burrows, Christine P Bird, Adam Frankish, Frances Lovell, Kevin L Howe, Jennifer L Ashurst, Robert S Fulton, Ralf Sudbrak, Gaiping Wen, Matthew C Jones, Matthew E Hurles, T Daniel Andrews, Carol E Scott, Stephen Searle, Juliane Ramser, Adam Whittaker, Rebecca Deadman, Nigel P Carter, Sarah E Hunt, Rui Chen, Andrew Cree, Preethi Gunaratne, Paul Havlak, Anne Hodgson, Michael L Metzker, Stephen Richards, Graham Scott, David Steffen, Erica Sodergren, David A Wheeler, Kim C Worley, Rachael Ainscough, Kerrie D Ambrose, M Ali Ansari-Lari, Swaroop Aradhya, Robert I S Ashwell, Anne K Babbage, Claire L Bagguley, Andrea Ballabio, Ruby Banerjee, Gary E Barker, Karen F Barlow, Ian P Barrett, Karen N Bates, David M Beare, Helen Beasley, Oliver Beasley, Alfred Beck, Graeme Bethel, Karin Blechschmidt, Nicola Brady, Sarah Bray-Allen, Anne M Bridgeman, Andrew J Brown, Mary J Brown, David Bonnin, Elspeth A Bruford, Christian Buhay, Paula Burch, Deborah Burford, Joanne Burgess, Wayne Burrill, John Burton, Jackie M Bye, Carol Carder, Laura Carrel, Joseph Chako, Joanne Chapman, Dean Chavez, Ellson Chen, Guan Chen, Yuan Chen, Zhijian Chen, Craig Chinault, Alfredo Ciccodicola, Sue Y Clark, Graham Clarke, Chris M Clee, Sheila Clegg, Kerstin Clerc-Blankenburg, Karen Clifford, Vicky Cobley, Charlotte G Cole, Jen S Conquer, Nicole Corby, Richard E Connor, Robert David, Joy Davies, Clay Davis, John Davis, Oliver Delgado, Denise Deshazo, Pawandeep Dhami, Yan Ding, Huyen Dinh, Steve Dodsworth, Heather Draper, Shannon Dugan-Rocha, Andrew Dunham, Matthew Dunn, K James Durbin, Ireena Dutta, Tamsin Eades, Matthew Ellwood, Alexandra Emery-Cohen, Helen Errington, Kathryn L Evans, Louisa Faulkner, Fiona Francis, John Frankland, Audrey E Fraser, Petra Galgoczy, James Gilbert, Rachel Gill, Gernot Glöckner, Simon Gregory, Susan Gribble, Coline Griffiths, Russell Grocock, Yanghong Gu, Rhian Gwilliam, Cerissa Hamilton, Elizabeth A Hart, Alicia Hawes, Paul D Heath, Katja Heitmann, Steffen Hennig, Judith Hernandez, Bernd Hinzmann, Sarah Ho, Michael Hoffs, Phillip J Howden, Elizabeth J Huckle, Jennifer Hume, Paul J Hunt, Adrienne R Hunt, Judith Isherwood, Leni Jacob, David Johnson, Sally Jones, Pieter de Jong, Shirin Joseph, Stephen Keenan, Susan Kelly, Joanne Kershaw, Ziad Khan, Petra Kioschis, Sven Klages, Andrew J Knights, Anna Kosiura, Christie Kovar-Smith, Gavin K Laird, Cordelia Langford, Stephanie Lawlor, Margaret Leversha, Lora Lewis, Wen Liu, Christine Lloyd, David M Lloyd, Hermela Loulseged, Jane E Loveland, Jamieson D Lovell, Ryan Lozado, Jing Lu, Rachael Lyne, Jie Ma, Manjula Maheshwari, Lucy H Matthews, Jennifer McDowall, Stuart McLaren, Amanda, Patrick Meidl, Thomas Meitinger, Sarah Milne, George Miner, Shailesh L Mistry, Margaret Morgan, Sidney Morris, Ines Müller, James C Mullikin, Ngoc Nguyen, Gabriele Nordsiek, Gerald Nyakatura, Christopher N O'Dell, Geoffery Okwuonu, Sophie Palmer, Richard Pandian, David Parker, Julia Parrish, Shiran Pasternak, Dina Patel, Alex V Pearce, Danita M Pearson, Sarah E Pelan, Lesette Perez, Keith M Porter, Yvonne Ramsey, Kathrin Reichwald, Susan Rhodes, Kerry A Ridler, David Schlessinger, Mary G Schueler, Harminder K Sehra, Charles, Hua Shen, Elizabeth M Sheridan, Ratna Shownkeen, Carl D Skuce, Michelle L Smith, Elizabeth C Sotheran, Helen E Steingruber, Charles A Steward, Roy Storey, R Mark Swann, David Swarbreck, Paul E Tabor, Stefan Taudien, Tineace Taylor, Brian Teague, Karen Thomas, Andrea Thorpe, Kirsten Timms, Alan Tracey, Steve Trevanion, Anthony C Tromans, Michele d'Urso, Daniel Verduzco, Donna Villasana, Lenee Waldron, Melanie Wall, Qiaoyan Wang, James Warren, Georgina L Warry, Xuehong Wei, Anthony West, Siobhan L Whitehead, Mathew N Whiteley, Jane E Wilkinson, David L Willey, Gabrielle Williams, Leanne Williams, Angela Williamson, Helen Williamson, Laurens Wilming, Rebecca L Woodmansey, Paul Wray, Jennifer Yen, Jingkun Zhang, Jianling Zhou, Huda Zoghbi, Sara Zorilla, David Buck, Richard Reinhardt, Annemarie Poustka, André Rosenthal, Hans Lehrach, Alfons Meindl, Patrick J Minx, Ladeana W Hillier, Huntington F Willard, Richard K Wilson, Robert H Waterston, Catherine M Rice, Mark Vaudin, Alan Coulson, David L Nelson, George Weinstock, John E Sulston, Richard Durbin, Tim Hubbard, Richard A Gibbs, Stephan Beck, Jane Rogers, and David R Bentley

    Nature 434(7031):325 (2005) PMID 15772651 PMCID PMC2665286

    The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise p...
  7. Mutations of the SBDS gene are present in most patients with Shwachman-Diamond syndrome.

    Blood 104(12):3588 (2004) PMID 15284109

    Shwachman-Diamond Syndrome (SDS) is a rare multisystem disorder characterized by exocrine pancreatic insufficiency, bone marrow dysfunction, and metaphyseal chondrodysplasia. Recent studies show that mutations of SBDS, a gene of unknown function, are present in the majority of patients with SDS....
  8. A pilot study of high-throughput, sequence-based mutational profiling of primary human acute myeloid leukemia cell genomes.

    PNAS 100(24):14275 (2003) PMID 14614138 PMCID PMC283582

    In this pilot study, we used primary human acute myeloid leukemia (AML) cell genomes as templates for exonic PCR amplification, followed by high-throughput resequencing, analyzing approximately 7 million base pairs of DNA from 140 AML samples and 48 controls. We identified six previously describ...
  9. Abundant gene conversion between arms of palindromes in human and ape Y chromosomes.

    Nature 423(6942):873 (2003) PMID 12815433

    Eight palindromes comprise one-quarter of the euchromatic DNA of the male-specific region of the human Y chromosome, the MSY. They contain many testis-specific genes and typically exhibit 99.97% intra-palindromic (arm-to-arm) sequence identity. This high degree of identity could be interpreted a...
  10. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes.

    Nature 423(6942):825 (2003) PMID 12815422

    The male-specific region of the Y chromosome, the MSY, differentiates the sexes and comprises 95% of the chromosome's length. Here, we report that the MSY is a mosaic of heterochromatic sequences and three classes of euchromatic sequences: X-transposed, X-degenerate and ampliconic. These classes...