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Research: Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites
- João L. Reis-Cunha,
- Samuel A. Pimenta-Carvalho,
- Laila V. Almeida,
- Anderson Coqueiro-dos-Santos,
- Catarina A. Marques,
- Jennifer A. Black,
- Jeziel Damasceno,
- Richard McCulloch,
- Daniella C. Bartholomeu,
- and Daniel C. Jeffares
Genome Res. March 2024 34: 441-453; Published in Advance April 11, 2024, doi:10.1101/gr.278550.123
...of the larger chromosomes (Marques et al. 2015; Damasceno et al. 2020, 2021). To circumvent this problem, Leishmania appears to confine duplication of the core to S phase with duplication of the subtelomeres occurring later, during late S, G2/M, and G1 stages of the cycle (Damasceno et al. 2020). Replication...
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Methods: A new strategy for genome assembly using short sequence reads and reduced representation libraries
- Andrew L. Young,
- Hatice Ozel Abaan,
- Daniel Zerbino,
- James C. Mullikin,
- Ewan Birney,
- and Elliott H. Margulies
Genome Res. February 2010 20: 249-256; doi:10.1101/gr.097956.109
...assembly of a D. melanogaster using a massively parallel short-read sequencing platform and reduced representation libraries. The reduced representation method simplifies the size and complexity of the assembly problem by breaking the into smaller portions, allowing us to assemble larger contigs than...
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PERSPECTIVE: Human Whole-Genome Shotgun Sequencing
- James L. Weber and
- Eugene W. Myers
Genome Res. May 1, 1997 7: 401-409; doi:10.1101/gr.7.5.401
...majority of human L1 elements are truncated with average length ∼0.7 kb ( Smit et al. 1995 ; A. Smit, pers. comm.). Note that the simulation does not solve an assembly problem over simulated data, but instead analyzes the nature of the sampling obtained. Details of the simulation, including source code...
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RESOURCE: Complete MHC Haplotype Sequencing for Common Disease Gene Mapping
- C. Andrew Stewart,
- Roger Horton,
- Richard J.N. Allcock,
- Jennifer L. Ashurst,
- Alexey M. Atrazhev,
- Penny Coggill,
- Ian Dunham,
- Simon Forbes,
- Karen Halls,
- Joanna M.M. Howson,
- Sean J. Humphray,
- Sarah Hunt,
- Andrew J. Mungall,
- Kazutoyo Osoegawa,
- Sophie Palmer,
- Anne N. Roberts,
- Jane Rogers,
- Sarah Sims,
- Yu Wang,
- Laurens G. Wilming,
- John F. Elliott,
- Pieter J. de Jong,
- Stephen Sawcer,
- John A. Todd,
- John Trowsdale,
- and Stephan Beck
Genome Res. June 2004 14: 1176-1187; Published in Advance May 12, 2004, doi:10.1101/gr.2188104
...hybridization membrane represents the colonies from 48 dishes through duplicate colonies (∼18,000 BAC clones per sheet). Further details about the two BAC libraries can be found at http://bacpac.chori.org/mhc501.htm and http://bacpac.chori.org/mhc502.htm . Mapping and Sequencing Genomic sequences (∼200 bases...
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LETTER: RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer
- Kazuhiro Shibata,
- Masayoshi Itoh,
- Katsunori Aizawa,
- Sumiharu Nagaoka,
- Nobuya Sasaki,
- Piero Carninci,
- Hideaki Konno,
- Junichi Akiyama,
- Katsuo Nishi,
- Tokuji Kitsunai,
- Hideo Tashiro,
- Mari Itoh,
- Noriko Sumi,
- Yoshiyuki Ishii,
- Shin Nakamura,
- Makoto Hazama,
- Tsutomu Nishine,
- Akira Harada,
- Rintaro Yamamoto,
- Hiroyuki Matsumoto,
- Sumito Sakaguchi,
- Takashi Ikegami,
- Katsuya Kashiwagi,
- Syuji Fujiwake,
- Kouji Inoue,
- Yoshiyuki Togawa,
- Masaki Izawa,
- Eiji Ohara,
- Masanori Watahiki,
- Yuko Yoneda,
- Tomokazu Ishikawa,
- Kaori Ozawa,
- Takumi Tanaka,
- Shuji Matsuura,
- Jun Kawai,
- Yasushi Okazaki,
- Masami Muramatsu,
- Yorinao Inoue,
- Akira Kira,
- and Yoshihide Hayashizaki
Genome Res. November 1, 2000 10: 1757-1771; doi:10.1101/gr.152600
.... To solve this problem, PMTs that are resistant to vibration noise were selected and used for the detection devices. Performance of the RISA Sequencer System Read Length and Reproducibility For the evaluation test, samples were prepared as described in Methods using 250 ng/well of CsCl purified pGEM-3ZF...
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PROGRESS: Toward a Complete Human Genome Sequence
- The Sanger Centre and
- The Washington University Genome Sequencing Center
Genome Res. November 1, 1998 8: 1097-1108; doi:10.1101/gr.8.11.1097
...) Short-insert libraries as a method of problem solving in sequencing. Genome Res. 8 : 562 – 566 . ↵ Mungall A.J. , Edwards C.A. , Ranby S.A. , Humphray S.J. , Heathcott R.W. , Clee C.M. , East C.L. , Holloway E. , Butler A.P. , Langford C.F. , et al. ( 1996 ) Physical mapping of chromosome 6: A strategy...
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ARTICLE: The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity
- James E. Galagan,
- Chad Nusbaum,
- Alice Roy,
- Matthew G. Endrizzi,
- Pendexter Macdonald,
- Will FitzHugh,
- Sarah Calvo,
- Reinhard Engels,
- Serge Smirnov,
- Deven Atnoor,
- Adam Brown,
- Nicole Allen,
- Jerome Naylor,
- Nicole Stange-Thomann,
- Kurt DeArellano,
- Robin Johnson,
- Lauren Linton,
- Paul McEwan,
- Kevin McKernan,
- Jessica Talamas,
- Andrea Tirrell,
- Wenjuan Ye,
- Andrew Zimmer,
- Robert D. Barber,
- Isaac Cann,
- David E. Graham,
- David A. Grahame,
- Adam M. Guss,
- Reiner Hedderich,
- Cheryl Ingram-Smith,
- H. Craig Kuettner,
- Joseph A. Krzycki,
- John A. Leigh,
- Weixi Li,
- Jinfeng Liu,
- Biswarup Mukhopadhyay,
- John N. Reeve,
- Kerry Smith,
- Timothy A. Springer,
- Lowell A. Umayam,
- Owen White,
- Robert H. White,
- Everly Conway de Macario,
- James G. Ferry,
- Ken F. Jarrell,
- Hua Jing,
- Alberto J.L. Macario,
- Ian Paulsen,
- Matthew Pritchett,
- Kevin R. Sowers,
- Ronald V. Swanson,
- Steven H. Zinder,
- Eric Lander,
- William W. Metcalf,
- and Bruce Birren
Genome Res. April 1, 2002 12: 532-542; doi:10.1101/gr.223902
...physiological and metabolic diversity, makes M. acetivorans a powerful model organism for the study of archaeal biology. [Sequence, data, annotations, and analyses are available at http://www-genome.wi.mit.edu/ . The sequence data described in this paper have been submitted to the GenBank data library under...
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LETTER: Comparative Genome Sequence Analysis of the Bpa/Str Region in Mouse and Man
- A.-M. Mallon,
- M. Platzer,
- R. Bate,
- G. Gloeckner,
- M.R.M. Botcherby,
- G. Nordsiek,
- M.A. Strivens,
- P. Kioschis,
- A. Dangel,
- D. Cunningham,
- R.N.A. Straw,
- P. Weston,
- M. Gilbert,
- S. Fernando,
- K. Goodall,
- G. Hunter,
- J.S. Greystrong,
- D. Clarke,
- C. Kimberley,
- M. Goerdes,
- K. Blechschmidt,
- A. Rump,
- B. Hinzmann,
- C.R. Mundy,
- W. Miller,
- A. Poustka,
- G.E. Herman,
- M. Rhodes,
- P. Denny,
- A. Rosenthal,
- and S.D.M. Brown
Genome Res. June 1, 2000 10: 758-775; doi:10.1101/gr.10.6.758
...Comparative Genome Sequence Analysis of the Bpa/Str Region in Mouse and Man A.-M. Mallon 1 , 7 , M. Platzer 2 , 7 , R. Bate 1 , G. Gloeckner 2 , M.R.M. Botcherby 3 , G. Nordsiek 2 , M.A. Strivens 1 , P. Kioschis...
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Method: Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs
- Nadin Rohland,
- Swapan Mallick,
- Matthew Mah,
- Robert Maier,
- Nick Patterson,
- and David Reich
Genome Res. November/December 2022 32: 2068-2078; Published in Advance December 14, 2022, doi:10.1101/gr.276728.122
...there is substantial room to make it better (reducing bias to a greater extent while filtering fewer SNPs). The demonstration of the filter also suggests a solution to the problem that has been a long-standing challenge for ancient human DNA studies: the difficulty of coanalyzing shotgun and 1240k enrichment data...
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Method: Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ
- Joseph W. Foley,
- Chunfang Zhu,
- Philippe Jolivet,
- Shirley X. Zhu,
- Peipei Lu,
- Michael J. Meaney,
- and Robert B. West
Genome Res. November 2019 29: 1816-1825; Published in Advance September 13, 2019, doi:10.1101/gr.234807.118
...the LCM may only capture part of the cell. For these reasons we do not propose LCM as a substitute for microﬂuidic single-cell methods. Rather, they are complementary approaches that solve different problems; microﬂuidic RNA-seq remains the best way to characterize thousands of cells from a single tissue...
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