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LaDeana Hillier

Research Profile

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Chemicals & Drugs

Genes & Molecular Sequences

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Evolution, Molecular

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TOP 3
Xinxian Deng; Carrie A Davis; Sevinc Ercan; Thomas R Gingeras; Joseph B Hiatt; LaDeana W Hillier; Jason D Lieb; Di Kim Nguyen; Brian Oliver; Valerie J Reinke; Felix Schlesinger; Jay Shendure; David Sturgill; Robert H Waterston; Christine M Disteche
Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster.
Zhi John Lu; Kevin Yip; Guilin Wang; Chong Shou; LaDeana W Hillier; Ekta Khurana; Ashish Agarwal; Raymond Auerbach; Joel S Rozowsky; Chao Cheng; Masaomi Kato; David M Miller; Frank Slack; Michael Snyder; Robert H Waterston; Valerie Reinke; Mark B Gerstein
Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.
Mary Ann Allen; LaDeana W Hillier; Robert H Waterston; Thomas Blumenthal
A global analysis of C. elegans trans-splicing.

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All Publications

2011: Xinxian Deng; Carrie A Davis; Sevinc Ercan; Thomas R Gingeras; Joseph B Hiatt; LaDeana W Hillier; Jason D Lieb; Di Kim Nguyen; Brian Oliver; Valerie J Reinke; Felix Schlesinger; Jay Shendure; David Sturgill; Robert H Waterston; Christine M Disteche
Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster.
Nature genetics 2011;43(12):1179-85.
2011: Zhi John Lu; Kevin Yip; Guilin Wang; Chong Shou; LaDeana W Hillier; Ekta Khurana; Ashish Agarwal; Raymond Auerbach; Joel S Rozowsky; Chao Cheng; Masaomi Kato; David M Miller; Frank Slack; Michael Snyder; Robert H Waterston; Valerie Reinke; Mark B Gerstein
Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.
Genome research 2011;21(2):276-85.
2011: Mary Ann Allen; LaDeana W Hillier; Robert H Waterston; Thomas Blumenthal
A global analysis of C. elegans trans-splicing.
Genome research 2011;21(2):255-64.
2011: M A M Groenen; LaDeana W Hillier; Hendrik-Jan Megens; William M Muir; Ron Okimoto; Adrianus Vereijken; Wesley C Warren; Yalda Zare; R P M A Crooijmans; Hans H Cheng
The development and characterization of a 60K SNP chip for chicken.
BMC genomics 2011;12(1):274.
2011: Ilka Engelmann; Aurélien Griffon; Laurent Tichit; Frédéric Montañana-Sanchis; Guilin Wang; Valerie Reinke; Robert H Waterston; LaDeana W Hillier; Jonathan J Ewbank
A comprehensive analysis of gene expression changes provoked by bacterial and fungal infection in C. elegans.
PloS one 2011;6(5):e19055.
2011: Liang Ye; George M Weinstock; Richard K Wilson; Lei Chen; David J Dooling; Kevin V Haub; LaDeana W Hillier; Devin P Locke; Elaine R Mardis; John C Martin; Jason R Miller; Patrick J Minx; Makedonka Mitreva; Nay Thane; Wesley C Warren
A vertebrate case study of the quality of assemblies derived from next-generation sequences.
Genome biology 2011;12(3):R31.
2010: Stephen Meader; LaDeana W Hillier; Devin Locke; Chris P Ponting; Gerton Lunter
Genome assembly quality: assessment and improvement using the neutral indel model.
Genome research 2010;20(5):675-84.
2010: Mei Zhong; Wei Niu; Zhi John Lu; Mihail Sarov; John I Murray; Judith Janette; Debasish Raha; Karyn L Sheaffer; Hugo Y K Lam; Elicia Preston; Cindie Slightham; LaDeana W Hillier; Trisha Brock; Ashish Agarwal; Raymond Auerbach; Anthony A Hyman; Mark Gerstein; Susan E Mango; Stuart K Kim; Robert H Waterston; Valerie Reinke; Michael Snyder
Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response.
PLoS genetics 2010;6(2):e1000848.
2010: Ashish Agarwal; David Koppstein; Joel S Rozowsky; Andrea Sboner; Lukas Habegger; LaDeana W Hillier; Rajkumar Sasidharan; Valerie Reinke; Robert H Waterston; Mark Gerstein
Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays.
BMC genomics 2010;11():383.
2009: LaDeana W Hillier; Valerie Reinke; Philip Green; Martin Hirst; Marco A Marra; Robert H Waterston
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans.
Genome research 2009;19(4):657-66.
2009: Tomas Marques-Bonet; Jeffrey M Kidd; ventura Mario; Tina Graves; Ze Cheng; LaDeana W Hillier; Zhaoshi Jiang; Carl Baker; Ray Malfavon-Borja; Lucinda A Fulton; Can Alkan; Gozde Aksay; Santhosh Girirajan; Priscillia Siswara; Lin Chen; Maria Francesca Cardone; Arcadi Navarro; Elaine R Mardis; Richard K Wilson; Evan E Eichler
A burst of segmental duplications in the genome of the African great ape ancestor.
Nature 2009;457(7231):877-81.
2009: Deanna M Church; LaDeana W Hillier
Back to Bermuda: how is science best served?
Genome biology 2009;10(4):105.
2008: Michael C Zody; Zhaoshi Jiang; Hon-Chung Fung; Francesca Antonacci; LaDeana W Hillier; Maria Francesca Cardone; Tina A Graves; Jeffrey M Kidd; Ze Cheng; Amr Abouelleil; Lin Chen; John Wallis; Jarret Glasscock; Richard K Wilson; Amy Denise Reily; Jaime Duckworth; ventura Mario; John Hardy; Wesley C Warren; Evan E Eichler
Evolutionary toggling of the MAPT 17q21.31 inversion region.
Nature genetics 2008;40(9):1076-83.
2008: LaDeana W Hillier; Gabor T Marth; Aaron R Quinlan; David Dooling; Ginger Fewell; Derek Barnett; Paul Fox; Jarret I Glasscock; Matthew Hickenbotham; Weichun Huang; vincent magrini; Ryan J Richt; Sacha N Sander; Donald A Stewart; Michael Stromberg; Eric F Tsung; Todd Wylie; Tim Schedl; Richard K Wilson; Elaine R Mardis
Whole-genome sequencing and variant discovery in C. elegans.
Nature methods 2008;5(2):183-8.
2008: Gonzalo R Ordoñez; LaDeana W Hillier; Wesley C Warren; Frank Grützner; Carlos López-Otín; Xose S Puente
Loss of genes implicated in gastric function during platypus evolution.
Genome biology 2008;9(5):R81.
2007: David J Begun; Alisha K Holloway; Kristian Stevens; LaDeana W Hillier; Yu-Ping Poh; Matthew W Hahn; Phillip M Nista; Corbin D Jones; Andrew D Kern; Colin N Dewey; Lior Pachter; Eugene Myers; Charles H Langley
Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.
PLoS biology 2007;5(11):e310.
2007: LaDeana W Hillier; Raymond D Miller; Scott E Baird; Asif Chinwalla; Lucinda A Fulton; Daniel C Koboldt; Robert H Waterston
Comparison of C. elegans and C. briggsae genome sequences reveals extensive conservation of chromosome organization and synteny.
PLoS biology 2007;5(7):e167.
2007: José M Ranz; Damien Maurin; Yuk S Chan; Marcin von Grotthuss; LaDeana W Hillier; John Roote; Michael Ashburner; Casey M Bergman
Principles of genome evolution in the Drosophila melanogaster species group.
PLoS biology 2007;5(6):e152.
2007: Michael Wendl; Scott Smith; Craig S Pohl; David J Dooling; Asif T Chinwalla; Kevin Crouse; Todd Hepler; Shin Leong; Lynn Carmichael; Mike Nhan; Benjamin J Oberkfell; Elaine R Mardis; LaDeana W Hillier; Richard K Wilson
Design and implementation of a generalized laboratory data model.
BMC bioinformatics 2007;8():362.
2006: Rene Warren; Dmitry Varabei; Darren Platt; Xiaoqiu Huang; David Messina; Shiaw-Pyng Yang; James W Kronstad; Martin I Krzywinski; Wesley C Warren; John W Wallis; LaDeana W Hillier; Asif T Chinwalla; Jacqueline E Schein; Asim S Siddiqui; Marco A Marra; Richard K Wilson; Steven J M Jones
Physical map-assisted whole-genome shotgun sequence assemblies.
Genome research 2006;16(6):768-75.
2006: Xiaoqiu Huang; Shiaw-Pyng Yang; Asif T Chinwalla; LaDeana W Hillier; Patrick J Minx; Elaine R Mardis; Richard K Wilson
Application of a superword array in genome assembly.
Nucleic acids research 2006;34(1):201-5.
2005: LaDeana W Hillier; Alan Coulson; John I Murray; Zhirong Bao; John E Sulston; Robert H Waterston
Genomics in C. elegans: so many genes, such a little worm.
Genome research 2005;15(12):1651-60.
2005: Xose S Puente; Ana Gutiérrez-Fernández; Gonzalo R Ordóñez; LaDeana W Hillier; Carlos López-Otín
Comparative genomic analysis of human and chimpanzee proteases.
Genomics 2005;86(6):638-47.
2005: Adam Siepel; Gill Bejerano; Jan Skov Pedersen; Angie S Hinrichs; Minmei Hou; Kate Rosenbloom; Hiram Clawson; John Spieth; LaDeana W Hillier; Stephen Richards; George M Weinstock; Richard K Wilson; Richard A Gibbs; W James Kent; Webb Miller; David Haussler
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
Genome research 2005;15(8):1034-50.
2004: Terrence S Furey; Mark Diekhans; Yontao Lu; Tina Graves; Lachlan Oddy; Jennifer Randall-Maher; LaDeana W Hillier; Richard K Wilson; David Haussler
Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing.
Genome research 2004;14(10B):2034-40.
2003: Xiaoqiu Huang; Jianmin Wang; Srinivas Aluru; Shiaw-Pyng Yang; LaDeana W Hillier
PCAP: a whole-genome assembly program.
Genome research 2003;13(9):2164-70.
2003: Daniel R Fuhrmann; Martin I Krzywinski; Readman Chiu; Parvaneh Saeedi; Jacqueline E Schein; Ian Bosdet; Asif T Chinwalla; LaDeana W Hillier; Robert H Waterston; John D McPherson; Steven J M Jones; Marco A Marra
Software for automated analysis of DNA fingerprinting gels.
Genome research 2003;13(5):940-53.
2003: Robert H Waterston; LaDeana W Hillier; Lucinda Fulton; Robert S Fulton; Tina Graves; Kymberlie H Pepin; Peer Bork; Mikita Suyama; David Torrents; Asif T Chinwalla; Elaine R Mardis; John D McPherson; Richard K Wilson
The human genome: genes, pseudogenes, and variation on chromosome 7.
Cold Spring Harbor symposia on quantitative biology 2003;68():13-22.
2001: Steven J M Jones; D L Riddle; A T Pouzyrev; Victor E Velculescu; LaDeana W Hillier; Sean R Eddy; S L Stricklin; David Baillie; Robert H Waterston; Marco A Marra
Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans.
Genome research 2001;11(8):1346-52.
2001: Michael Wendl; Ian F Korf; Asif T Chinwalla; LaDeana W Hillier
Automated processing of raw DNA sequence data.
IEEE engineering in medicine and biology magazine : the quarterly magazine of the Engineering in Medicine & Biology Society 2001;20(4):41-8.
2001: Paul F Cliften; LaDeana W Hillier; Lucinda Fulton; Tina Graves; Tracie L Miner; Warren Gish; Robert H Waterston; Mark Johnston
Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis.
Genome research 2001;11(7):1175-86.
2001: Michael Wendl; Marco A Marra; LaDeana W Hillier; Asif T Chinwalla; Richard K Wilson; Robert H Waterston
Theories and applications for sequencing randomly selected clones.
Genome research 2001;11(2):274-80.
1999: Marco A Marra; Tamara Kucaba; LaDeana W Hillier; Robert H Waterston
High-throughput plasmid DNA purification for 3 cents per sample.
Nucleic acids research 1999;27(24):e37.
1999: Gabor T Marth; Ian F Korf; M D Yandell; R T Yeh; Z Gu; H Zakeri; N O Stitziel; LaDeana W Hillier; Pui-Yan Kwok; Warren Gish
A general approach to single-nucleotide polymorphism discovery.
Nature genetics 1999;23(4):452-6.
1999: M Marra; Tamara Kucaba; Mandeep Sekhon; LaDeana W Hillier; Robert A Martienssen; A Chinwalla; J Crockett; J Fedele; H Grover; C Gund; W Richard McCombie; K McDonald; John McPherson; N Mudd; LD Parnell; Jacqueline E Schein; R Seim; P Shelby; Robert H Waterston; R Wilson
zA map for sequence analysis of the Arabidopsis thaliana genome.
Nature genetics 1999;22(3):265-70.
1999: J D Parsons; E Buehler; LaDeana W Hillier
DNA sequence chromatogram browsing using JAVA and CORBA.
Genome research 1999;9(3):277-81.
1998: Michael Wendl; S Dear; D Hodgson; LaDeana W Hillier
Automated sequence preprocessing in a large-scale sequencing environment.
Genome research 1998;8(9):975-84.
1998: Patricia Taillon-Miller; Z Gu; Q Li; LaDeana W Hillier; Pui-Yan Kwok
Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms.
Genome research 1998;8(7):748-54.
1998: Ian D Manger; Adrian Hehl; Stephen Parmley; L David Sibley; M Marra; LaDeana W Hillier; Robert H Waterston; John C Boothroyd
Expressed sequence tag analysis of the bradyzoite stage of Toxoplasma gondii: identification of developmentally regulated genes.
Infection and immunity 1998;66(4):1632-7.
1998: S Dear; Richard Durbin; LaDeana W Hillier; Gabor T Marth; J Thierry-Mieg; R Mott
Sequence assembly with CAFTOOLS.
Genome research 1998;8(3):260-7.
1998: B Ewing; LaDeana W Hillier; Michael Wendl; Phil Green
Base-calling of automated sequencer traces using phred. I. Accuracy assessment.
Genome research 1998;8(3):175-85.
1998: Marco A Marra; LaDeana W Hillier; Robert H Waterston
Expressed sequence tags--ESTablishing bridges between genomes.
Trends in genetics : TIG 1998;14(1):4-7.
1998: James W Ajioka; John C Boothroyd; Brian P Brunk; Adrian Hehl; LaDeana W Hillier; Ian D Manger; M Marra; G C Overton; David S Roos; Kiew-Lian Wan; Robert H Waterston; L David Sibley
Gene discovery by EST sequencing in Toxoplasma gondii reveals sequences restricted to the Apicomplexa.
Genome research 1998;8(1):18-28.
1997: Patricia Taillon-Miller; I Bauer-Sardiña; H Zakeri; LaDeana W Hillier; D G Mutch; Pui-Yan Kwok
The homozygous complete hydatidiform mole: a unique resource for genome studies.
Genomics 1997;46(2):307-10.
1997: Marco A Marra; Tamara Kucaba; Nicole L Dietrich; Eric Green; B Brownstein; Richard K Wilson; K M McDonald; LaDeana W Hillier; John D McPherson; Robert H Waterston
High throughput fingerprint analysis of large-insert clones.
Genome research 1997;7(11):1072-84.
1997: SL Chissoe; Marco A Marra; LaDeana W Hillier; R Brinkman; Richard K Wilson; Robert H Waterston
Representation of cloned genomic sequences in two sequencing vectors: correlation of DNA sequence and subclone distribution.
Nucleic acids research 1997;25(15):2960-6.
1996: M L Cooper; D R Maffitt; J D Parsons; LaDeana W Hillier; David States
Lane tracking software for four-color fluorescence-based electrophoretic gel images.
Genome research 1996;6(11):1110-7.
1996: LaDeana W Hillier; GG Lennon; M Becker; MF Bonaldo; B Chiapelli; S Chissoe; N Dietrich; T DuBuque; A Favello; W Gish; M Hawkins; M Hultman; Tamara Kucaba; M Lacy; M Le; N Le; E Mardis; B Moore; M Morris; J Parsons; CK Prange; L Rifkin; T Rohlfing; K Schellenberg; M Bento Soares; F Tan; J Thierry-Meg; E Trevaskis; K Underwood; P Wohldman; R Waterston; R Wilson; Marco A Marra
Generation and analysis of 280,000 human expressed sequence tags.
Genome research 1996;6(9):807-28.
1995: Mark Vaudin; A Roopra; LaDeana W Hillier; R Brinkman; John E Sulston; Richard K Wilson; Robert H Waterston
The construction and analysis of M13 libraries prepared from YAC DNA.
Nucleic acids research 1995;23(4):670-4.
1995: L L Fulton; LaDeana W Hillier; Richard K Wilson
Large-scale complementary DNA sequencing methods.
Methods in cell biology 1995;48():571-82.
1995: A Favello; LaDeana W Hillier; Richard K Wilson
Genomic DNA sequencing methods.
Methods in cell biology 1995;48():551-69.
1993: P Green; D Lipman; LaDeana W Hillier; Robert H Waterston; D States; J M Claverie
Ancient conserved regions in new gene sequences and the protein databases.
Science (New York, N.Y.) 1993;259(5102):1711-6.
1992: Robert H Waterston; C Martin; M Craxton; C Huynh; A Coulson; LaDeana W Hillier; R Durbin; P Green; R Shownkeen; N Halloran
A survey of expressed genes in Caenorhabditis elegans.
Nature genetics 1992;1(2):114-23.
1992: John E Sulston; Z Du; K Thomas; R Wilson; LaDeana W Hillier; R Staden; N Halloran; P Green; J Thierry-Mieg; L Qiu
The C. elegans genome sequencing project: a beginning.
Nature 1992;356(6364):37-41.
1991: T Gleeson; LaDeana W Hillier
A trace display and editing program for data from fluorescence based sequencing machines.
Nucleic acids research 1991;19(23):6481-3.