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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
Brownstein CA,
Beggs AH,
Homer N,
Merriman B,
Yu TW,
Flannery KC,
Dechene ET,
Towne MC,
Savage SK,
Price EN,
Holm IA,
Luquette LJ,
Lyon E,
Majzoub J,
Neupert P,
McCallie D,
Szolovits P,
Willard HF,
Mendelsohn NJ,
Temme R,
Finkel RS,
Yum SW,
Medne L,
Sunyaev SR,
Adzhubey I,
Cassa CA,
de Bakker PI,
Duzkale H,
Dworzy Ski P,
Fairbrother W,
Francioli L,
Funke BH,
Giovanni MA,
Handsaker RE,
Lage K,
Lebo MS,
Lek M,
Leshchiner I,
Macarthur DG,
McLaughlin HM,
Murray MF,
Pers TH,
Polak PP,
Raychaudhuri S,
Rehm HL,
Soemedi R,
Stitziel NO,
Vestecka S,
Supper J,
Gugenmus C,
Klocke B,
Hahn A,
Schubach M,
Menzel M,
Biskup S,
Freisinger P,
Deng M,
Braun M,
Perner S,
Smith RJ,
Andorf JL,
Huang J,
Ryckman K,
Sheffield VC,
Stone EM,
Bair T,
Black-Ziegelbein EA,
Braun TA,
Darbro B,
Deluca AP,
Kolbe DL,
Scheetz TE,
Shearer AE,
Sompallae R,
Wang K,
Bassuk AG,
Edens E,
Mathews K,
Moore SA,
Shchelochkov OA,
Trapane P,
Bossler A,
Campbell CA,
Heusel JW,
Kwitek A,
Maga T,
Panzer K,
Wassink T,
Van Daele D,
Azaiez H,
Booth K,
Meyer N,
Segal MM,
Williams MS,
Tromp G,
White P,
Corsmeier D,
Fitzgerald-Butt S,
Herman G,
Lamb-Thrush D,
McBride KL,
Newsom D,
Pierson CR,
Rakowsky AT,
Maver A,
Lovre IL,
Palanda IA,
Peterlin B,
Torkamani A,
Wedell A,
Huss M,
Alexeyenko A,
Lindvall JM,
Magnusson M,
Nilsson D,
Stranneheim H,
Taylan F,
Gilissen C,
Hoischen A,
van Bon B,
Yntema H,
Nelen M,
Zhang W,
Sager J,
Zhang L,
Blair K,
Kural D,
Cariaso M,
Lennon GG,
Javed A,
Agrawal S,
Ng PC,
Sandhu KS,
Krishna S,
Veeramachaneni V,
Isakov O,
Halperin E,
Friedman E,
Shomron N,
Glusman G,
Roach JC,
Caballero J,
Cox HC,
Mauldin D,
Ament SA,
Rowen L,
Richards DR,
Lucas FA,
Gonzalez-Garay ML,
Caskey CT,
Bai Y,
Huang Y,
Fang F,
Zhang Y,
Wang Z,
Barrera J,
Garcia-Lobo JM,
Gonzalez-Lamuno D,
Llorca J,
Rodriguez MC,
Varela I,
Reese MG,
De La Vega FM,
Kiruluta E,
Cargill M,
Hart RK,
Sorenson JM,
Lyon GJ,
Stevenson DA,
Bray BE,
Moore BM,
Eilbeck K,
Yandell M,
Zhao H,
Hou L,
Chen X,
Yan X,
Chen M,
Li C,
Yang C,
Gunel M,
Li P,
Kong Y,
Alexander AC,
Albertyn ZI,
Boycott KM,
Bulman DE,
Gordon PM,
Innes AM,
Knoppers BM,
Majewski J,
Marshall CR,
Parboosingh JS,
Sawyer SL,
Samuels ME,
Schwartzentruber J,
Kohane IS,
Margulies DM

Genome Biology
  15 (3): R53; Mar 25 2014   NLM
[Abstract]
[DOI] [Full Text]

Improvement of the oryza sativa nipponbare reference genome using next generation sequence and optical map data
Kawahara Y,
de la Bastide M,
Cabal R,
Hamilton JP,
Kanamori H,
McCombie WR,
Ouyang S,
Schwartz DC,
Tanaka T,
Wu J,
Zhou S,
Childs KL,
Davidson RM,
Lin H,
Quesada-Ocampo L,
Vaillancourt B,
Sakai H,
Lee SS,
Kim J,
Numa H,
Itoh T,
Buell CR,
Matsumoto T

Rice
  6 (1): 1-10; Feb 6 2013   Springer
[Abstract]
[DOI] [Full Text]

Fluorescent Arc/Arg3.1 indicator mice: A versatile tool to study brain activity changes in vitro and in vivo
Grinevich V,
Kolleker A,
Eliava M,
Takada N,
Takuma H,
Fukazawa Y,
Shigemoto R,
Kuhl D,
Waters J,
Seeburg P,
Osten P

Journal of Neuroscience Methods
  184 (1): 25-36; Oct 2009  
[Abstract]
[DOI] [Full Text] [PDF]

The rice annotation project database (RAP-DB): 2008 update
Tanaka T,
Antonio BA,
Kikuchi S,
Matsumoto T,
Nagamura Y,
Numa H,
Sakai H,
Wu J,
Itoh T,
Sasaki T,
Aono R,
Fujii Y,
Habara T,
Harada E,
Kanno M,
Kawahara Y,
Kawashima H,
Kubooka H,
Matsuya A,
Nakaoka H,
Saichi N,
Sanbonmatsu R,
Sato Y,
Shinso Y,
Suzuki M,
Takeda JI,
Tanino M,
Todokoro F,
Yamaguchi K,
Yamamoto N,
Yamasaki C,
Imanishi T,
Okido T,
Tada M,
Ikeo K,
Tateno Y,
Gojobori T,
Lin YC,
Wei FJ,
Hsing YI,
Zhao Q,
Han B,
Kramer MR,
McCombie RW,
Lonsdale D,
ODonovan CC,
Whitfield EJ,
Apweiler R,
Koyanagi KO,
Khurana JP,
Raghuvanshi S,
Singh NK,
Tyagi AK,
Haberer G,
Fujisawa M,
Hosokawa S,
Ito Y,
Ikawa H,
Shibata M,
Yamamoto M,
Bruskiewich RM,
Hoen DR,
Bureau TE,
Namiki N,
Ohyanagi H,
Sakai Y,
Nobushima S,
Sakata K,
Barrero RA,
Souvorov A,
Smith-White B,
Tatusova T,
An S,
An G,
Oota S,
Fuks G,
Messing J,
Christie KR,
Lieberherr D,
Kim H,
Zuccolo A,
Wing RA,
Nobuta K,
Green PJ,
Lu C,
Meyers BC,
Chaparro C,
Piegu B,
Panaud O

Nucleic Acids Research
  36 (0): D1028-D1033; Jan 2008   PMCID: PMC2238920
[Abstract]
[DOI] [Full Text] [PDF]

The map-based sequence of the rice genome
Matsumoto T,
Wu JZ,
Kanamori H,
Katayose Y,
Fujisawa M,
Namiki N,
Mizuno H,
Yamamoto K,
Antonio BA,
Baba T,
Sakata K,
Nagamura Y,
Aoki H,
Arikawa K,
Arita K,
Bito T,
Chiden Y,
Fujitsuka N,
Fukunaka R,
Hamada M,
Harada C,
Hayashi A,
Hijishita S,
Honda M,
Hosokawa S,
Ichikawa Y,
Idonuma A,
Iijima M,
Ikeda M,
Ikeno M,
Ito K,
Ito S,
Ito T,
Ito Y,
Iwabuchi A,
Kamiya K,
Karasawa W,
Kurita K,
Katagiri S,
Kikuta A,
Kobayashi H,
Kobayashi N,
Machita K,
Maehara T,
Masukawa M,
Mizubayashi T,
Mukai Y,
Nagasaki H,
Nagata Y,
Naito S,
Nakashima M,
Nakama Y,
Nakamichi Y,
Nakamura M,
Meguro A,
Negishi M,
Ohta I,
Ohta T,
Okamoto M,
Ono N,
Saji S,
Sakaguchi M,
Sakai K,
Shibata M,
Shimokawa T,
Song JY,
Takazaki Y,
Terasawa K,
Tsugane M,
Tsuji K,
Ueda S,
Waki K,
Yamagata H,
Yamamoto M,
Yamamoto S,
Yamane H,
Yoshiki S,
Yoshihara R,
Yukawa K,
Zhong HS,
Yano M,
Sasaki T,
Yuan QP,
Shu OT,
Liu J,
Jones KM,
Gansberger K,
Moffat K,
Hill J,
Bera J,
Fadrosh D,
Jin SH,
Johri S,
Kim M,
Overton L,
Reardon M,
Tsitrin T,
Vuong H,
Weaver B,
Ciecko A,
Tallon L,
Jackson J,
Pai G,
Van Aken S,
Utterback T,
Reidmuller S,
Feldblyum T,
Hsiao J,
Zismann V,
Iobst S,
de Vazeille AR,
Buell CR,
Ying K,
Li Y,
Lu TT,
Huang YC,
Zhao Q,
Feng Q,
Zhang L,
Zhu JJ,
Weng QJ,
Mu J,
Lu YQ,
Fan DL,
Liu YL,
Guan JP,
Zhang YJ,
Yu SL,
Liu XH,
Zhang Y,
Hong GF,
Han B,
Choisne N,
Demange N,
Orjeda G,
Samain S,
Cattolico L,
Pelletier E,
Couloux A,
Segurens B,
Wincker P,
DHont A,
Scarpelli C,
Weissenbach J,
Salanoubat M,
Quetier F,
Yu Y,
Kim HR,
Rambo T,
Currie J,
Collura K,
Luo MZ,
Yang TJ,
Ammiraju JS,
Engler F,
Soderlund C,
Wing RA,
Palmer LE,
de la Bastide M,
Spiegel L,
Nascimento L,
Zutavern T,
OShaughnessy A,
Dike S,
Dedhia N,
Preston R,
Balija V,
McCombie WR,
Chow TY,
Chen HH,
Chung MC,
Chen CS,
Shaw JF,
Wu HP,
Hsiao KJ,
Chao YT,
Chu MK,
Cheng CH,
Hour AL,
Lee PF,
Lin SJ,
Lin YC,
Liou JY,
Liu SM,
Hsing YI,
Raghuvanshi S,
Mohanty A,
Bharti AK,
Gaur A,
Gupta V,
Kumar D,
Ravi V,
Vij S,
Kapur A,
Khurana P,
Khurana JP,
Tyagi AK,
Gaikwad K,
Singh A,
Dalal V,
Srivastava S,
Dixit A,
Pal AK,
Ghazi IA,
Yadav M,
Pandit A,
Bhargava A,
Sureshbabu K,
Batra K,
Sharma TR,
Mohapatra T,
Singh NK,
Messing J,
Nelson AB,
Fuks G,
Kavchok S,
Keizer G,
Llaca EL,
Song RT,
Tanyolac B,
Young S,
Il KH,
Hahn JH,
Sangsakoo G,
Vanavichit A,
de Mattos LA,
Zimmer PD,
Malone G,
Dellagostin O,
de Oliveira AC,
Bevan M,
Bancroft I,
Minx P,
Cordum H,
Wilson R,
Cheng ZK,
Jin WW,
Jiang JM,
Leong SA,
Iwama H,
Gojobori T,
Itoh T,
Niimura Y,
Fujii Y,
Habara T,
Sakai H,
Sato Y,
Wilson G,
Kumar K,
McCouch S,
Juretic N,
Hoen D,
Wright S,
Bruskiewich R,
Bureau T,
Miyao A,
Hirochika H,
Nishikawa T

Nature
  436 (7052): 793-800; Aug 2005  
[Abstract]
[DOI] [Full Text] [PDF]

Experience and activity-dependent maturation of perisomatic GABAergic innervation in primary visual cortex during a postnatal critical period
Chattopadhyaya B,
Di Cristo G,
Higashiyama H,
Knott GW,
Kuhlman SJ,
Welker E,
Huang ZJ

J Neurosci
  24 (43): 9598-611; Oct 27 2004  
[Abstract]
[DOI]

Ankyrin-based subcellular gradient of neurofascin, an immunoglobulin family protein, directs GABAergic innervation at purkinje axon initial segment
Ango F,
di Cristo G,
Higashiyama H,
Bennett V,
Wu P,
Huang ZJ

Cell
  119 (2): 257-72; Oct 15 2004  
[Abstract]
[DOI]

The GAOLAOZHUANGREN1 gene encodes a putative glycosyltransferase that is critical for normal development and carbohydrate metabolism
Shao MH,
Zheng HQ,
Hu Y,
Liu DH,
Jang JC,
Ma H,
Huang H

Plant and Cell Physiology
  45 (10): 1453-1460; Oct 2004  
[Abstract]
[Full Text]

Identification, cDNA cloning, and targeted deletion of p70, a novel, ubiquitously expressed SH3 domain-containing protein
Carpino N,
Kobayashi R,
Zang H,
Takahashi Y,
Jou ST,
Feng J,
Nakajima H,
Ihle JN

Molecular and Cellular Biology
  22 (21): 7491-7500; Nov 2002  
[Full Text]

Homolog interaction during meiotic prophase I in Arabidopsis requires the SOLO DANCERS gene encoding a novel cyclin-like protein
Azumi Y,
Liu DH,
Zhao DZ,
Li WX,
Wang GF,
Hu Y,
Ma H

Embo Journal
  21 (12): 3081-3095; Jun 2002  
[Full Text]

The Arabidopsis ATK1 gene is required for spindle morphogenesis in male meiosis
Chen CB,
Marcus A,
Li WX,
Hu Y,
Calzada JP,
Grossniklaus U,
Cyr RJ,
Ma H

Development
  129 (10): 2401-2409; May 2002  
[Full Text]

Identification of ter94, Drosophila VCP, as a modulator of polyglutamine-induced neurodegeneration
Higashiyama H,
Hirose F,
Yamaguchi M,
Inoue YH,
Fujikake N,
Matsukage A,
Kakizuka A

Cell Death and Differentiation
  9 (3): 264-273; Mar 2002  
[Full Text]

Arabidopsis genes essential for seedling viability: isolation of insertional mutants and molecular cloning
Budziszewski GJ,
Lewis SP,
Glover LW,
Reineke J,
Jones G,
Ziemnik LS,
Lonowski J,
Nyfeler B,
Aux G,
Zhou Q,
McElver J,
Patton DA,
Martienssen R,
Grossniklaus U,
Ma H,
Law M,
Levin JZ

Genetics
  159 (4): 1765-78; Dec 2001  
[Abstract]
[Full Text]

The Arabidopsis kinesin, KATA, is a minus-end directed kinesin involved in male meiosis
Marcus AI,
Chen C,
Hu Y,
Calzada JP,
Grossniklauss U,
Ma H,
Cyr RJ

Molecular Biology of the Cell
  12 (0): 436A-436A; Nov 2001  
[Full Text]

Identification, sequence analysis and expression studies of novel anther-specific genes of Arabidopsis thaliana
Rubinelli P,
Hu Y,
Ma H

Plant Mol Biol
  37 (4): 607-19; Jul 1998  
[Abstract]
[Full Text]

To be, or not to be, a flower--control of floral meristem identity
Ma H

Trends Genet
  14 (1): 26-32; Jan 1998  
[Abstract]
[Full Text]

Specific interactions between the K domains of AG and AGLs, members of the MADS domain family of DNA binding proteins
Fan HY,
Hu Y,
Tudor M,
Ma H

Plant J
  12 (5): 999-1010; Nov 1997  
[Abstract]
[Full Text]

The on and off of floral regulatory genes
Ma H

Cell
  89 (6): 821-4; Jun 13 1997  
[Full Text]

The G protein alpha subunit (GP alpha1) is associated with the ER and the plasma membrane in meristematic cells of Arabidopsis and cauliflower
Weiss CA,
White E,
Huang H,
Ma H

FEBS Lett
  407 (3): 361-7; May 5 1997  
[Abstract]
[Full Text]

Polycomb in plants
Ma H

Trends Genet
  13 (5): 167; May 1997  
[Full Text]

Determination of Arabidopsis floral meristem identity by AGAMOUS
Mizukami Y,
Ma H

Plant Cell
  9 (3): 393-408; Mar 1997  
[Abstract]
[Full Text]

FON1, an Arabidopsis gene that terminates floral meristem activity and controls flower organ number
Huang H,
Ma H

Plant Cell
  9 (2): 115-34; Feb 1997  
[Abstract]
[Full Text]

Specific expression of the AGL1 MADS-box gene suggests regulatory functions in Arabidopsis gynoecium and ovule development
Flanagan CA,
Hu Y,
Ma H

Plant J
  10 (2): 343-53; Aug 1996  
[Abstract]
[Full Text]

Functional domains of the floral regulator AGAMOUS: characterization of the DNA binding domain and analysis of dominant negative mutations
Mizukami Y,
Huang H,
Tudor M,
Hu Y,
Ma H

Plant Cell
  8 (5): 831-45; May 1996  
[Abstract]
[Full Text]

DNA binding properties of two Arabidopsis MADS domain proteins: binding consensus and dimer formation
Huang H,
Tudor M,
Su T,
Zhang Y,
Hu Y,
Ma H

Plant Cell
  8 (1): 81-94; Jan 1996  
[Abstract]
[Full Text]

GTP-binding proteins in plants: new members of an old family
Ma H

Plant Mol Biol
  26 (5): 1611-36; Dec 1994  
[Abstract]
[Full Text]

Spatially and temporally regulated expression of the MADS-box gene AGL2 in wild-type and mutant arabidopsis flowers
Flanagan CA,
Ma H

Plant Mol Biol
  26 (2): 581-95; Oct 1994  
[Abstract]
[Full Text]

Isolation of cDNAs encoding guanine nucleotide-binding protein beta-subunit homologues from maize (ZGB1) and Arabidopsis (AGB1)
Weiss CA,
Garnaat CW,
Mukai K,
Hu Y,
Ma H

Proc Natl Acad Sci U S A
  91 (20): 9554-8; Sep 27 1994  
[Abstract]
[Full Text]

The unfolding drama of flower development: recent results from genetic and molecular analyses
Ma H

Genes Dev
  8 (7): 745-56; Apr 1 1994  
[DOI] [Full Text]

Regulated Expression of the Arabidopsis G-Protein Alpha-Subunit Gene Gpa1
Huang H,
Weiss CA,
Ma H

International Journal of Plant Sciences
  155 (1): 3-14; Jan 1994  
[Abstract]
[DOI]

Immunolocalization of the G protein alpha subunit encoded by the GPA1 gene in Arabidopsis
Weiss CA,
Huang H,
Ma H

Plant Cell
  5 (11): 1513-28; Nov 1993  
[Abstract]


Isolation and characterization of the binding sequences for the product of the Arabidopsis floral homeotic gene AGAMOUS
Huang H,
Mizukami Y,
Hu Y,
Ma H

Nucleic Acids Res
  21 (20): 4769-76; Oct 11 1993  
[Abstract]


Protein phosphorylation in plants: enzymes, substrates and regulators
Ma H

Trends Genet
  9 (7): 228-30; Jul 1993  


Characterization of Agl3, a Mads-Box Gene with Non-Flower-Specific Expression
Weiss C,
Huang H,
Ma H

Journal of Cellular Biochemistry
  (0): 37-37; Jan 1993  
[Full Text]

Functional-Analysis of the Arabidopsis Floral Homeotic Gene Agamous in Transgenic Plants
Mizukami Y,
Ma H

Journal of Cellular Biochemistry
  (0): 15-15; Jan 1993  
[Full Text]

Agl1 and Agl2, 2 Agamous-Related Mads-Box Genes, Are Differentially Expressed During Flower Development
Flanagan CA,
Ma H

Journal of Cellular Biochemistry
  (0): 14-14; Jan 1993  
[Full Text]

Ectopic expression of the floral homeotic gene AGAMOUS in transgenic Arabidopsis plants alters floral organ identity
Mizukami Y,
Ma H

Cell
  71 (1): 119-31; Oct 2 1992  
[Abstract]


Vectors for Plant Transformation and Cosmid Libraries
Ma H,
Yanofsky MF,
Klee HJ,
Bowman JL,
Meyerowitz EM

Gene
  117 (2): 161-167; Aug 1992  
[Abstract]
[Full Text]

Isolation and sequence analysis of TGA1 cDNAs encoding a tomato G protein alpha subunit
Ma H,
Yanofsky MF,
Huang H

Gene
  107 (2): 189-95; Nov 15 1991  
[Abstract]
[Full Text]


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