Volume 3; Issue 1

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BMC Medical Genomics
Volume 3; Issue 1

BMC Medical Genomics

Volume 3; Issue 1

1

Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information

Yonqing Zhang, Supriyo De, John R Garner, Kirstin Smith, S Alex Wang, Kevin G Becker

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.02 MB

english, 2010

2

Mutation screening of melatonin-related genes in patients with autism spectrum disorders

Lina Jonsson, Elin Ljunggren, Anna Bremer, Christin Pedersen, Mikael Landén, Kent Thuresson, MaiBritt Giacobini, Jonas Melke

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.11 MB

english, 2010

3

CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations

Yuri Kotliarov, Serdar Bozdag, Hangjiong Cheng, Stefan Wuchty, Jean-Claude Zenklusen, Howard A Fine

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 939 KB

english, 2010

4

Astrocytes derived from trisomic human embryonic stem cells express markers of astrocytic cancer cells and premalignant stem-like progenitors

Sailesh Gopalakrishna-Pillai, Linda E Iverson

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 2.12 MB

english, 2010

5

Signaling pathway networks mined from human pituitary adenoma proteomics data

Xianquan Zhan, Dominic M Desiderio

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 4.08 MB

english, 2010

6

Genomics and proteomics approaches to the study of cancer-stroma interactions

Flávia C Rodrigues-Lisoni, Paulo Peitl, Alessandra Vidotto, Giovana M Polachini, José V Maniglia, Juliana Carmona-Raphe, Bianca R Cunha, Tiago Henrique, Caique F Souza, Rodrigo AP Teixeira, Erica E Fu

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.59 MB

english, 2010

7

Peripheral blood gene expression patterns discriminate among chronic inflammatory diseases and healthy controls and identify novel targets

Bertalan Mesko, Szilard Poliska, Andrea Szegedi, Zoltan Szekanecz, Karoly Palatka, Maria Papp, Laszlo Nagy

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 2.08 MB

english, 2010

8

MUC1-associated proliferation signature predicts outcomes in lung adenocarcinoma patients

Dhara M MacDermed, Nikolai N Khodarev, Sean P Pitroda, Darrin C Edwards, Charles A Pelizzari, Lei Huang, Donald W Kufe, Ralph R Weichselbaum

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.61 MB

english, 2010

9

Predicting environmental chemical factors associated with disease-related gene expression data

Chirag J Patel, Atul J Butte

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 944 KB

english, 2010

10

Molecular analysis of endothelial progenitor cell (EPC) subtypes reveals two distinct cell populations with different identities

Reinhold J Medina, Christina L O'Neill, Mark Sweeney, Jasenka Guduric-Fuchs, Tom A Gardiner, David A Simpson, Alan W Stitt

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 4.31 MB

english, 2010

11

Gene profiling of the erythro- and megakaryoblastic leukaemias induced by the Graffi murine retrovirus

Veronique Voisin, Philippe Legault, Paulina Salazar Diana Ospina, Yaacov Ben-David, Eric Rassart

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.81 MB

english, 2010

12

Human difference in the genomic era: Facilitating a socially responsible dialogue

Sarah Knerr, Edward Ramos, Juleigh Nowinski, Keianna Dixon, Vence L Bonham

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 490 KB

english, 2010

13

SEURAT: Visual analytics for the integrated analysis of microarray data

Alexander Gribov, Martin Sill, Sonja Lück, Frank Rücker, Konstanze Döhner, Lars Bullinger, Axel Benner, Antony Unwin

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.27 MB

english, 2010

14

A combined genome-wide linkage and association approach to find susceptibility loci for platelet function phenotypes in European American and African American families with coronary artery disease

Rasika A Mathias, Yoonhee Kim, Heejong Sung, Lisa R Yanek, VJ Mantese, J Enrique Hererra-Galeano, Ingo Ruczinski, Alexander F Wilson, Nauder Faraday, Lewis C Becker, Diane M Becker

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 2.05 MB

english, 2010

15

An algorithm for classifying tumors based on genomic aberrations and selecting representative tumor models

Xin Lu, Ke Zhang, Charles Van Sant, John Coon, Dimitri Semizarov

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 3.53 MB

english, 2010

16

Examining smoking-induced differential gene expression changes in buccal mucosa

Doris M Kupfer, Vicky L White, Marita C Jenkins, Dennis Burian

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 2.04 MB

english, 2010

17

Pathway analysis comparison using Crohn's disease genome wide association studies

David Ballard, Clara Abraham, Judy Cho, Hongyu Zhao

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.04 MB

english, 2010

18

A gene expression signature of RAS pathway dependence predicts response to PI3K and RAS pathway inhibitors and expands the population of RAS pathway activated tumors

Andrey Loboda, Michael Nebozhyn, Rich Klinghoffer, Jason Frazier, Michael Chastain, William Arthur, Brian Roberts, Theresa Zhang, Melissa Chenard, Brian Haines, Jannik Andersen, Kumiko Nagashima, Clou

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.46 MB

english, 2010

19

Effect of methylene blue on the genomic response to reperfusion injury induced by cardiac arrest and cardiopulmonary resuscitation in porcine brain

Cécile Martijn, Lars Wiklund

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 4.31 MB

english, 2010

20

Decreased expression of GRAF1/OPHN-1-L in the X-linked alpha thalassemia mental retardation syndrome

Vincenza Barresi, Angela Ragusa, Marco Fichera, Nicolò Musso, Lucia Castiglia, Giancarlo Rappazzo, Salvatore Travali, Teresa Mattina, Corrado Romano, Guido Cocchi, Daniele F Condorelli

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 701 KB

english, 2010

21

Transcriptomic epidemiology of smoking: the effect of smoking on gene expression in lymphocytes

Jac C Charlesworth, Joanne E Curran, Matthew P Johnson, Harald HH Göring, Thomas D Dyer, Vincent P Diego, Jack W Kent, Michael C Mahaney, Laura Almasy, Jean W MacCluer, Eric K Moses, John Blangero

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 901 KB

english, 2010

22

Association of adipocyte genes with ASP expression: a microarray analysis of subcutaneous and omental adipose tissue in morbidly obese subjects

Robin E MacLaren, Wei Cui, HuiLing Lu, Serge Simard, Katherine Cianflone

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 701 KB

english, 2010

23

Identification of protein-coding and non-coding RNA expression profiles in CD34+and in stromal cells in refractory anemia with ringed sideroblasts

Mariana O Baratti, Yuri B Moreira, Fabiola Traina, Fernando F Costa, Sergio Verjovski-Almeida, Sara T Olalla-Saad

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.72 MB

english, 2010

24

Regulation of early signaling and gene expression in the α-particle and bystander response of IMR-90 human fibroblasts

Shanaz A Ghandhi, Lihua Ming, Vladimir N Ivanov, Tom K Hei, Sally A Amundson

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.24 MB

english, 2010

25

A sequence-based approach to identify reference genes for gene expression analysis

Raj Chari, Kim M Lonergan, Larissa A Pikor, Bradley P Coe, Chang Qi Zhu, Timothy HW Chan, Calum E MacAulay, Ming-Sound Tsao, Stephen Lam, Raymond T Ng, Wan L Lam

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 584 KB

english, 2010

26

Genome-wide DNA methylation analysis for diabetic nephropathy in type 1 diabetes mellitus

Christopher G Bell, Andrew E Teschendorff, Vardhman K Rakyan, Alexander P Maxwell, Stephan Beck, David A Savage

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.14 MB

english, 2010

27

Co-expressed immune and metabolic genes in visceral and subcutaneous adipose tissue from severely obese individuals are associated with plasma HDL and glucose levels: a microarray study

Marcel GM Wolfs, Sander S Rensen, Elinda J Bruin-Van Dijk, Froukje J Verdam, Jan-Willem Greve, Bahram Sanjabi, Marcel Bruinenberg, Cisca Wijmenga, Timon W van Haeften, Wim A Buurman, Lude Franke, Mart

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 2.23 MB

english, 2010

28

Genetic integrity of the human Y chromosome exposed to groundwater arsenic

Safdar Ali, Sher Ali

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.85 MB

english, 2010

29

Impact of RNA degradation on gene expression profiling

Lennart Opitz, Gabriela Salinas-Riester, Marian Grade, Klaus Jung, Peter Jo, Georg Emons, B Michael Ghadimi, Tim Beißbarth, Jochen Gaedcke

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.09 MB

english, 2010

30

The NRF2-mediated oxidative stress response pathway is associated with tumor cell resistance to arsenic trioxide across the NCI-60 panel

Qian Liu, Hao Zhang, Lisa Smeester, Fei Zou, Matt Kesic, Ilona Jaspers, Jingbo Pi, Rebecca C Fry

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 3.33 MB

english, 2010

31

A towards-multidimensional screening approach to predict candidate genes of rheumatoid arthritis based on SNP, structural and functional annotations

Liangcai Zhang, Wan Li, Leilei Song, Lina Chen

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.86 MB

english, 2010

32

Analyzing the regulation of metabolic pathways in human breast cancer

Gunnar Schramm, Eva-Maria Surmann, Stefan Wiesberg, Marcus Oswald, Gerhard Reinelt, Roland Eils, Rainer König

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.07 MB

english, 2010

33

Genome-wide methylation and expression profiling identifies promoter characteristics affecting demethylation-induced gene up-regulation in melanoma

Jill C Rubinstein, Nam Tran, Shuangge Ma, Ruth Halaban, Michael Krauthammer

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.91 MB

english, 2010

34

Impairment of circulating endothelial progenitors in Down syndrome

Valerio Costa, Linda Sommese, Amelia Casamassimi, Roberta Colicchio, Claudia Angelini, Valentina Marchesano, Lara Milone, Bartolomeo Farzati, Alfonso Giovane, Carmela Fiorito, Monica Rienzo, Marco Pic

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 2.00 MB

english, 2010

35

Evaluation of the bacterial diversity of Pressure ulcers using bTEFAP pyrosequencing

Drake M Smith, David E Snow, Eric Rees, Ann M Zischkau, J Delton Hanson, Randall D Wolcott, Yan Sun, Jennifer White, Shashi Kumar, Scot E Dowd

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.12 MB

english, 2010

36

Polymorphisms in folate-metabolizing genes, chromosome damage, and risk of Down syndrome in Italian women: identification of key factors using artificial neural networks

Fabio Coppedè, Enzo Grossi, Francesca Migheli, Lucia Migliore

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 675 KB

english, 2010

37

LNCaP Atlas: Gene expression associated within vivoprogression to castration-recurrent prostate cancer

Tammy L Romanuik, Gang Wang, Olena Morozova, Allen Delaney, Marco A Marra, Marianne D Sadar

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 981 KB

english, 2010

38

Molecular signature of response and potential pathways related to resistance to the HSP90 inhibitor, 17AAG, in breast cancer

Magdalena Zajac, Gonzalo Gomez, Javier Benitez, Beatriz Martínez-Delgado

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.55 MB

english, 2010

39

Gene regulatory network reveals oxidative stress as the underlying molecular mechanism of type 2 diabetes and hypertension

Jesmin, Mahbubur SM Rashid, Hasan Jamil, Raquel Hontecillas, Josep Bassaganya-Riera

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 5.88 MB

english, 2010

40

Chemokine gene expression in lung CD8 T cells correlates with protective immunity in mice immunized intra-nasally with Adenovirus-85A

Lian N Lee, Dilair Baban, Edward O Ronan, Jiannis Ragoussis, Peter CL Beverley, Elma Z Tchilian

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 669 KB

english, 2010

41

Admixture mapping of end stage kidney disease genetic susceptibility using estimated mutual information ancestry informative markers

Liran I Shlush, Sivan Bercovici, Walter G Wasser, Guennady Yudkovsky, Alan Templeton, Dan Geiger, Karl Skorecki

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 728 KB

english, 2010

42

Hepatic microRNA expression is associated with the response to interferon treatment of chronic hepatitis C

Yoshiki Murakami, Masami Tanaka, Hidenori Toyoda, Katsuyuki Hayashi, Masahiko Kuroda, Atsushi Tajima, Kunitada Shimotohno

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.22 MB

english, 2010

43

Literature-based discovery of diabetes- and ROS-related targets

Junguk Hur, Kelli A Sullivan, Adam D Schuyler, Yu Hong, Manjusha Pande, David J States, H V Jagadish, Eva L Feldman

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.45 MB

english, 2010

44

Insight in modulation of inflammation in response to diclofenac intervention: a human intervention study

Marjan J van Erk, Suzan Wopereis, Carina Rubingh, Trinette van Vliet, Elwin Verheij, Nicole HP Cnubben, Theresa L Pedersen, John W Newman, Age K Smilde, van der Jan Greef, Henk FJ Hendriks, Ben van Om

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.49 MB

english, 2010

45

Genotator: A disease-agnostic tool for genetic annotation of disease

Dennis P Wall, Rimma Pivovarov, Mark Tong, Jae-Yoon Jung, Vincent A Fusaro, Todd F DeLuca, Peter J Tonellato

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.20 MB

english, 2010

46

Multi-cancer computational analysis reveals invasion-associated variant of desmoplastic reaction involving INHBA, THBS2 and COL11A1

Hoon Kim, John Watkinson, Vinay Varadan, Dimitris Anastassiou

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 732 KB

english, 2010

47

Conversion of a molecular classifier obtained by gene expression profiling into a classifier based on real-time PCR: a prognosis predictor for gliomas

Satoru Kawarazaki, Kazuya Taniguchi, Mitsuaki Shirahata, Yoji Kukita, Manabu Kanemoto, Nobuhiro Mikuni, Nobuo Hashimoto, Susumu Miyamoto, Jun A Takahashi, Kikuya Kato

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 490 KB

english, 2010

48

Concomitant heterochromatinisation and down-regulation of gene expression unveils epigenetic silencing ofRELBin an aggressive subset of chronic lymphocytic leukemia in males

Jean-Brice Marteau, Odile Rigaud, Thibaut Brugat, Nathalie Gault, Laurent Vallat, Mogens Kruhoffer, Torben F Orntoft, Florence Nguyen-Khac, Sylvie Chevillard, Hélène Merle-Beral, Jozo Delic

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 3.20 MB

english, 2010

49

Enrichment of ultraconserved elements among genomic imbalances causing mental delay and congenital anomalies

Francisco Martínez, Sandra Monfort, Mónica Roselló, Silvestre Oltra, David Blesa, Ramiro Quiroga, Sonia Mayo, Carmen Orellana

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 238 KB

english, 2010

50

An empirical Bayes model for gene expression and methylation profiles in antiestrogen resistant breast cancer

Jaesik Jeong, Lang Li, Yunlong Liu, Kenneth P Nephew, Tim Hui-Ming Huang, Changyu Shen

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 718 KB

english, 2010

51

Gene expression profiling in whole blood identifies distinct biological pathways associated with obesity

Sujoy Ghosh, Robert Dent, Mary-Ellen Harper, Shelby A Gorman, Joan S Stuart, Ruth McPherson

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.25 MB

english, 2010

52

Disease-associated alleles in genome-wide association studies are enriched for derived low frequency alleles relative to HapMap and neutral expectations

Joseph Lachance

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 830 KB

english, 2010

53

Comparative gene expression profiling analysis of urothelial carcinoma of the renal pelvis and bladder

Zhongfa Zhang, Kyle A Furge, Ximing J Yang, Bin T Teh, Donna E Hansel

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.28 MB

english, 2010

54

Birt-Hogg-Dubé renal tumors are genetically distinct from other renal neoplasias and are associated with up-regulation of mitochondrial gene expression

Jeff A Klomp, David Petillo, Natalie M Niemi, Karl J Dykema, Jindong Chen, Ximing J Yang, Annika Sääf, Peter Zickert, Markus Aly, Ulf Bergerheim, Magnus Nordenskjöld, Sophie Gad, Sophie Giraud, Yves D

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 484 KB

english, 2010

55

Gene expression signatures in childhood acute leukemias are largely unique and distinct from those of normal tissues and other malignancies

Anna Andersson, Patrik Edén, Tor Olofsson, Thoas Fioretos

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 3.12 MB

english, 2010

56

Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASL®platform

Monica M Reinholz, Jeanette E Eckel-Passow, S Keith Anderson, Yan W Asmann, Michael A Zschunke, Ann L Oberg, Ann E McCullough, Amylou C Dueck, Beiyun Chen, Craig S April, Eliza Wickham-Garcia, Robert

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.40 MB

english, 2010

57

Gene expression profiling of subcutaneous adipose tissue in morbid obesity using a focused microarray: Distinct expression of cell-cycle- and differentiation-related genes

Sara Rodríguez-Acebes, Nuria Palacios, José I Botella-Carretero, Nuria Olea, Lorena Crespo, Roberto Peromingo, Diego Gómez-Coronado, Miguel A Lasunción, Clotilde Vázquez, Javier Martínez-Botas

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 721 KB

english, 2010

58

Primate-specific evolution of noncoding element insertion intoPLA2G4Cand human preterm birth

Jevon Plunkett, Scott Doniger, Thomas Morgan, Ritva Haataja, Mikko Hallman, Hilkka Puttonen, Ramkumar Menon, Edward Kuczynski, Errol Norwitz, Victoria Snegovskikh, Aarno Palotie, Leena Peltonen, Vinet

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.37 MB

english, 2010

59

mspecLINE: bridging knowledge of human disease with the proteome

Jeremy Handcock, Eric W Deutsch, John Boyle

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.44 MB

english, 2010

60

Molecular sampling of prostate cancer: a dilemma for predicting disease progression

Andrea Sboner, Francesca Demichelis, Stefano Calza, Yudi Pawitan, Sunita R Setlur, Yujin Hoshida, Sven Perner, Hans-Olov Adami, Katja Fall, Lorelei A Mucci, Philip W Kantoff, Meir Stampfer, Swen-Olof

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 1.34 MB

english, 2010

61

Genotypes and haplotypes in the insulin-like growth factors, their receptors and binding proteins in relation to plasma metabolic levels and mammographic density

Margarethe Biong, Inger T Gram, Ilene Brill, Fredrik Johansen, Hiroko K Solvang, Grethe IG Alnaes, Toril Fagerheim, Yngve Bremnes, Stephen J Chanock, Laurie Burdett, Meredith Yeager, Giske Ursin, Vess

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 334 KB

english, 2010

62

Dynamic cross-talk analysis among TNF-R, TLR-4 and IL-1R signalings in TNFα-induced inflammatory responses

Shih-Kuang Yang, Yu-Chao Wang, Chun-Cheih Chao, Yung-Jen Chuang, Chung-Yu Lan, Bor-Sen Chen

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 2.08 MB

english, 2010

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