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1.

1634
Accesses

Research article   Open Access Highly Accessed

Global analysis of DNA methylation in early-stage liver fibrosis

Yoko Komatsu, Tsuyoshi Waku, Naoya Iwasaki, Wakana Ono, Chie Yamaguchi, Junn Yanagisawa BMC Medical Genomics 2012, 5:5 (27 January 2012)

Abstract | Full text | PDF | PubMed

2.

996
Accesses

Research article   Open Access Highly Accessed

The effects of MicroRNA transfections on global patterns of gene expression in ovarian cancer cells are functionally coordinated

Shubin W Shahab, Lilya V Matyunina, Christopher G Hill, Lijuan Wang, Roman Mezencev, L Walker, John F McDonald BMC Medical Genomics 2012, 5:33 (1 August 2012)

Abstract | Full text | PDF | PubMed

3.

850
Accesses

Research article   Open Access Highly Accessed

Systems analysis of human brain gene expression: mechanisms for HIV-associated neurocognitive impairment and common pathways with Alzheimer's disease

Andrew J Levine, Jeremy A Miller, Paul Shapshak, Benjamin Gelman, Elyse J Singer, Charles H Hinkin, Deborah Commins, Susan Morgello, Igor Grant, Steve Horvath BMC Medical Genomics 2013, 6:4 (13 February 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

Re-analysis of existing transcriptomic datasets from the brains of patients with HIV-associated neurocognitive impairment, using a systems biology approach, corroborates their results but also identifies possible co-expression networks linked to neurocognitive impairment in HIV and Alzheimer’s disease.

4.

842
Accesses

Review   Open Access Highly Accessed

Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases

Douglas B Kell BMC Medical Genomics 2009, 2:2 (8 January 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Douglas Kell reviews the role of iron-catalysed free radicals in disease, which underpin the behavior of many physiological and pathological processes, and considers the need for better understanding using an integrative, systems-level approach.

5.

810
Accesses

Technical advance   Open Access Highly Accessed

Noninvasive Fetal Trisomy (NIFTY) test: an advanced noninvasive prenatal diagnosis methodology for fetal autosomal and sex chromosomal aneuploidies

Fuman Jiang, Jinghui Ren, Fang Chen, Yuqiu Zhou, Jiansheng Xie, Shan Dan, Yue Su, Jianhong Xie, Baomin Yin, Wen Su, Huakun Zhang, Wei Wang, Xianghua Chai, Linhua Lin, Hui Guo, Qiyun Li, Peipei Li, Yuying Yuan, Xiaoyu Pan, Yihan Li, Lifu Liu, Huifei Chen, Zhaoling Xuan, Shengpei Chen, Chunlei Zhang, Hongyun Zhang, Zhongming Tian, Zhengyu Zhang, Hui Jiang, Lijian Zhao, Weimou Zheng, Songgang Li, Yingrui Li, Jun Wang, Jian Wang, Xiuqing Zhang et al. BMC Medical Genomics 2012, 5:57 (1 December 2012)

Abstract | Full text | PDF | PubMed

6.

781
Accesses

Research article   Open Access Highly Accessed

PAM50 Breast Cancer Subtyping by RT-qPCR and Concordance with Standard Clinical Molecular Markers

Roy RL Bastien, Álvaro Rodríguez-Lescure, Mark TW Ebbert, Aleix Prat, Blanca Munárriz, Leslie Rowe, Patricia Miller, Manuel Ruiz-Borrego, Daniel Anderson, Bradley Lyons, Isabel Álvarez, Tracy Dowell, David Wall, Miguel Seguí, Lee Barley, Kenneth M Boucher, Emilio Alba, Lisa Pappas, Carole A Davis, Ignacio Aranda, Christiane Fauron, Inge J Stijleman, José Palacios, Antonio Antón, Eva Carrasco, Rosalía Caballero, Matthew J Ellis, Torsten O Nielsen, Charles M Perou, Mark Astill, Philip S Bernard, Miguel Martín et al. BMC Medical Genomics 2012, 5:44 (4 October 2012)

Abstract | Full text | PDF | PubMed

7.

752
Accesses

Research article   Open Access Highly Accessed

Multilocus loss of DNA methylation in individuals with mutations in the histone H3 Lysine 4 Demethylase KDM5C

Daria Grafodatskaya, Barian HY Chung, Darci T Butcher, Andrei L Turinsky, Sarah J Goodman, Sana Choufani, Yi-An Chen, Youliang Lou, Chunhua Zhao, Rageen Rajendram, Fatima E Abidi, Cindy Skinner, James Stavropoulos, Carolyn A Bondy, Jill Hamilton, Shoshana Wodak, Stephen W Scherer, Charles E Schwartz, Rosanna Weksberg BMC Medical Genomics 2013, 6:1 (28 January 2013)

Abstract | Full text | PDF | PubMed

8.

561
Accesses

Database   Open Access

The Roche Cancer Genome Database 2.0

Jan Küntzer, Daniela Maisel, Hans-Peter Lenhof, Stefan Klostermann, Helmut Burtscher BMC Medical Genomics 2011, 4:43 (17 May 2011)

Abstract | Full text | PDF | PubMed |  Editor’s summary

The enlarged Roche Cancer Genome Database integrates information from a number of human mutation databases and mutation data curated from the literature, with an improved interface and search functionality over the earlier version.

9.

505
Accesses

Research article   Open Access

Genomic profiling of rectal adenoma and carcinoma by array-based comparative genomic hybridization

Zhi-Zhou Shi, Yue-Ming Zhang, Li Shang, Jia-Jie Hao, Tong-Tong Zhang, Bo-Shi Wang, Jian-Wei Liang, Xi Chen, Ying Zhang, Gui-Qi Wang, Ming-Rong Wang, Yu Zhang BMC Medical Genomics 2012, 5:52 (16 November 2012)

Abstract | Full text | PDF | PubMed

10.

470
Accesses

Research article   Open Access Highly Accessed

Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifs

Perry Evans, William Dampier, Lyle Ungar, Aydin Tozeren BMC Medical Genomics 2009, 2:27 (18 May 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

11.

462
Accesses

Research article   Open Access Highly Accessed

Targeted high throughput sequencing in clinical cancer Settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity

Martin Kerick, Melanie Isau, Bernd Timmermann, Holger Sültmann, Ralf Herwig, Sylvia Krobitsch, Georg Schaefer, Irmgard Verdorfer, Georg Bartsch, Helmut Klocker, Hans Lehrach, Michal R Schweiger BMC Medical Genomics 2011, 4:68 (29 September 2011)

Abstract | Full text | PDF | PubMed

12.

448
Accesses

Research article   Open Access

Pivotal role of the muscle-contraction pathway in cryptorchidism and evidence for genomic connections with cardiomyopathy pathways in RASopathies

Carlo V Cannistraci, Jernej Ogorevc, Minja Zorc, Timothy Ravasi, Peter Dovc, Tanja Kunej BMC Medical Genomics 2013, 6:5 (14 February 2013)

Abstract | Provisional PDF | PubMed

13.

386
Accesses

Proceedings   Open Access

Potential roles of microRNAs in regulating long intergenic noncoding RNAs

Liran Juan, Guohua Wang, Milan Radovich, Bryan P Schneider, Susan E Clare, Yadong Wang, Yunlong Liu BMC Medical Genomics 2013, 6(Suppl 1):S7 (23 January 2013)

Abstract | Full text | PDF | PubMed

14.

367
Accesses

Research article   Open Access

Next-generation text-mining mediated generation of chemical response-specific gene sets for interpretation of gene expression data

Kristina M Hettne, André Boorsma, Dorien A M van Dartel, Jelle J Goeman, Esther de Jong, Aldert H Piersma, Rob H Stierum, Jos C Kleinjans, Jan A Kors BMC Medical Genomics 2013, 6:2 (29 January 2013)

Abstract | Full text | PDF | PubMed

15.

348
Accesses

Research article   Open Access

Subtypes of primary colorectal tumors correlate with response to targeted treatment in colorectal cell lines

Andreas Schlicker, Garry Beran, Christine M Chresta, Gael McWalter, Alison Pritchard, Susie Weston, Sarah Runswick, Sara Davenport, Kerry Heathcote, Denis Alferez Castro, George Orphanides, Tim French, Lodewyk FA Wessels BMC Medical Genomics 2012, 5:66 (31 December 2012)

Abstract | Full text | PDF | PubMed

16.

347
Accesses

Proceedings   Open Access

A novel method for the normalization of microRNA RT-PCR data

Rehman Qureshi, Ahmet Sacan BMC Medical Genomics 2013, 6(Suppl 1):S14 (23 January 2013)

Abstract | Full text | PDF | PubMed

17.

320
Accesses

Research article   Open Access Highly Accessed

MicroRNA profiling of diverse endothelial cell types

Matthew N McCall, Oliver A Kent, Jianshi Yu, Karen Fox-Talbot, Ari L Zaiman, Marc K Halushka BMC Medical Genomics 2011, 4:78 (2 November 2011)

Abstract | Full text | PDF | PubMed

18.

319
Accesses

Research article   Open Access Highly Accessed

Human breast cancer associated fibroblasts exhibit subtype specific gene expression profiles

Julia Tchou, Andrew V Kossenkov, Lisa Chang, Celine Satija, Meenhard Herlyn, Louise C Showe, Ellen Puré BMC Medical Genomics 2012, 5:39 (6 September 2012)

Abstract | Full text | PDF | PubMed

19.

293
Accesses

Research article   Open Access Highly Accessed

A systematic comparison and evaluation of high density exon arrays and RNA-seq technology used to unravel the peripheral blood transcriptome of sickle cell disease

Nalini Raghavachari, Jennifer Barb, Yanqin Yang, Poching Liu, Kimberly Woodhouse, Daniel Levy, Christopher J O‘Donnell, Peter J Munson, Gregory J Kato BMC Medical Genomics 2012, 5:28 (29 June 2012)

Abstract | Full text | PDF | PubMed | F1000 Biology

20.

292
Accesses

Review   Open Access Highly Accessed

Completion of the swine genome will simplify the production of swine as a large animal biomedical model

Eric M Walters, Eckhard Wolf, Jeffery J Whyte, Jiude Mao, Simone Renner, Hiroshi Nagashima, Eiji Kobayashi, Jianguo Zhao, Kevin D Wells, John K Critser, Lela K Riley, Randall S Prather BMC Medical Genomics 2012, 5:55 (15 November 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Eric M Walters and colleagues review the pig as a large animal biomedical model and how the publication of the swine genome sequence will further advance its utility for understanding human disease, transgenesis and xenotransplantation.

21.

273
Accesses

Research article   Open Access Highly Accessed

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, Cloud Paweletz, Bethany Lynch, Igor Feldman, Hongyue Dai, Pearl Huang, James Watters BMC Medical Genomics 2010, 3:26 (30 June 2010)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

22.

256
Accesses

Research article   Open Access Highly Accessed

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 BMC Medical Genomics 2010, 3:36 (9 August 2010)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

23.

256
Accesses

Research article   Open Access Highly Accessed

DNA methylation differences at growth related genes correlate with birth weight: a molecular signature linked to developmental origins of adult disease?

Nahid Turan, Mohamed F Ghalwash, Sunita Katari, Christos Coutifaris, Zoran Obradovic, Carmen Sapienza BMC Medical Genomics 2012, 5:10 (12 April 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Profiling of inter-individual DNA methylation differences in neonates has identified 23 genes that account for 70-87% of variance in birth weight, whilst traditional gene expression profiling identified a far smaller proportion.

24.

250
Accesses

Research   Open Access

Recursive SVM biomarker selection for early detection of breast cancer in peripheral blood

Fan Zhang, Howard L Kaufman, Youping Deng, Renee Drabier BMC Medical Genomics 2013, 6(Suppl 1):S4 (23 January 2013)

Abstract | Full text | PDF | PubMed

25.

243
Accesses

Research article   Open Access Highly Accessed

Structural, functional and molecular analysis of the effects of aging in the small intestine and colon of C57BL/6J mice

Wilma T Steegenga, Nicole JW de Wit, Mark V Boekschoten, Noortje IJssennagger, Carolien Lute, Shohreh Keshtkar, Mechteld M Bromhaar, Ellen Kampman, Lisette C de Groot, Michael Muller BMC Medical Genomics 2012, 5:38 (28 August 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

The small intestine and colons of aging mice do not show marked changes in expression of genes involved in metabolic processes, however immune response and inflammation gene expression increases and aging-induced global hypomethylation is also present.

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