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  1. Long noncoding RNAs (lncRNAs) are widely involved in the initiation and development of cancer. Although some computational methods have been proposed to identify cancer-related lncRNAs, there is still a demand...

    Authors: Xuan Zhang, Jun Wang, Jing Li, Wen Chen and Changning Liu
    Citation: BMC Medical Genomics 2018 11(Suppl 6):120
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  2. Identification of cancer subtypes is of great importance to facilitate cancer diagnosis and therapy. A number of methods have been proposed to integrate multi-sources data to identify cancer subtypes in recent...

    Authors: Yang Guo, Yang Qi, Zhanhuai Li and Xuequn Shang
    Citation: BMC Medical Genomics 2018 11(Suppl 6):119
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  3. Gene expression-based profiling has been used to identify biomarkers for different breast cancer subtypes. However, this technique has many limitations. IsomiRs are isoforms of miRNAs that have critical roles ...

    Authors: Chaowang Lan, Hui Peng, Eileen M. McGowan, Gyorgy Hutvagner and Jinyan Li
    Citation: BMC Medical Genomics 2018 11(Suppl 6):118
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  4. Human cancers are complex ecosystems composed of cells with distinct molecular signatures. Such intratumoral heterogeneity poses a major challenge to cancer diagnosis and treatment. Recent advancements of sing...

    Authors: Yanglan Gan, Ning Li, Guobing Zou, Yongchang Xin and Jihong Guan
    Citation: BMC Medical Genomics 2018 11(Suppl 6):117
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  5. Micro-RNAs (miRNAs) play a significant role in regulating gene expression under physiological and pathological conditions such as cancers. However, it remains a challenging problem to discover the target messe...

    Authors: Lujia Chen and Xinghua Lu
    Citation: BMC Medical Genomics 2018 11(Suppl 6):116
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  6. Gene co-expression network (GCN) mining is a systematic approach to efficiently identify novel disease pathways, predict novel gene functions and search for potential disease biomarkers. However, few studies h...

    Authors: Shunian Xiang, Zhi Huang, Tianfu Wang, Zhi Han, Christina Y. Yu, Dong Ni, Kun Huang and Jie Zhang
    Citation: BMC Medical Genomics 2018 11(Suppl 6):115
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  7. Recent studies demonstrated that long non-coding RNAs (lncRNAs) could be intricately implicated in cancer-related molecular networks, and related to cancer occurrence, development and prognosis. However, clini...

    Authors: Jun Wang, Xuan Zhang, Wen Chen, Jing Li and Changning Liu
    Citation: BMC Medical Genomics 2018 11(Suppl 6):114
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  8. Current knowledge and data on miRNA-lncRNA interactions is still limited and little effort has been made to predict target lncRNAs of miRNAs. Accumulating evidences suggest that the interaction patterns betwee...

    Authors: Zhi-An Huang, Yu-An Huang, Zhu-Hong You, Zexuan Zhu and Yiwen Sun
    Citation: BMC Medical Genomics 2018 11(Suppl 6):113
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  9. Forty-two percent of patients experience disease comorbidity, contributing substantially to mortality rates and increased healthcare costs. Yet, the possibility of underlying shared mechanisms for diseases rem...

    Authors: Haiquan Li, Jungwei Fan, Francesca Vitali, Joanne Berghout, Dillon Aberasturi, Jianrong Li, Liam Wilson, Wesley Chiu, Minsu Pumarejo, Jiali Han, Colleen Kenost, Pradeep C. Koripella, Nima Pouladi, Dean Billheimer, Edward J. Bedrick and Yves A. Lussier
    Citation: BMC Medical Genomics 2018 11(Suppl 6):112
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 6

  10. There is a clear need for assays that can predict the risk of metastatic prostate cancer following curative procedures. Importantly these assays must be analytically robust in order to provide quality data for...

    Authors: Paul Wallace Medlow, Christopher James Steele, Andrena Marie McCavigan, Wesley Reardon, Christopher Michael Brown, Shauna May Lambe, Felipe Augusto Andre Ishiy, Steven Michael Walker, Gemma Elizabeth Logan, Olaide Yaqeen Raji, Viktor Berge, Betina Katz, Elaine Williamson Kay, Katherine Sheehan, Ronald William Watson, Denis Paul Harkin…
    Citation: BMC Medical Genomics 2018 11:125
    Content type: Research article Published on:

  11. Silver-Russell Syndrome (SRS) is a rare growth-related genetic disorder mainly characterized by prenatal and postnatal growth failure. Although molecular causes are not clear in all cases, the most common mech...

    Authors: Yerai Vado, Javier Errea-Dorronsoro, Isabel Llano-Rivas, Nerea Gorria, Arrate Pereda, Blanca Gener, Laura Garcia-Naveda and Guiomar Perez de Nanclares
    Citation: BMC Medical Genomics 2018 11:124
    Content type: Case report Published on:

  12. The etiology of more than half of all patients with X-linked intellectual disability remains elusive, despite array-based comparative genomic hybridization, whole exome or genome sequencing. Since short read m...

    Authors: Alena Zablotskaya, Hilde Van Esch, Kevin J. Verstrepen, Guy Froyen and Joris R. Vermeesch
    Citation: BMC Medical Genomics 2018 11:123
    Content type: Research article Published on:

  13. Chromosome translocations are a hallmark of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Additional genomic aberrations are also crucial in both BCP-ALL leukemogenesis and treatment management. Her...

    Authors: Thayana Conceição Barbosa, Bruno Almeida Lopes, Caroline Barbieri Blunck, Marcela Braga Mansur, Adriana Vanessa Santini Deyl, Mariana Emerenciano and Maria S. Pombo-de-Oliveira
    Citation: BMC Medical Genomics 2018 11:122
    Content type: Case report Published on:

  14. Biliary atresia (BA), a fibrosing disorder of the developing biliary tract leading to liver failure in infancy, has an elevated incidence in indigenous New Zealand (NZ) Māori. We investigated a high rate of BA...

    Authors: Sophia R. Cameron-Christie, Justin Wilde, Andrew Gray, Rick Tankard, Melanie Bahlo, David Markie, Helen M. Evans and Stephen P. Robertson
    Citation: BMC Medical Genomics 2018 11:121
    Content type: Research article Published on:

  15. Non-alcoholic fatty liver disease (NAFLD) is a major health burden in need for new medication. To identify potential drug targets a genomic study was performed in lipid-laden primary human hepatocyte (PHH) and...

    Authors: Stephanie Breher-Esch, Nishika Sahini, Anna Trincone, Christin Wallstab and Jürgen Borlak
    Citation: BMC Medical Genomics 2018 11:111
    Content type: Research article Published on:

  16. Large-scale “omics” datasets have not been leveraged and integrated with functional analyses to discover potential drivers of cardiomyopathy. This study addresses the knowledge gap.

    Authors: Nzali V. Campbell, David A. Weitzenkamp, Ian L. Campbell, Ronald F. Schmidt, Chindo Hicks, Michael J. Morgan, David C. Irwin and John J. Tentler
    Citation: BMC Medical Genomics 2018 11:110
    Content type: Research article Published on:

  17. Myocardial infarction (MI) is a multifactorial disease with complex pathogenesis, mainly the result of the interplay of genetic and environmental risk factors. The regulation of thrombosis, inflammation and ch...

    Authors: Panagiota Kontou, Athanasia Pavlopoulou, Georgia Braliou, Spyridoula Bogiatzi, Niki Dimou, Sripal Bangalore and Pantelis Bagos
    Citation: BMC Medical Genomics 2018 11:109
    Content type: Research article Published on:

  18. Molecular analyses such as whole-genome sequencing have become routine and are expected to be transformational for future healthcare and lifestyle decisions. Population-wide implementation of such analyses is,...

    Authors:
    Citation: BMC Medical Genomics 2018 11:108
    Content type: Research article Published on:

    The Data Descriptor to this article has been published in Scientific Data 2019 6:257

  19. Non-small cell lung cancer (NSCLC) represents more than about 80% of the lung cancer. The early stages of NSCLC can be treated with complete resection with a good prognosis. However, most cases are detected at...

    Authors: Dan Li, William Yang, Yifan Zhang, Jack Y Yang, Renchu Guan, Dong Xu and Mary Qu Yang
    Citation: BMC Medical Genomics 2018 11(Suppl 5):106
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  20. Human Down syndrome (DS) is usually caused by genomic micro-duplications and dosage imbalances of human chromosome 21. It is associated with many genomic and phenotype abnormalities. Even though human DS occur...

    Authors: Bing Feng, William Hoskins, Yan Zhang, Zibo Meng, David C. Samuels, Jiandong Wang, Ruofan Xia, Chao Liu, Jijun Tang and Yan Guo
    Citation: BMC Medical Genomics 2018 11(Suppl 5):105
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  21. Breast cancer is the most common type of invasive cancer in woman. It accounts for approximately 18% of all cancer deaths worldwide. It is well known that somatic mutation plays an essential role in cancer dev...

    Authors: Yifan Zhang, William Yang, Dan Li, Jack Y Yang, Renchu Guan and Mary Qu Yang
    Citation: BMC Medical Genomics 2018 11(Suppl 5):104
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  22. A protein family has similar and diverse functions locally conserved. An aligned pattern cluster (APC) can reflect the conserved functionality. Discovering aligned residue associations (ARAs) in APCs can revea...

    Authors: Pei-Yuan Zhou, Antonio Sze-To and Andrew K. C. Wong
    Citation: BMC Medical Genomics 2018 11(Suppl 5):103
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  23. The right dataset is essential to obtain the right insights in data science; therefore, it is important for data scientists to have a good understanding of the availability of relevant datasets as well as the ...

    Authors: Jingyi Shi, Mingna Zheng, Lixia Yao and Yaorong Ge
    Citation: BMC Medical Genomics 2018 11(Suppl 5):102
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  24. Miniature inverted-repeat transposable element (MITE) is a type of class II non-autonomous transposable element playing a crucial role in the process of evolution in biology. There is an urgent need to develop...

    Authors: Jialu Hu, Yan Zheng and Xuequn Shang
    Citation: BMC Medical Genomics 2018 11(Suppl 5):101
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  25. The clinical decision support system can effectively break the limitations of doctors’ knowledge and reduce the possibility of misdiagnosis to enhance health care. The traditional genetic data storage and anal...

    Authors: Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Chao Wang and Xuehai Zhou
    Citation: BMC Medical Genomics 2018 11(Suppl 5):100
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  26. With the development of sequencing technology, more and more long non-coding RNAs (lncRNAs) have been identified. Some lncRNAs have been confirmed that they play an important role in the process of development...

    Authors: Jingpu Zhang, shuai Zou and Lei Deng
    Citation: BMC Medical Genomics 2018 11(Suppl 5):99
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  27. While continental level ancestry is relatively simple using genomic information, distinguishing between individuals from closely associated sub-populations (e.g., from the same continent) is still a difficult ...

    Authors: Tanjin T. Toma, Jeremy M. Dawson and Donald A. Adjeroh
    Citation: BMC Medical Genomics 2018 11(Suppl 5):0
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  28. The integration of high-quality, genome-wide analyses offers a robust approach to elucidating genetic factors involved in complex human diseases. Even though several methods exist to integrate heterogeneous om...

    Authors: Haley R. Eidem, Jacob L. Steenwyk, Jennifer H. Wisecaver, John A. Capra, Patrick Abbot and Antonis Rokas
    Citation: BMC Medical Genomics 2018 11:107
    Content type: Technical advance Published on:

  29. Recent large-scale cancer sequencing studies have discovered many novel cancer driver genes (CDGs) in human cancers. Some studies also suggest that CDG mutations contribute to cancer-associated epigenomic and ...

    Authors: Ahrim Youn, Kyung In Kim, Raul Rabadan, Benjamin Tycko, Yufeng Shen and Shuang Wang
    Citation: BMC Medical Genomics 2018 11:98
    Content type: Research article Published on:

  30. BAP1 is a histone deubiquitinase that acts as a tumor and metastasis suppressor associated with disease progression in human cancer. We have used the “Calling Card System” of transposase-directed transposon in...

    Authors: Matthew Yen, Zongtai Qi, Xuhua Chen, John A. Cooper, Robi D. Mitra and Michael D. Onken
    Citation: BMC Medical Genomics 2018 11:97
    Content type: Research article Published on:

  31. Glioblastoma multiforme, the most prevalent and aggressive brain tumour, has a poor prognosis. The molecular mechanisms underlying gliomagenesis remain poorly understood. Therefore, molecular research, includi...

    Authors: Pengfei Xu, Jian Yang, Junhui Liu, Xue Yang, Jianming Liao, Fanen Yuan, Yang Xu, Baohui Liu and Qianxue Chen
    Citation: BMC Medical Genomics 2018 11:96
    Content type: Research article Published on:

  32. Nucleotide Excision Repair (NER) is a major pathway of mammalian DNA repair that is associated with drug resistance and has not been well characterized in acute lymphoblastic leukemia (ALL). The objective of t...

    Authors: Omar M. Ibrahim, Homood M. As Sobeai, Stephen G. Grant and Jean J. Latimer
    Citation: BMC Medical Genomics 2018 11:95
    Content type: Database Published on:

  34. Whole-exome sequencing (WES) has become an invaluable tool for genetic diagnosis in paediatrics. However, it has not been widely adopted in the prenatal setting. This study evaluated the use of WES in prenatal...

    Authors: Gordon K C Leung, Christopher C Y Mak, Jasmine L F Fung, Wilfred H S Wong, Mandy H Y Tsang, Mullin H C Yu, Steven L C Pei, K S Yeung, Gary T K Mok, C P Lee, Amelia P W Hui, Mary H Y Tang, Kelvin Y K Chan, Anthony P Y Liu, Wanling Yang, P C Sham…
    Citation: BMC Medical Genomics 2018 11:93
    Content type: Research article Published on:

  35. Verheij syndrome is a rare microdeletion syndrome of chromosome 8q24.3 that harbors PUF60, SCRIB, and NRBP2 genes. Subsequently, loss of function mutations in PUF60 have been found in children with clinical featu...

    Authors: Qiong Xu, Chun-yang Li, Yi Wang, Hui-ping Li, Bing-bing Wu, Yong-hui Jiang and Xiu Xu
    Citation: BMC Medical Genomics 2018 11:92
    Content type: Case report Published on:

  36. Detection of copy number variants (CNVs) is an important aspect of clinical testing for several disorders, including Duchenne muscular dystrophy, and is often performed using multiplex ligation-dependent probe...

    Authors: Velina Kozareva, Clayton Stroff, Maxwell Silver, Jonathan F. Freidin and Nigel F. Delaney
    Citation: BMC Medical Genomics 2018 11:91
    Content type: Technical advance Published on:

  37. Noninvasive prenatal screening (NIPS) of common aneuploidies using cell-free DNA from maternal plasma is part of routine prenatal care and is widely used in both high-risk and low-risk patient populations. Hig...

    Authors: Kristjan Eerik Kaseniit, Gregory J Hogan, Kevin M D’Auria, Carrie Haverty and Dale Muzzey
    Citation: BMC Medical Genomics 2018 11:90
    Content type: Research article Published on:

  39. Logistic regression is a popular technique used in machine learning to construct classification models. Since the construction of such models is based on computing with large datasets, it is an appealing idea ...

    Authors: Charlotte Bonte and Frederik Vercauteren
    Citation: BMC Medical Genomics 2018 11(Suppl 4):86
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  41. Practical applications for data analysis may require combining multiple databases belonging to different owners, such as health centers. The analysis should be performed without violating privacy of neither th...

    Authors: Peeter Laud and Alisa Pankova
    Citation: BMC Medical Genomics 2018 11(Suppl 4):84
    Content type: Technical advance Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  42. Security concerns have been raised since big data became a prominent tool in data analysis. For instance, many machine learning algorithms aim to generate prediction models using training data which contain se...

    Authors: Andrey Kim, Yongsoo Song, Miran Kim, Keewoo Lee and Jung Hee Cheon
    Citation: BMC Medical Genomics 2018 11(Suppl 4):83
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  43. One of the 3 tracks of iDASH Privacy & Security Workshop 2017 competition was to execute a whole genome variants search on private genomic data. Particularly, the search application was to find the top most si...

    Authors: Sergiu Carpov and Thibaud Tortech
    Citation: BMC Medical Genomics 2018 11(Suppl 4):82
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  44. One of the tasks in the 2017 iDASH secure genome analysis competition was to enable training of logistic regression models over encrypted genomic data. More precisely, given a list of approximately 1500 patien...

    Authors: Hao Chen, Ran Gilad-Bachrach, Kyoohyung Han, Zhicong Huang, Amir Jalali, Kim Laine and Kristin Lauter
    Citation: BMC Medical Genomics 2018 11(Suppl 4):81
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  45. Bladder cancer has numerous genomic features that are potentially actionable by targeted agents. Nevertheless, both pre-clinical and clinical research using molecular targeted agents have been very limited in ...

    Authors: Adnan Ahmad Ansari, Inkeun Park, Inki Kim, Sojung Park, Sung-Min Ahn and Jae-lyun Lee
    Citation: BMC Medical Genomics 2018 11:88
    Content type: Database Published on:

  46. Mutations occurring in the orthodenticle homeobox 2 gene (OTX2) are responsible for a rare genetic syndrome, characterized mainly by microphthalmia/anophthalmia associated with extra-ocular defects such as brain ...

    Authors: Anna Pichiecchio, Giovanni Vitale, Camilla Caporali, Cecilia Parazzini, Donatella Milani, Maria Paola Recalcati, Laura D’Amico, Sabrina Signorini, Umberto Balottin and Stefano Bastianello
    Citation: BMC Medical Genomics 2018 11:87
    Content type: Case report Published on:

  47. The transition from ductal carcinoma in situ (DCIS) to invasive breast carcinoma (IBC) is an important step during breast carcinogenesis. Understanding its molecular changes may help to identify high-risk DCIS...

    Authors: Silke Schultz, Harald Bartsch, Karl Sotlar, Karina Petat-Dutter, Michael Bonin, Steffen Kahlert, Nadia Harbeck, Ulrich Vogel, Harald Seeger, Tanja Fehm and Hans J. Neubauer
    Citation: BMC Medical Genomics 2018 11:80
    Content type: Research article Published on:

  48. Alzheimer’s disease (AD) is one of the most common neurodegenerative diseases that causes problems related to brain function. To some extent it is understood on a molecular level how AD arises, however there a...

    Authors: Jason E. Miller, Manu K. Shivakumar, Younghee Lee, Seonggyun Han, Emrin Horgousluoglu, Shannon L. Risacher, Andrew J. Saykin, Kwangsik Nho and Dokyoon Kim
    Citation: BMC Medical Genomics 2018 11(Suppl 3):76
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 3

  49. Understanding the effect of human genetic variations on disease can provide insight into phenotype-genotype relationships, and has great potential for improving the effectiveness of personalized medicine. Whil...

    Authors: Ann G. Cirincione, Kaylyn L. Clark and Maricel G. Kann
    Citation: BMC Medical Genomics 2018 11(Suppl 3):75
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 3

  50. RNA-seq is the most commonly used sequencing application. Not only does it measure gene expression but it is also an excellent media to detect important structural variants such as single nucleotide variants (...

    Authors: Naresh Prodduturi, Aditya Bhagwate, Jean-Pierre A. Kocher and Zhifu Sun
    Citation: BMC Medical Genomics 2018 11(Suppl 3):67
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 3

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