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Regulation of the SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE genes/microRNA 156 Module by the Homeodomain Proteins PENNYWISE and POUND-FOOLISH in Arabidopsis

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Molecular Plant 2011年第6期4卷 1123-1132页

作者： Shruti Lal Leo Bryan Pacis Harley M.S. Smith Genetics Genomics and Bioinformatics Graduate Program University of California Riverside CA 92521 USA Center for Plant Cell Biology Institute of Integrative Genome Biology Department of Botany and Plant Sciences University of California Riverside CA 92521 USA

The morphology of inflorescences is regulated in part by the temporal and spatial events that regulate flower specification. In Arabidopsis, an endogenous flowering time pathway mediated by a subset of SQUAMOSA PROMOTER- BINDING PROTEIN-LIKE （SPL） transcription factors, including SPL3, SPL4, and SPL5, function to specify flowers by activating floral meristem identity genes. During shoot development, SPL3, SPL4, and SPL5 are post-transcriptionally regulated by microRNA156 （miR156）. The photoperiod regulated florigenic signal, FLOWERING LOCUS T （FT）, promotes floral induction, in part by activating SPL3, SPL4, and SPL5. In turn, these SPLs function in parallel with FT to specify flower meristems. Two related BELLl-like homeobox genes PENNYWISE （PNY） and POUND-FOOLISH （PNF） expressed in the shoot apical meristem are absolutely required for the specification of floral meristems. Genetic studies show that the floral specification function of FT depends upon PNYand PNF; however, the interplay between these homeodomain proteins and SPLs is not known. In this manuscript, we show that the photoperiodic floral induction of SPL3, SPL4, and SPL5 is dependent upon PNY and PNE Further, PNY and PNF also control SPL3, SPL4, and SPL5 expression by negatively regulating miR156. Lastly, ectopic expres- sion of SPL4 partially rescues the pny pnf non-flower-producing phenotype, while overexpression of SPL3 or SPL5 in pny pnf plants was unable to restore flower specification. These results suggest that：（1） SPL3, SPL4, and SPL5 function is dependent upon PNY and PNF, or （2） expression of multiple SPLs is required for floral specification in pny pnf plants.

关键词： Development meristem homeodomain flowering microRNA.

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Comprehensive genomic profiling of the lung transcriptome in emphysema and idiopathic pulmonary fibrosis using RNA-Seq

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BMC Proc 2012年第SUPPL 6期6卷 P21-P21页

作者： Rebecca L Kusko John Brothers, II Gang Liu Lingqi Luo Brenda Juan Guardela John Tedrow Yuriy Aleksyev Ivana V Yang Mick Correll Mark Geraci John Quackenbush Frank Sciurba Marc Lenburg David A Schwartz Jennifer Beane Naftali Kaminski Avrum Spira Genetics and Genomics Graduate Program Boston University School of Medicine Boston MA USA Bioinformatics Program Boston University Boston MA USA Division of Computational Biomedicine Department of Medicine Boston University School of Medicine Boston MA USA Simmons Center for Interstitial Lung Disease and Department of Medicine University of Pittsburgh Medical Center Pittsburgh PA USA Department of Pathology and Laboratory Medicine Boston University School of Medicine Boston MA USA Center for Genes Environment and Health and Department of Medicine National Jewish Health Denver CO USA Dana-Farber Cancer Institute and Harvard School of Public Health Boston MA USA Department of Medicine University of Colorado School of Medicine Aurora CO USA

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Next generation sequencing for profiling expression of miRNAs: technical progress and applications in drug development

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Journal of Biomedical Science and Engineering 2011年第10期4卷 666-676页

作者： Jie Liu Steven F. Jennings Weida Tong Huixiao Hong University of Arkansas at Little Rock/University of Arkansas for Medical Sciences Bioinformatics Graduate Program Little Rock USA.

miRNAs are non-coding RNAs that play a regulatory role in expression of genes and are associated with diseases. Quantitatively measuring expression levels of miRNAs can help understanding the mechanisms of human diseases and discovering new drug targets. There are three major methods that have been used to measure the expression levels of miRNAs: real-time reverse transcription PCR (qRT-PCR), microarray, and the newly introduced next-generation sequencing (NGS). NGS is not only suitable for profiling of known miRNAs that qRT-PCR and microarray can do too but also able to detect unknown miRNAs that the other two methods are incapable. Profiling of miRNAs by NGS has been progressed rapidly and is a promising field for applications in drug development. This paper will review the technical advancement of NGS for profiling miRNAs, including comparative analyses between different platforms and software packages for analyzing NGS data. Examples and future perspectives of applications of NGS profiling miRNAs in drug development will be discussed.

关键词： MiRNAs Next-Generation Sequencing Expression Data Analysis Drug Development

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Moving beyond gene expression: identification of lung-disease-associated novel transcripts and alternative splicing by RNA sequencing

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BMC Proceedings 2012年第6期6卷 1-2页

作者： John Brothers II Paola Sebastiani Marc Lenburg Avrum Spira Rebecca Kusko Yuriy Alekesyev Gang Liu Lingqi Luo Jennifer Beane Brenda Juan Guardela John Tedrow Frank Sciurba Naftali Kaminski Ivana V Yang David A Schwartz Mick Correll John Quackenbush Mark Geraci Bioinformatics Program Boston University Boston MA 02115 USA Genetics and Genomics Graduate Program Boston University School of Medicine Boston MA 02118 USA Department of Medicine Boston University School of Medicine Section of Computational Biomedicine Boston MA 02118 USA Department of Pathology and Laboratory Medicine Boston University School of Medicine Boston MA 02118 USA Simmons Center for Interstitial Lung Disease and Department of Medicine University of Pittsburgh Medical Center Pittsburgh PA 15213 USA Center for Genes Environment and Health and Department of Medicine National Jewish Health Denver CO 80206 USA Dana-Farber Cancer Institute and Harvard School of Public Health Boston MA 02115 USA Department of Medicine University of Colorado School of Medicine Aurora CO 80045 USA

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Characterizing the small RNA transcriptome associated with COPD and ILD using next-generation sequencing

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BMC Proceedings 2012年第6期6卷 1-2页

作者： Joshua D Campbell Joseph Gerrein Marc E Lenburg Avrum Spira Lingqi Luo Gang Liu Ji Xiao Jennifer Beane Brenda J Guardela John Tedrow Frank Sciurba Naftali Kaminski Yuriy O Aleksyev Ivana V Yang David A Schwartz Mick Correll John Quackenbush Mark Geraci Bioinformatics Graduate Program Boston University Boston MA USA Section of Computational Biomedicine Boston University Boston MA USA Department of Pathology and Laboratory Medicine Boston University School of Medicine Boston MA USA Simmons Center for Interstitial Lung Disease and Department of Medicine University of Pittsburgh Medical Center Pittsburgh PA USA Center for Genes Environment and Health and Department of Medicine National Jewish Health Denver CO USA Dana-Farber Cancer Institute and Harvard School of Public Health Boston MA USA Department of Medicine University of Colorado School of Medicine Aurora CO USA

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Expression of G protein-coupled receptors and related proteins in HEK293, AtT20, BV2, and N18 cell lines as revealed by microarray analysis

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BMC Genomics 2011年第1期12卷 1-14页

作者： Atwood, Brady K. Lopez, Jacqueline Wager-Miller, James Mackie, Ken Straiker, Alex Department of Psychological and Brain Sciences The Gill Center for Biomolecular Science Indiana University Bloomington IN United States Center for Genomics and Bioinformatics Indiana University Bloomington IN United States Graduate Program in Neurobiology and Behavior University of Washington Seattle WA United States

Background: G protein coupled receptors (GPCRs) are one of the most widely studied gene superfamilies. Thousands of GPCR research studies have utilized heterologous expression systems such as human embryonic kidney cells (HEK293). Though often treated as 'blank slates', these cell lines nevertheless endogenously express GPCRs and related signaling proteins. The outcome of a given GPCR study can be profoundly influenced by this largely unknown complement of receptors and/or signaling proteins. Little easily accessible information exists that describes the expression profiles of the GPCRs in cell lines. What is accessible is often limited in scope - of the hundreds of GPCRs and related proteins, one is unlikely to find information on expression of more than a dozen proteins in a given cell line. Microarray technology has allowed rapid analysis of mRNA levels of thousands of candidate genes, but though often publicly available, the results can be difficult to efficiently access or even to ***: To bridge this gap, we have used microarrays to measure the mRNA levels of a comprehensive profile of non-chemosensory GPCRs and over a hundred GPCR signaling related gene products in four cell lines frequently used for GPCR research: HEK293, AtT20, BV2, and ***: This study provides researchers an easily accessible mRNA profile of the endogenous signaling repertoire that these four cell lines possess. This will assist in choosing the most appropriate cell line for studying GPCRs and related signaling proteins. It also provides a better understanding of the potential interactions between GPCRs and those signaling proteins. © 2011 Atwood et al;licensee BioMed Central Ltd.

关键词： HEK293 Cell AtT20 Cell GPCR Signaling Frizzle Receptor Related Signaling Protein

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A Bayesian model for SNP discovery based on next-generation sequencing data

A Bayesian model for SNP discovery based on next-generation ...

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IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)

作者： Yanxun Xu Xiaofeng Zheng Yuan Yuan Marcos R Estecio Jean-Pierre Issa Yuan Ji Shoudan Liang Department of Statistics Rice University Houston TX USA Department of Bioinformatics and Computational Biology University of Texas M.D. Anderson Cancer Center Houston TX USA Graduate Program in Structural and Computational Biology and Molecular Biophysics Baylor College of Medicine Houston TX USA Department of Biochemistry and Molecular Biology University of Texas M.D. Anderson Cancer Center Houston TX USA Fels Institute for Cancer Research and Molecular Biology Temple University Philadelphia PA USA CCRI NorthShore University HealthSystem Chicago IL USA

ISBN: (纸本)9781467352345

A single-nucleotide polymorphism (SNP) is a single base change in the DNA sequence and is the most common polymorphism. Since some SNPs have a major influence on disease susceptibility, detecting SNPs plays an important role in biomedical research. To take fully advantage of the next-generation sequencing (NGS) technology and detect SNP more effectively, we propose a Bayesian approach that computes a posterior probability of hidden nucleotide variations at each covered genomic position. The position with higher posterior probability of hidden nucleotide variation has a higher chance to be a SNP. We apply the proposed method to detect SNPs in two cell lines: the prostate cancer cell line PC3 and the embryonic stem cell line H1. A comparison between our results with dbSNP database shows a high ratio of overlap (≥95 %). The positions that are called only under our model but not in dbSNP may serve as candidates for new SNPs.

关键词： comparison candidates generation Single nucleotide polymorphism sequence number protection a posteriori probability DNA Sequence Bayesian inference Disease Susceptibility Analyses, Sequence

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Abstracts from the 3rd International Genomic Medicine Conference (3rd IGMC 2015) : Jeddah, Kingdom of Saudi Arabia. 30 November - 3 December 2015

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BMC genomics 2016年第6期17 Suppl 6卷 487页

作者： Jerry W. Shay Noriko Homma Ruyun Zhou Muhammad Imran Naseer Adeel G. Chaudhary Mohammed Al-Qahtani Nobutaka Hirokawa Maryam Goudarzi Albert J. Fornace Saleh Baeesa Deema Hussain Mohammed Bangash Fahad Alghamdi Hans-Juergen Schulten Angel Carracedo Ishaq Khan Hanadi Qashqari Nawal Madkhali Mohamad Saka Kulvinder S. Saini Awatif Jamal Jaudah Al-Maghrabi Adel Abuzenadah Adeel Chaudhary Mohammed Al Qahtani Ghazi Damanhouri Heba Alkhatabi Anne Goodeve Laura Crookes Nikolas Niksic Nicholas Beauchamp Adel M. Abuzenadah Jim Vaught Bruce Budowle Mourad Assidi Abdelbaset Buhmeida Leena Merdad Sudhir Kumar Sayaka Miura Karen Gomez Mahmood Rasool Ahmed Rebai Sajjad Karim Hend F. Nour Eldin Heba Abusamra Elham M. Alhathli Nada Salem Mohammed H. Al-Qahtani Hossam Faheem Ashok Agarwa Eberhard Nieschlag Joachim Wistuba Oliver S. Damm Mohd A. Beg Taha A. Abdel-Meguid Hisham A. Mosli Osama S. Bajouh Serdar Coskun Muhammad Abu-Elmagd Ashraf Dallol Sahar Hakamy Wejdan Al-Qahtani Asia Al-Harbi Shireen Hussain Burak Ozkosem Rick DuBois Safia S. Messaoudi Maryam T. Dandana Touhami Mahjoub Wassim Y. Almawi S. Abdalla M. Nabil Al-Aama Asmaa Elzawahry Tsuyoshi Takahashi Sachiyo Mimaki Eisaku Furukawa Rie Nakatsuka Isao Kurosaka Takahiko Nishigaki Hiromi Nakamura Satoshi Serada Tetsuji Naka Seiichi Hirota Tatsuhiro Shibata Katsuya Tsuchihara Toshirou Nishida Mamoru Kato Sajid Mehmood Naeem Mahmood Ashraf Awais Asif Muhammad Bilal Malik Siddique Mehmood Aadil Hussain Qazi Mohammad Sajid Jamal Mughees Uddin Siddiqui Mohammad A. Alzohairy Mohammad A. Al Karaawi Taoufik Nedjadi Heba Al-Khattabi Adel Al-Ammari Ahmed Al-Sayyad Hédia Zitouni Nozha Raguema Marwa Ben Ali Wided Malah Raja Lfalah Wassim Almawi Mohammed Elanbari Andrey Ptitsyn Sana Mahjoub Rabeb El Ghali Bechir Achour Nidhal Ben Amor Brahim N’siri Hamid Morjani Esam Azhar Vera Chayeb Maryam Dendena Hedia Zitouni Khedija Zouari-Limayem Bassem Refaat Ahmed M. Ashshi Sarah A. Batwa Hazem Ramadan Amal Awad Ahmed Ateya Adel Galal Ahmed El-Shemi Ahmad Ashshi Mohammed Basalamah Youjin Na Cha University of Texas Southwestern Medical Center Dallas USA Department of Cell Biology and Anatomy Graduate School of Medicine the University of Tokyo Tokyo Japan Center of Excellence in Genomic Medicine Research King Abdulaziz University Jeddah Saudi Arabia Department of Biochemistry and Molecular & Cellular Biology Lombardi Comprehensive Cancer Center Georgetown University Washington USA Department of Oncology Lombardi Comprehensive Cancer Center Georgetown University Washington USA Department of Radiation Medicine Lombardi Comprehensive Cancer Center Georgetown University Washington USA Center of Excellence in Genomic Medicine Research (CEGMR) King Abdulaziz University Jeddah Kingdom of Saudi Arabia King Fahd Medical Research Centre King Abdulaziz University Jeddah Saudi Arabia Centre of Excellence in Genomic Medicine Research King Abdulaziz University Jeddah Saudi Arabia Sheffield Diagnostic Genetic Service Sheffield Children’s NHS Foundation Trust Western Bank Sheffield UK Center of Innovations in Personalized Medicine King Abdulaziz University Jeddah Saudi Arabia President ISBER Editor-in-Chief Biopreservation & Biobanking ᅟ USA Institute of Applied Genetics Department of Molecular and Medical Genetics University of North Texas Health Science Center Fort Worth USA Department of Dental Public Health Faculty of Dentistry King Abdulaziz University Jeddah Saudi Arabia Institute for Genomics and Evolutionary Medicine Temple University Philadelphia USA Center of Excellence in Genomic Medicine King Abdulaziz University Jeddah Kingdom of Saudi Arabia Laboratory of Molecular and Cellular Screening Processes (Bioinformatics Group) Centre of Biotechnology of Sfax Sfax Tunisia Fujitsu Technology Solutions International ᅟ ᅟ Case Western Reserve University School of Medicine and Lerner College of Medicine Cleveland Clinic Foundation Cleveland USA American Center for Reproductive Medicine Andrology Center Cleveland USA Center for Reproductive Medicine and

O1 Regulation of genes by telomere length over long distances Jerry W. Shay O2 The microtubule destabilizer KIF2A regulates the postnatal establishment of neuronal circuits in addition to prenatal cell survival, cell migration, and axon elongation, and its loss leading to malformation of cortical development and severe epilepsy Noriko Homma, Ruyun Zhou, Muhammad Imran Naseer, Adeel G. Chaudhary, Mohammed Al-Qahtani, Nobutaka Hirokawa O3 Integration of metagenomics and metabolomics in gut microbiome research Maryam Goudarzi, Albert J. Fornace Jr. O4 A unique integrated system to discern pathogenesis of central nervous system tumors Saleh Baeesa, Deema Hussain, Mohammed Bangash, Fahad Alghamdi, Hans-Juergen Schulten, Angel Carracedo, Ishaq Khan, Hanadi Qashqari, Nawal Madkhali, Mohamad Saka, Kulvinder S. Saini, Awatif Jamal, Jaudah Al-Maghrabi, Adel Abuzenadah, Adeel Chaudhary, Mohammed Al Qahtani, Ghazi Damanhouri O5 RPL27A is a target of miR-595 and deficiency contributes to ribosomal dysgenesis Heba Alkhatabi O6 Next generation DNA sequencing panels for haemostatic and platelet disorders and for Fanconi anaemia in routine diagnostic service Anne Goodeve, Laura Crookes, Nikolas Niksic, Nicholas Beauchamp O7 Targeted sequencing panels and their utilization in personalized medicine Adel M. Abuzenadah O8 International biobanking in the era of precision medicine Jim Vaught O9 Biobank and biodata for clinical and forensic applications Bruce Budowle, Mourad Assidi, Abdelbaset Buhmeida O10 Tissue microarray technique: a powerful adjunct tool for molecular profiling of solid tumors Jaudah Al-Maghrabi O11 The CEGMR biobanking unit: achievements, challenges and future plans Abdelbaset Buhmeida, Mourad Assidi, Leena Merdad O12 Phylomedicine of tumors Sudhir Kumar, Sayaka Miura, Karen Gomez O13 Clinical implementation of pharmacogenomics for colorectal cancer treatment Angel Carracedo, Mahmood Rasool O14 From association to causality: translation of GWAS findings for genomic me

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Proceedings of the 3rd IPLeiria's International Health Congress Abstracts

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BMC HEALTH SERVICES RESEARCH 2016年第3期16卷 111-242页

作者： [Anonymous] Health Sciences Research Unit: Nursing Collegue of College of Health Technology of Coimbra Coimbra Portugal Sisters Hospitallers of the Sacred Heart of Jesus Casa de Saúde Rainha Santa Isabel Coimbra Portugal Research Unit for Sport and Physical Activity Faculty of Sport Sciences and Physical Education University of Coimbra Coimbra Portugal Complementary Sciences- INESCC Coimbra Portugal CUF Hospitals Lisbon Portugal Breast Unit Champalimaud Clinical Center Lisbon Portugal Swiss Centre for Medical Simulation & Swiss Association of Simulation in Healthcare Basel Switzerland Basel University Hospital Basel Switzerland HELPO Association Cascais Portugal Centro de Linguística Universidade de Lisboa Lisboa Portugal Centro Superior de Estudios Universitarios La Salle Madrid Spain Universidade da Madeira Funchal Portugal Serviço de Saúde da Região Autónoma da Madeira E.P.E. Funchal Portugal Escola Superior de Enfermagem de Lisboa Lisboa Portugal Instituto Superior Miguel Torga Coimbra Portugal Centro de Investigação do Núcleo de Estudos e Intervenção Cognitivo Comportamental Universidade de Coimbra Coimbra Portugal Escola Superior de Saúde de Leiria & Unidade de Investigação em Saúde Instituto Politécnico de Leiria Leiria Portugal National School of Public Health & Centro de Investigação em Saúde Pública Universidade Nova de Lisboa Lisboa Portugal Agrarian Superior School Polytechnic Institute of Viseu Viseu Portugal Laboratory of Microbiology Department of Biological Sciences Faculty of Pharmacy University of Porto Porto Portugal Unit for Multidisciplinary Biomedical Research Institute of Biomedical Sciences Abel Salazar University of Porto Porto Portugal Agrupamento de Centros de Saúde (ACES) Baixo Mondego Figueira da Foz Portugal Universidade de Trás-os-Montes e Alto Douro Vila Real Portugal Centro de Salud La Paz Badajoz España Centro de Salud San Fernando Badajoz España Complejo Hospitalario Universitario de Badajoz Badajoz España Hospital Don Beni

S1 Health literacy and health education in adolescence Catarina Cardoso Tomás S2 The effect of a walking program on the quality of life and well-being of people with schizophrenia Emanuel Oliveira, D. Sousa, M. Uba-Chupel, G. Furtado, C. Rocha, A. Teixeira, P. Ferreira S3 Diagnosis and innovative treatments - the way to a better medical practice Celeste Alves S4 Simulation-based learning and how it is a high contribution Stefan Gisin S5 Formative research about acceptability, utilization and promotion of a home fortification programme with micronutrient powders (MNP) in the Autonomous Region of Príncipe, São Tomé and Príncipe Elisabete Catarino, Nelma Carvalho, Tiago Coucelo, Luís Bonfim, Carina Silva S6 Safety culture of the patient: a reflexion about the therapeutic approach on the patient with vocal pathology Débora Franco S7 About wine, fortune cookies and patient experience Jesús Alcoba González O1 The psychological impact on the emergency crews after the disaster event on February 20, 2010 Helena G. Jardim, Rita Silva O2 Musculoskeletal disorders in midwives Cristina L. Baixinho, Mª Helena Presado, Mª Fátima Marques, Mário E. Cardoso O3 Negative childhood experiences and fears of compassion: Implications for psychological difficulties in adolescence Marina Cunha, Joana Mendes, Ana Xavier, Ana Galhardo, Margarida Couto O4 Optimal age to give the first dose of measles vaccine in Portugal João G. Frade, Carla Nunes, João R. Mesquita, Maria S. Nascimento, Guilherme Gonçalves O5 Functional assessment of elderly in primary care Conceição Castro, Alice Mártires, Mª João Monteiro, Conceição Rainho O6 Smoking and coronary events in a population of Spanish health-care centre: An observational study Francisco P. Caballero, Fatima M. Monago, Jose T. Guerrero, Rocio M. Monago, Africa P. Trigo, Milagros L. Gutierrez, Gemma M. Milanés, Mercedes G. Reina, Ana G. Villanueva, Ana S. Piñero, Isabel R. Aliseda, Francisco B. Ramirez O7 Prevalence of musculoskeletal injuries in Por

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Modularity detection in protein-protein interaction networks

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BMC Research Notes 2011年第1期4卷 1-6页

作者： Narayanan, Tejaswini Gersten, Merril Subramaniam, Shankar Grama, Ananth Department of Electrical and Computer Engineering University of California San Diego United States Graduate Program in Bioinformatics and Systems Biology University of California San Diego United States Department of Bioengineering University of California San Diego United States Department of Computer Science Purdue University West Lafayette IN United States

Background: Many recent studies have investigated modularity in biological networks, and its role in functional and structural characterization of constituent biomolecules. A technique that has shown considerable promise in the domain of modularity detection is the Newman and Girvan (NG) algorithm, which relies on the number of shortest-paths across pairs of vertices in the network traversing a given edge, referred to as the betweenness of that edge. The edge with the highest betweenness is iteratively eliminated from the network, with the betweenness of the remaining edges recalculated in every iteration. This generates a complete dendrogram, from which modules are extracted by applying a quality metric called modularity denoted by Q. This exhaustive computation can be prohibitively expensive for large networks such as Protein-Protein Interaction Networks. In this paper, we present a novel optimization to the modularity detection algorithm, in terms of an efficient termination criterion based on a target edge betweenness value, using which the process of iterative edge removal may be terminated. Results: We validate the robustness of our approach by applying our algorithm on real-world protein-protein interaction networks of Yeast, *** and Drosophila, and demonstrate that our algorithm consistently has significant computational gains in terms of reduced runtime, when compared to the NG algorithm. Furthermore, our algorithm produces modules comparable to those from the NG algorithm, qualitatively and quantitatively. We illustrate this using comparison metrics such as module distribution, module membership cardinality, modularity Q, and Jaccard Similarity Coefficient. Conclusions: We have presented an optimized approach for efficient modularity detection in networks. The intuition driving our approach is the extraction of holistic measures of centrality from graphs, which are representative of inherent modular structure of the underlying network, and the applic

关键词： Biological Network Jaccard Index Input Network High Betweenness Jaccard Similarity Coefficient

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