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  1. Content type: Research

    In this paper, we consider the problem of learning the genetic interaction map, i.e., the topology of a directed acyclic graph (DAG) of genetic interactions from noisy double-knockout (DK) data. Based on a set...

    Authors: Fabio Nikolay, Marius Pesavento, George Kritikos and Nassos Typas

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2017 2017:10

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  2. Content type: Research

    This paper addresses the question of biomarker discovery in proteomics. Given clinical data regarding a list of proteins for a set of individuals, the tackled problem is to extract a short subset of proteins t...

    Authors: Noura Dridi, Audrey Giremus, Jean-Francois Giovannelli, Caroline Truntzer, Melita Hadzagic, Jean-Philippe Charrier, Laurent Gerfault, Patrick Ducoroy, Bruno Lacroix, Pierre Grangeat and Pascal Roy

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2017 2017:9

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  3. Content type: Review

    Stochastic hybrid systems (SHS) have attracted a lot of research interests in recent years. In this paper, we review some of the recent applications of SHS to biological systems modeling and analysis. Due to t...

    Authors: Xiangfang Li, Oluwaseyi Omotere, Lijun Qian and Edward R. Dougherty

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2017 2017:8

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  4. Content type: Research

    Tagging biomedical entities such as gene, protein, cell, and cell-line is the first step and an important pre-requisite in biomedical literature mining. In this paper, we describe our hybrid named entity taggi...

    Authors: Gurusamy Murugesan, Sabenabanu Abdulkadhar, Balu Bhasuran and Jeyakumar Natarajan

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2017 2017:7

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  5. Content type: Review

    The reductionist approach of dissecting biological systems into their constituents has been successful in the first stage of the molecular biology to elucidate the chemical basis of several biological processe...

    Authors: Danila Vella, Italo Zoppis, Giancarlo Mauri, Pierluigi Mauri and Dario Di Silvestre

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2017 2017:6

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  6. Content type: Research

    Electrocardiogram is a slow signal to acquire, and it is prone to noise. It can be inconvenient to collect large number of ECG heartbeats in order to train a reliable biometric system; hence, this issue might ...

    Authors: Wael Louis, Shahad Abdulnour, Sahar Javaher Haghighi and Dimitrios Hatzinakos

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2017 2017:5

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  7. Content type: Research

    Autism spectrum disorder (ASD) is a developmental disorder that significantly impairs patients’ ability to perform normal social interaction and communication. Moreover, the diagnosis procedure of ASD is highl...

    Authors: Jianbo Yuan, Chester Holtz, Tristram Smith and Jiebo Luo

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2017 2017:3

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  8. Content type: Research

    Gene expression time series data are usually in the form of high-dimensional arrays. Unfortunately, the data may sometimes contain missing values: for either the expression values of some genes at some time po...

    Authors: Oyetunji E. Ogundijo, Abdulkadir Elmas and Xiaodong Wang

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2017 2017:2

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  9. Content type: Research

    Methods based on correlation and partial correlation are today employed in the reconstruction of a statistical interaction graph from high-throughput omics data. These dedicated methods work well even for the ...

    Authors: Nurgazy Sulaimanov and Heinz Koeppl

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2016 2016:19

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  10. Content type: Research

    Online community-based health services accumulate a huge amount of unstructured health question answering (QA) records at a continuously increasing pace. The ability to organize these health QA records has bee...

    Authors: Mohammad Akbari, Xia Hu, Liqiang Nie and Tat-Seng Chua

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2016 2016:18

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  11. Content type: Research

    Identifying the residues in a protein that are involved in protein-protein interaction and identifying the contact matrix for a pair of interacting proteins are two computational tasks at different levels of a...

    Authors: Tianchuan Du, Li Liao and Cathy H. Wu

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2016 2016:17

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  12. Content type: Research

    The rapidly expanding corpus of medical research literature presents major challenges in the understanding of previous work, the extraction of maximum information from collected data, and the identification of...

    Authors: Victor Andrei and Ognjen Arandjelović

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2016 2016:16

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  13. Content type: Research

    Principal component analysis (PCA) is a dimensionality reduction and data analysis tool commonly used in many areas. The main idea of PCA is to represent high-dimensional data with a few representative compone...

    Authors: Inci M. Baytas, Kaixiang Lin, Fei Wang, Anil K. Jain and Jiayu Zhou

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2016 2016:15

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  14. Content type: Research

    Prediabetes is a major epidemic and is associated with adverse cardio-cerebrovascular outcomes. Early identification of patients who will develop rapid progression of atherosclerosis could be beneficial for im...

    Authors: Xia Hu, Peter D. Reaven, Aramesh Saremi, Ninghao Liu, Mohammad Ali Abbasi, Huan Liu and Raymond Q. Migrino

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2016 2016:14

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  15. Content type: Research

    Recent years have witnessed an increasing interest in the application of machine learning to clinical informatics and healthcare systems. A significant amount of research has been done on healthcare systems ba...

    Authors: Kuan Wang and Jiebo Luo

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2016 2016:13

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  16. Content type: Research

    By 2050, it is estimated that the number of worldwide Alzheimer’s disease (AD) patients will quadruple from the current number of 36 million, while no proven disease-modifying treatments are available. At pres...

    Authors: Yan Jin, Yi Su, Xiao-Hua Zhou and Shuai Huang

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2016 2016:12

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  17. Content type: Research

    Simulation study in systems biology involving computational experiments dealing with Wnt signaling pathways abound in literature but often lack a pedagogical perspective that might ease the understanding of be...

    Authors: Shriprakash Sinha

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2016 2017:1

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  18. Content type: Research

    Event-related potentials (ERPs) are widely used in brain-computer interface applications and in neuroscience.  Normal EEG activity is rich in background noise, and therefore, in order to detect ERPs, it is usu...

    Authors: William Giroldini, Luciano Pederzoli, Marco Bilucaglia, Simone Melloni and Patrizio Tressoldi

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2016 2016:11

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  19. Content type: Research

    Viral evolution remains to be a main obstacle in the effectiveness of antiviral treatments. The ability to predict this evolution will help in the early detection of drug-resistant strains and will potentially...

    Authors: Mostafa A. Salama, Aboul Ella Hassanien and Ahmad Mostafa

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2016 2016:10

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  20. Content type: Research

    With increasingly “big” data available in biomedical research, deriving accurate and reproducible biology knowledge from such big data imposes enormous computational challenges. In this paper, motivated by rec...

    Authors: Yijie Wang and Xiaoning Qian

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2016 2016:9

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  21. Content type: Research

    RNA interference (RNAi) screening is extensively used in the field of reverse genetics. RNAi libraries constructed using random oligonucleotides have made this technology affordable. However, the new methodolo...

    Authors: Kenta Kamatuka, Masahiro Hattori and Tomoyasu Sugiyama

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2016 2016:7

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  22. Content type: Research

    Tumor size, as indicated by the T-category, is known as a strong prognostic indicator for breast cancer. It is common practice to distinguish the T1 and T2 groups at a tumor size of 2.0 cm. We investigated the...

    Authors: Hiroko K. Solvang, Arnoldo Frigessi, Fateme Kaveh, Margit L. H. Riis, Torben Lüders, Ida R. K. Bukholm, Vessela N. Kristensen and Bettina K. Andreassen

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2016 2016:6

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  23. Content type: Research

    Module identification has been studied extensively in order to gain deeper understanding of complex systems, such as social networks as well as biological networks. Modules are often defined as groups of verti...

    Authors: Siamak Zamani Dadaneh and Xiaoning Qian

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2016 2016:5

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  24. Content type: Research

    Ever since the introduction of the Watson-Crick model, numerous efforts have been made to fully characterize the digital information content of the DNA. However, it became increasingly evident that variations ...

    Authors: Dawit Nigatu, Werner Henkel, Patrick Sobetzko and Georgi Muskhelishvili

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2016 2016:4

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  25. Content type: Research

    The toxicity and efficacy of more than 30 anticancer agents present very high variations, depending on the dosing time. Therefore, the biologists studying the circadian rhythm require a very precise method for...

    Authors: Mircea Dumitru, Ali Mohammad-Djafari and Simona Baghai Sain

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2016 2016:3

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  26. Content type: Research

    In classification, prior knowledge is incorporated in a Bayesian framework by assuming that the feature-label distribution belongs to an uncertainty class of feature-label distributions governed by a prior dis...

    Authors: Amin Zollanvari and Edward R. Dougherty

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2016 2016:2

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  27. Content type: Research

    The discrete coefficient of determination (CoD) measures the nonlinear interaction between discrete predictor and target variables and has had far-reaching applications in Genomic Signal Processing. Previous w...

    Authors: Ting Chen and Ulisses M. Braga-Neto

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2016 2016:1

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  28. Content type: Research

    Leishmania devices its survival strategy by suppressing the host’s immune functions. The antigen molecules produced by Leishmania interferes with the host’s cell signaling cascades and co...

    Authors: Piyali Ganguli, Saikat Chowdhury, Shomeek Chowdhury and Ram Rup Sarkar

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2015 2015:13

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  29. Content type: Research

    Study of signaling networks is important for a better understanding of cell behaviors e.g., growth, differentiation, metabolism, proptosis, and gaining deeper insights into the molecular mechanisms of complex ...

    Authors: Lipi Acharya, Robert Reynolds and Dongxiao Zhu

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2015 2015:12

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  30. Content type: Research

    Biological networks inherently have uncertain topologies. This arises from many factors. For instance, interactions between molecules may or may not take place under varying conditions. Genetic or epigenetic m...

    Authors: Haitham Gabr, Juan Carlos Rivera-Mulia, David M. Gilbert and Tamer Kahveci

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2015 2015:10

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  31. Content type: Research

    Boolean networks are an important class of computational models for molecular interaction networks. Boolean canalization, a type of hierarchical clustering of the inputs of a Boolean function, has been extensi...

    Authors: David Murrugarra and Elena S. Dimitrova

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2015 2015:9

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  32. Content type: Research

    Network-based analyses are commonly used as powerful tools to interpret the findings of genome-wide association studies (GWAS) in a functional context. In particular, identification of disease-associated funct...

    Authors: Marzieh Ayati, Sinan Erten, Mark R. Chance and Mehmet Koyutürk

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2015 2015:7

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  33. Content type: Research

    Bayesian networks have become popular for modeling probabilistic relationships between entities. As their structure can also be given a causal interpretation about the studied system, they can be used to learn...

    Authors: Antti Larjo and Harri Lähdesmäki

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2015 2015:6

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  34. Content type: Research

    Soybean (Glycine max) is a major source of vegetable oil and protein for both animal and human consumption. The completion of soybean genome sequence led to a number of transcriptomic studies (RNA-seq), which pro...

    Authors: Jie Hou, Gary Stacey and Jianlin Cheng

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2015 2015:5

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  35. Content type: Review

    Recent findings have elucidated that the regulation of messenger RNA (mRNA) levels is due to the synergistic and antagonist actions of transcription factors (TFs) and microRNAs (miRNAs). Mutual interactions am...

    Authors: Pietro H Guzzi, Maria Teresa Di Martino, Pierosandro Tagliaferri, Pierfrancesco Tassone and Mario Cannataro

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2015 2015:4

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  36. Content type: Review

    Biological network alignment aims to find regions of topological and functional (dis)similarities between molecular networks of different species. Then, network alignment can guide the transfer of biological k...

    Authors: Fazle E Faisal, Lei Meng, Joseph Crawford and Tijana Milenković

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2015 2015:3

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  37. Content type: Research

    This paper presents a fusion-based neural network (NN) classification algorithm for 40-Hz auditory steady state response (ASSR) ensemble averaged signals which were recorded from eight human subjects for obser...

    Authors: Gulzar A Khuwaja, Sahar Javaher Haghighi and Dimitrios Hatzinakos

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2015 2015:2

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  38. Content type: Research

    Typically, a vast amount of experience and data is needed to successfully determine cancer prognosis in the face of (1) the inherent stochasticity of cell dynamics, (2) incomplete knowledge of healthy cell reg...

    Authors: Mohammadmahdi R Yousefi and Lori A Dalton

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2015 2015:1

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  39. Content type: Research

    Discovery and validation of protein biomarkers with high specificity is the main challenge of current proteomics studies. Different mass spectrometry models are used as shotgun tools for the discovery of bioma...

    Authors: Esmaeil Atashpaz-Gargari, Ulisses M Braga-Neto and Edward R Dougherty

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:17

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  40. Content type: Research

    Accurate prediction of cancer prognosis based on gene expression data is generally difficult, and identifying robust prognostic markers for cancer remains a challenging problem. Recent studies have shown that ...

    Authors: Navadon Khunlertgit and Byung-Jun Yoon

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:19

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  41. Content type: Research

    The waveforms of the pupillary light reflex (PLR) can be analyzed in a diagnostic test that allows for differentiation between disorders affecting photoreceptors and disorders affecting retinal ganglion cells,...

    Authors: Minoru Nakayama, Wioletta Nowak, Hitoshi Ishikawa, Ken Asakawa and Yoshiaki Ichibe

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:18

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  42. Content type: Research

    Convex bootstrap error estimation is a popular tool for classifier error estimation in gene expression studies. A basic question is how to determine the weight for the convex combination between the basic boot...

    Authors: Thang Vu, Chao Sima, Ulisses M Braga-Neto and Edward R Dougherty

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:15

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  43. Content type: Research

    Drugs that target specific proteins are a major paradigm in cancer research. In this article, we extend a modeling framework for drug sensitivity prediction and combination therapy design based on drug perturb...

    Authors: Noah Berlow, Lara Davis, Charles Keller and Ranadip Pal

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:14

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  44. Content type: Research

    Challenging tasks are encountered in the field of bioinformatics. The choice of the genomic sequence’s mapping technique is one the most fastidious tasks. It shows that a judicious choice would serve in examin...

    Authors: Imen Messaoudi, Afef Elloumi Oueslati and Zied Lachiri

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:16

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  45. Content type: Research

    The Dialogue for Reverse Engineering Assessments and Methods (DREAM) project was initiated in 2006 as a community-wide effort for the development of network inference challenges for rigorous assessment of reve...

    Authors: Peng Li, Ping Gong, Haoni Li, Edward J Perkins, Nan Wang and Chaoyang Zhang

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:12

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