研究生生物信息學(xué)考試題目

1Bioinformatics examination1. Final examination schedule: 09/12/2014-7/01/2015, four weeks.2. Choose any ONE of the five proposed questions, and write a report on design andimplementation3. Report sectionsa) Title page: title and personal information (including your name, student ID#,major, the class number, and contact information).b) Abstract: 250 words; Keywords: 3-5 wordsc) Introduction: 2-3 paragraphsd) Design and Implementation: at least include a flowcharte) References: please refer to the format of Bioinformatics.4. Requirementsa) Total words: 2000-2500 words (not include reference)b) If you choose the template of Bioinformatics (either word or LaTex), pleasedisregard the format requirements below.c) Format requirements: Font size: Arial, 12 (宋體，5 號); Line spacing, double; andParagraph after, 6pt5. Scoresa) Fail: if the duplication rate 30 % in any two of reports, two would be consideredas plagiarization (score: 0). Never plagiarize your report.b) Bonus: +10 if written in English, please make sure that it is readable; and +10 ifLaTex usedc) Bonus: -10 if absent one time; and -20 if absent two times6. Please send your report in both the paper and electronic versions NO LATER THAN7/01/2015. The signed paper should be deposited to the Molecular Genetics Lab atthe 3rd floors, East building, and the compressedelectronic file should be sent to Mr.XXX at XXXX126.com1Question #1RNA editing is one of the post- or co-transcriptional processes with modification of RNAnucleotides from their genome-encoded sequence. In humans, the most prevalent type of RNAediting is mediated by double-strand RNA (dsRNA)-specific adenosine deaminase acting onRNA (ADAR) enzymes, which converts adenosines to inosines (A to I editing). Since I isinterpreted as guanosine (G) during splicing and translation, A to I changes in protein-codingsequences may lead to codon changes, and thus alter functional properties of the proteins. RNAediting has been linked to a wide range of human diseases, including cancer, neurologicaldisorders, metabolic diseases, viral infection, and autoimmune disorder.Suppose we aim to study the RNA editome for prostate cancer using next-generationsequencing technology. Suppose we have collected prostate cancer tissues and the adjacentnon-cancer tissues from 20 prostate patients, please design a pipeline to detect (or identify)RNA editing sites by comparing RNA-seq variants with its counterparts on the genome.2Question #2Suppose a family of four members was collected in clinical practice (fig. 1), including anaffected mother, an unaffected father, an affected offspring (daughter, founder), and anunaffected offspring. The affected family contains a series ofclinical features and had not been diagnosed with a knowndisease (i.e., an unidentified syndrome).Suppose we aim to study the genetic basis of thisfamily using the technology of whole-exome sequencing.Please design a study and pipeline to identify the causalmutations that may underline this unidentified syndrome.Fig.1.Pedigree.3Question #3The APOBEC3B gene is a member of the cytidine deaminase gene family, whichencodes proteins that are structurally and functionally related to the C to U RNA-editing cytidinedeaminase APOBEC1. It is thought that the proteins may be RNA editing enzymes and haveroles in growth or cell cycle control.Suppose we aim to perform a bioinformatics analysis on both the mRNA and proteinsequence of APOBEC3B. Please design a pipeline to download both sequences from onlinedatabase, analyze its promoter regions and transcription factor binding sites, and proteindomain. Furthermore, construct an atomic-resolution model of APOBEC1 from its amino acidsequence (i.e., the protein 3D structure) by homology modeling.Note: please include your results in the report (the Results Section) if it waschoose.4Question #4Electronic medical records (EMR) are a systematic collection of electronic healthinformation about an individual patient or population, which is stored in a digit format. Everythingrelated to a patients care were stored in the EMR, including demographic information, clinicalnotes, laboratory reports, and other accessory tests (e.g., CT, and X-ray).Suppose we aim to construct an EMR database system, please state the procedureshow to design and implement such a system. In addition, given the constructed databasecontaining 2,000 patients, who have consulted in the Division of Cardiovascular Diseases,please design a study to classify these patients with and without coronary heart disease (CHD)using natural language processing (NLP) and evaluate your classification procedures.5Question #5Gene expression profiling refers to the measurement of the expression of thousands ofgenes at once, which is used to create a global picture of cellular function at the levels oftranscriptome. The technologies of DNA microarray (analog) and transcriptome sequencing(RNA-seq, digital) have been used to measures