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University of Illinois, Urbana Champaign - ENGL - 481
engl 481assignment 8Short Annotation #3: RussellDue Date: Wenesday, April 12, In Class Format: One page, single spaced In the context of this course, the purposes of an annotation are multiple: to be descriptive enough so as to stand in for
University of Illinois, Urbana Champaign - ENGL - 481
engl 481assignment 6Short Annotation #2: Wiley, Wesley, WilliamsDue Date: Wednesday, March 29th, hard copy in class Format: One page, single spaced In the context of this course, the purposes of an annotation are multiple: to be descriptive
University of Illinois, Urbana Champaign - ENGL - 481
engl 481assignment 10Composition Theory and Practice Final ProjectDue Dates: Monday, April 24 Proposal Due (electronic submission before class) Wednesday, May 3 Completed Project Due (by 5:00 pm) Proposal: 1 page typed, single spaced, sketches
University of Illinois, Urbana Champaign - ENGL - 481
engl 481assignment 3Long Annotation #1: SircDue Dates: pp. 1-32, Monday, Jan. 30th, before class, electronic submissionpp. 33-67, Wednesday, Feb. 1, before class, electronic submission pp. 69-119, Monday, Feb. 6, before class, electronic submis
University of Illinois, Urbana Champaign - ENGL - 481
engl 481assignment 2Short Annotation #1: Lutz and DeemerDue Date: Friday, January 27th, In Class Format: One page, single spaced In the context of this course, the purposes of an annotation are multiple: to be descriptive enough so as to st
Cincinnati - LESSON - 8
C+ Programming Applied to Robotics, Mark Aull Lesson 8: Laser Measurement System lab activity The Sick Laser Measurement System is a method of detecting obstacles. It can operate in a few different operating modes, but I've always run it at the 1 ang
Cincinnati - LESSON - 1
C+ Programming Applied to Robotics, Mark Aull Lesson 1: Intro to Visual Studio, C+ file types C+ uses several file types. Source code, the human readable or high level language, is stored primarily in .cpp files, but also .h files. .cpp files contain
Cincinnati - EH - 3
Users Manual for the gimmR (Gaussian Infinite Mixture Model in R) packageSupport web page: http:/eh3.uc.edu/gimmOutline1. 2. 3. 4. 5. 6. Introduction Using the package Formatting data for simple model Analyzing data with replicates Using Context-
Cincinnati - EH - 3
Users Manual for the gimmR (Gaussian Infinite Mixture Model in R) packageOutline1. 2. 3. 4. 5. Introduction Using the package Formatting data for simple model Analyzing data with replicates Using Context-Specific Infinite Mixture Model (CSIMM)1.
Cincinnati - EH - 3
Users Manual for the gimmR package (Gaussian Innite Mixture Model in R)Mario Medvedovic, Vinayak Kumar September 28, 20061IntroductionThis package serves as the interface between the low level procedures for clustering gene expression data usi
Cincinnati - EH - 3
Examples of using gimmR package (Gaussian Innite Mixture Model in R)Mario Medvedovic, Vinayak Kumar September 29, 20061IntroductiongimmR serves as the interface for running low level procedures for clustering gene expression data using the Bay
Cincinnati - EH - 3
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Cincinnati - EH - 3
CLUSTERING MULTINOMIAL OBSERVATIONS VIA FINITE AND INFINITE MIXTURE MODELS AND MCMC ALGORITHMSMario Medvedovic, University of Cincinnati Medical Center Mario Medvedovic, Department of Environmental Health, University of Cincinnati Medical Center, 3
Cincinnati - EH - 3
DNA Microarrays and Computational Analysis of DNA Microarray Data in Cancer ResearchMario Medvedovic, Jonathan Wiest 1. 2. 3. Introduction Applications of microarrays Analysis of gene expression microarrays a. Data normalization b. Detecting differe
Cincinnati - EH - 3
Principal Investigator/Program Director (Last, First, Middle):BIOGRAPHICAL SKETCHProvide the following information for the key personnel and other significant contributors in the order listed on Form Page 2. Follow this format for each person. DO
Cincinnati - EH - 3
Breast Cancer Genomics Informaticshttp:/eh3.uc.edu/BreastCancerKaustubh Shinde1, Xiangdong Liu1,2, Maureen Sartor1, Prachi Kothiyal2, Mario Medvedovic1,21Department 2Divisionof Environmental Health, University of Cincinnati, 3223 Eden Avenue ML
Cincinnati - EH - 3
Original PapersLRpath: A logistic regression approach for identifying enriched biological groups in gene expression dataMaureen A Sartor1, George D. Leikauf2 and Mario Medvedovic3,4*1 2Center for Computational Medicine and Biology, University o
Cincinnati - EH - 3
Supplemental Information Bayesian context-specific infinite mixture model for clustering of gene expression profiles across diverse microarray datasetsXiangdong Liu, Siva Sivaganesan, Ka Yee Yeung, Junhai Guo, Roger Bumgarner, Mario Medvedovic* *Mar
Cincinnati - EH - 3
Clustering Mutational Spectra via Classi cation Likelihood and Markov Chain Monte Carlo AlgorithmsMario MEDVEDOVIC, Paul SUCCOP, Rakesh SHUKLA, and Kathleen DIXONWe have analyzed a set of 39 mutational spectra of the supF gene that were generated b
Cincinnati - EH - 3
Gene ExpressionContext-specific infinite mixtures for clustering gene expression profiles across diverse microarray datasetLiu, X.1,2, Sivaganesan, S.3, Yeung, K.Y.4, Guo, J.1, Bumgarner, R.E.4, MedvedovicMario1,2*Department of Environmental Heal
Cincinnati - EH - 3
1412qq q q q qexpns[controls, 1]q q10q q q q q q qq q q q q q q q q q q qq682468 Index101214
Cincinnati - EH - 3
N_noninf = 100, sd = 0.71.0 True Positive Rate 0.2 0.4 0.6 0.8contextselection Euclidean distance Pearson correlation 0.0 0.000.010.020.030.040.05False Positive RateN_noninf = 50, sd = 0.71.0 True Positive Rate 0.2 0.4 0.6 0.8cont
Cincinnati - EH - 3
Before subtracting batch effect01234BrControlE2ICIBefore subtracting batch effect1.5 0.0 0.5 1.0BrControlE2ICIAfter subtracting batch effect4 0 1 2 3BrControlE2ICIAfter subtracting batch effect1.5 0.0 0.5 1.
Cincinnati - EH - 3
sd = 0.31.0 True Positive Rate 0.2 0.4 0.6 0.8contextselection Euclidean distance Pearson correlation 0.0 0.000.010.020.030.040.05False Positive Ratesd = 0.41.0 True Positive Rate 0.2 0.4 0.6 0.8contextselection Euclidean distance
Cincinnati - EH - 3
01020304050Br_3 Control_2 Control_1 Control_3 Control_4 ICI_2 ICI_4 ICI_1 Br_2 Br_1 Br_4 ICI_3 E2_3 E2_2 E2_1 E2_4
Cincinnati - EH - 3
0.00.51.01.5sampleLFF1121.CEL HFS862 AIN1147.CEL LFF808.CEL LFS3780.CEL HFF848 LFF854 HFS1107.CEL LFO1106.CEL HFS861 FO1146.CEL LFO817.CEL HFS860 LFO319 HFF302 LFF3560.CEL HFS374.CEL LFO368.CEL LFS864 HFS322 LFS326 LFB3370 LFF853 LFF851 HFB
Cincinnati - EH - 3
Color Key2 1012Row ZScore5947_at 80176_at 220323_at 79827_at 1440_at 2744_at 6280_at 5266_at 7075_at 27286_at 4318_at 23136_at 26353_at 2633_at 5698_at 3569_at 57722_at 344887_at 6318_at 10950_at 624_at 339479_at 5793_at 1645_at 23648_at
Cincinnati - EH - 3
N_noninf = 100, sd = 0.31.0 True Positive Rate 0.2 0.4 0.6 0.8contextselection Euclidean distance Pearson correlation 0.0 0.000.010.020.030.040.05False Positive RateN_noninf = 100, sd = 0.41.0 True Positive Rate 0.2 0.4 0.6 0.8con
Cincinnati - EH - 12
Height 0.7 SAHA02.CEL Control5A1.CEL Control5A.CEL HDAC4204.CEL MS27501.CEL MS27501.CEL HDAC4204.CEL Control5A.CEL SAHA02.CEL Control5A1.CEL MS27501.CEL Control5A1.CEL Control5A.CEL SAHA02.CEL HDAC4204.CEL 0.8 1.05HeightHeightHeight 0.7 SAHA02.
Cincinnati - EH - 3
7632LP5622LP6631LP8641LP2591LP11522LP1531LP9511LP10521LP13651LP16R672 L4612LP3592LP12711LP14652LP15662LP LP1A.CEL LP1A.CEL LP1A.CEL LP1A.CEL LP1A.CEL LP2A.CEL LP1.CEL LP2A.CEL LP2A.CEL LP2A.CEL LP2A.CEL LP1A.CEL LP1A.CEL
Cincinnati - EH - 3
Fcnb5 0 1 2 3 41 Control2 E23 ICI4 BrSlfn38 0 2 4 61 Control2 E23 ICI4 BrPde6h012341 Control2 E23 ICI4 BrPkia0123451 Control2 E23 ICI4 BrAp2m110 0 2 4 6 81 Control2 E23 ICI4 Br
Cincinnati - EH - 3
Rab3d024681 Control2 E23 ICI4 BrTrpm401234561 Control2 E23 ICI4 BrHprt10 0 2 4 6 81 Control2 E23 ICI4 BrIl6ra8 0 2 4 61 Control2 E23 ICI4 BrIl11ra1012345671 Control
Cincinnati - EH - 3
Chrd01234561 Control2 E23 ICI4 BrNov024681 Control2 E23 ICI4 Br
Cincinnati - EH - 3
Ar024681 Control2 E23 ICIKcnmb10123451 Control2 E23 ICIHoxd10_predicted024681 Control2 E23 ICIRGD1305645_predicted01234561 Control2 E23 ICI
Cincinnati - EH - 3
Me1024681 Control2 E23 ICI4 BrChm024681 Control2 E23 ICI4 BrHspa4l_predicted6 0 1 2 3 4 51 Control2 E23 ICI4 BrTmeff101234561 Control2 E23 ICI4 Br
Cincinnati - EH - 3
Vtn6 0 1 2 3 4 51 Control2 E23 ICI4 BrRGD1305928_predicted012341 Control2 E23 ICI4 BrClca3_predicted0246810121 Control2 E23 ICI4 Br
Cincinnati - EH - 11
LN2510 8 6 4 2Percent of Total0CS9210 8 6 4 2 0 2 0 2 4smoothed reporter level [log2]
Cincinnati - EH - 3
LN2510 8 6 4 2Percent of Total0CS9210 8 6 4 2 0 2 0 2 4smoothed reporter level [log2]
Cincinnati - EH - 3
Examples of using gimmR package (Gaussian Innite Mixture Model in R)Mario Medvedovic, Vinayak Kumar November 22, 20061IntroductiongimmR serves as the interface for running low level procedures for clustering gene expression data using the Baye
Cincinnati - EH - 3
Users Manual for the gimmR package (Gaussian Innite Mixture Model in R)Mario Medvedovic, Vinayak Kumar September 7, 20061IntroductionThis package serves as the interface between the low level procedures for clustering gene expression data usin
Cincinnati - EH - 3
051015202564679_at 292746_at 679942_at 360914_at 81506_at 303817_at 64455_at 305846_at 81526_at 298077_at 311803_at 300455_at 303772_at 85496_at 114851_at 498736_at 304785_at 286922_at 292485_at 312192_at 308836_at 25098_at 613220_at 2426
Cincinnati - EH - 3
Color Key and Histogram2000Count0 0.45001000150000.2 0.4Valuemyeloid leukemia fac similar tomotifconta myosin, myozenin polypep similar to Calseques1 tripartite C type 2 typ myosin, light1, polyp hemochromatosis(fa troponin heavy s
Cincinnati - EH - 3
Color Key and Histogram2500Count0 0.4500150000.2 0.4Valuehypothetical component malic enzyme member 6 complement protein LOC ELOVL family 1 comple retroviral RIKEN origin expressed Mphaseintegration site phosphoprotein exonuclease 1
Cincinnati - EH - 3
# genes with correct GO annotation 10 1e33 1e26 1e19 1e12 1e05 FDR threshold 20 50 100 200 500 1000
Cincinnati - EH - 3
Before removing Batch Effect0.0 log(sd) 1.5 1.0 0.5AIN HFB HFF HFO HFS LFB LFF LFO LFS3.0 22.52.0468 mean101214After removing Batch Effect0.0 log(sd) 1.5 1.0 0.5AIN HFB HFF HFO HFS LFB LFF LFO LFS3.0 22.52.0468 m
Cincinnati - EH - 3
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Cincinnati - EH - 3
Rab3d024681 Control2 E23 ICI4 BrTrpm401234561 Control2 E23 ICI4 BrHprt10 0 2 4 6 81 Control2 E23 ICI4 BrIl6ra8 0 2 4 61 Control2 E23 ICI4 BrIl11ra1012345671 Control
Cincinnati - EH - 3
Cxcl2024681 Control2 E23 ICI4 BrAps0123451 Control2 E23 ICI4 BrSlfn38 0 2 4 61 Control2 E23 ICI4 BrCcl285 0 1 2 3 41 Control2 E23 ICI4 BrNfil302461 Control2 E23 ICI4 Br
Cincinnati - EH - 3
Me18 0 2 4 61 Control2 E23 ICIChm024681 Control2 E23 ICIPeci024681 Control2 E23 ICIHspa4l_predicted6 0 1 2 3 4 51 Control2 E23 ICIRGD1559882_predicted6 0 1 2 3 4 51 Control2 E23 ICISncaip
Cincinnati - EH - 3
Rab3d024681 Control2 E23 ICI4 BrTrpm401234561 Control2 E23 ICI4 BrHprt10 0 2 4 6 81 Control2 E23 ICI4 BrIl6ra8 0 2 4 61 Control2 E23 ICI4 BrIl11ra1012345671 Control
Cincinnati - EH - 3
Cxcl2024681 Control2 E23 ICI4 BrAps0123451 Control2 E23 ICI4 BrSlfn38 0 2 4 61 Control2 E23 ICI4 BrCasp4012345671 Control2 E23 ICI4 BrTimp110 0 2 4 6 81 Control2 E2
Cincinnati - EH - 3
Ppp1r14a7 0 1 2 3 4 5 61 Control2 E23 ICI4 BrFmo27 0 1 2 3 4 5 61 Control2 E23 ICI4 BrImpa202461 Control2 E23 ICI4 BrArl4a012345671 Control2 E23 ICI4 BrCol7a1_predicted6 0 1 2 3 4 5
Cincinnati - EH - 3
Cxcl2024681 Control2 E23 ICI4 BrAps0123451 Control2 E23 ICI4 BrCasp4012345671 Control2 E23 ICI4 BrTimp110 0 2 4 6 81 Control2 E23 ICI4 BrS100a8024681 Control
Cincinnati - EH - 3
Zdhhc27 0 1 2 3 4 5 61 Control2 E23 ICI4 BrAbca3024681 Control2 E23 ICI4 BrRGD1560559_predicted10 0 2 4 6 81 Control2 E23 ICI4 BrFuk_predicted7 0 1 2 3 4 5 61 Control2 E23 ICI4 BrSema4a10 0 2 4 6
Cincinnati - EH - 3
Prss88 0 2 4 61 Control2 E23 ICI4 BrKrt2802468101 Control2 E23 ICI4 BrSlc18a1012345671 Control2 E23 ICI4 BrPkig024681 Control2 E23 ICI4 BrPsen102461 Control2 E
Cincinnati - EH - 3
Atp6v1b202468101 Control2 E23 ICI4 BrRGD1562168_predicted8 0 2 4 61 Control2 E23 ICI4 Br
Cincinnati - EH - 3
Slfn38 0 2 4 61 Control2 E23 ICI4 BrCcl176 0 1 2 3 4 51 Control2 E23 ICI4 BrMx16 0 1 2 3 4 51 Control2 E23 ICI4 BrOas1b012341 Control2 E23 ICI4 BrRT1N3012341 Control2 E23 ICI4 Br
Cincinnati - EH - 3
Peci024681 Control2 E23 ICI4 BrRGD1559882_predicted6 0 1 2 3 4 51 Control2 E23 ICI4 BrSncaip_predicted012341 Control2 E23 ICI4 BrPwwp2_predicted024681 Control2 E23 ICI4 BrLOC49833
Cincinnati - EH - 3
Cfh024681 Control2 E23 ICI4 BrCd2008 0 2 4 61 Control2 E23 ICI4 BrBgn10 0 2 4 6 81 Control2 E23 ICI4 BrDpysl2024681 Control2 E23 ICI4 BrDpt_predicted024681 Control2 E23 ICI
Cincinnati - EH - 3
Chek17 0 1 2 3 4 5 61 Control2 E23 ICI4 BrGnai101234561 Control2 E23 ICI4 BrMlstd28 0 2 4 61 Control2 E23 ICI4 BrRGD1303074024681 Control2 E23 ICI4 BrLamp38 0 2 4 61 Control2 E2