updated the cv

muschellij2 · Jan 11, 2018 · 5faadb7 · 5faadb7
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diff --git a/Current_CV.pdf b/Current_CV.pdf
diff --git a/Modern_CV.pdf b/Modern_CV.pdf
diff --git a/R_packages.Rnw b/R_packages.Rnw
@@ -2,25 +2,50 @@
 
 <<echo = FALSE, results = "hide", message=FALSE, error=FALSE, warning=FALSE>>=
 if (!require(cranlogs)) {
-library(devtools)
-install_github("metacran/cranlogs")
+  library(devtools)
+  install_github("metacran/cranlogs")
+  library(cranlogs)
 }
 library(plyr)
 first_date = "2014-01-10"
 today = Sys.Date()
 long_today = format(Sys.time(), "%B %d, %Y")
-packs = c("fslr", "WhiteStripe", "brainR",
-          "matlabr","spm12r", "rscopus",
-          "diffr", "neurobase", "freesurfer",
-          "papayar", "oasis", "neurohcp", "kirby21.base",
-           "kirby21.fmri",  "kirby21.t1")
+# packs = c("brainR", "diffr", "freesurfer", "fslr", 
+#           "kirby21.base", "kirby21.fmri", 
+#           "kirby21.t1", "matlabr", "neurobase", "neurohcp", 
+#           "oasis", "papayar", "rscopus", "spm12r", "WhiteStripe")
+# from crandb
+packs = c("brainR", "cifti", "diffr", "fedreporter", "freesurfer", "fslr", 
+"gcite", "gifti", "glassdoor", "kirby21.base", "kirby21.fmri", 
+"kirby21.t1", "matlabr", "neurobase", "neurohcp", "neurovault", 
+"papayar", "rscopus", "spm12r", "stapler", "WhiteStripe")
+# from muschpack
+gh = c("alvin", "biobankr", 
+       "dcm2niir", "dcmtk", "dhs", "drammsr", 
+       "extrantsr", "ggneuro", "ghtravis", 
+       "gluc", "greedyreg", "ichseg", "itksnapr", 
+       "jhudsl", "kirby21.asl", "kirby21.det2", "kirby21.dti", 
+       "kirby21.flair", "kirby21.mt", "kirby21.smri", "kirby21.survey", 
+       "kirby21.t2", "kirby21.vaso", "leanpubr", "lungct", "malf.templates", 
+       "neuroc.deps", "neurocInstall", "rcamino", 
+       "robex", "smri.process")
+# packs = c(packs, gh)
+packs = sort(unique(packs))
+
 packs = unique(packs)
 dl = cran_downloads( from = first_date, to = today,
 	packages = packs)
 dl = ddply(dl, .(package), summarise, count = sum(count))
 desc <- sapply(packs, function(x) {
-	read.dcf(file = system.file("DESCRIPTION", package = x),
-                   fields = c("Package", "Title"))
+  fname = system.file("DESCRIPTION", package = x)
+  if (fname == "") {
+    print(x)
+    devtools::install_github(paste0("muschellij2/", x))
+    fname = system.file("DESCRIPTION", package = x)
+    # return(NULL)
+  }
+  
+  read.dcf(file = fname, fields = c("Package", "Title"))
 })
 desc = t(desc)
 colnames(desc) = c("package", "title")

diff --git a/R_packages.tex b/R_packages.tex
@@ -2,24 +2,30 @@
 
 
 
-All download counts are from RStudio CRAN logs and are accurate as of September 06, 2017.
+All download counts are from RStudio CRAN logs and are accurate as of January 11, 2018.
 \newline
 
-\cventry{}{\href{http://cran.r-project.org/web/packages/fslr/index.html}{fslr}: Wrapper Functions for FSL (FMRIB Software Library) from \newline Functional MRI of the Brain (FMRIB)}{\newline Downloads: 14002}{}{}{}
-\cventry{}{\href{http://cran.r-project.org/web/packages/brainR/index.html}{brainR}: Helper functions to misc3d and rgl packages for brain imaging}{\newline Downloads: 11424}{}{}{}
-\cventry{}{\href{http://cran.r-project.org/web/packages/WhiteStripe/index.html}{WhiteStripe}: White Matter Normalization for Magnetic Resonance \newline Images using Whitestripe}{\newline Downloads: 7357}{}{}{}
-\cventry{}{\href{http://cran.r-project.org/web/packages/matlabr/index.html}{matlabr}: An Interface for MATLAB using System Calls}{\newline Downloads: 6139}{}{}{}
-\cventry{}{\href{http://cran.r-project.org/web/packages/rscopus/index.html}{rscopus}: Scopus Database API Interface}{\newline Downloads: 5927}{}{}{}
-\cventry{}{\href{http://cran.r-project.org/web/packages/diffr/index.html}{diffr}: Display Differences Between Two Files using Codediff Library}{\newline Downloads: 5355}{}{}{}
-\cventry{}{\href{http://cran.r-project.org/web/packages/neurobase/index.html}{neurobase}: Neuroconductor Base Package with Helper Functions for \newline nifti Objects}{\newline Downloads: 4793}{}{}{}
-\cventry{}{\href{http://cran.r-project.org/web/packages/spm12r/index.html}{spm12r}: Wrapper Functions for SPM (Statistical Parametric Mapping) \newline Version 12 from the Wellcome Trust Centre for Neuroimaging}{\newline Downloads: 3973}{}{}{}
-\cventry{}{\href{http://cran.r-project.org/web/packages/oasis/index.html}{oasis}: Multiple Sclerosis Lesion Segmentation using Magnetic \newline Resonance Imaging (MRI)}{\newline Downloads: 3230}{}{}{}
-\cventry{}{\href{http://cran.r-project.org/web/packages/papayar/index.html}{papayar}: View Medical Research Images using the Papaya \newline JavaScript Library}{\newline Downloads: 2436}{}{}{}
-\cventry{}{\href{http://cran.r-project.org/web/packages/freesurfer/index.html}{freesurfer}: Wrapper Functions for Freesurfer}{\newline Downloads: 1947}{}{}{}
-\cventry{}{\href{http://cran.r-project.org/web/packages/kirby21.t1/index.html}{kirby21.t1}: Example T1 Structural Data from the Multi-Modal MRI \newline Reproducibility Resource}{\newline Downloads: 1301}{}{}{}
-\cventry{}{\href{http://cran.r-project.org/web/packages/kirby21.base/index.html}{kirby21.base}: Example Data from the Multi-Modal MRI \newline Reproducibility Resource}{\newline Downloads: 1142}{}{}{}
-\cventry{}{\href{http://cran.r-project.org/web/packages/kirby21.fmri/index.html}{kirby21.fmri}: Example Functional Imaging Data from the Multi-Modal \newline MRI Reproducibility Resource}{\newline Downloads: 968}{}{}{}
-\cventry{}{\href{http://cran.r-project.org/web/packages/neurohcp/index.html}{neurohcp}: Human Connectome Project Interface}{\newline Downloads: 567}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/fslr/index.html}{fslr}: Wrapper Functions for FSL (FMRIB Software Library) from \newline Functional MRI of the Brain (FMRIB)}{\newline Downloads: 15030}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/brainR/index.html}{brainR}: Helper Functions to misc3d and rgl Packages for Brain Imaging}{\newline Downloads: 13086}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/WhiteStripe/index.html}{WhiteStripe}: White Matter Normalization for Magnetic Resonance \newline Images using Whitestripe}{\newline Downloads: 8510}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/rscopus/index.html}{rscopus}: Scopus Database API Interface}{\newline Downloads: 8279}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/matlabr/index.html}{matlabr}: An Interface for MATLAB using System Calls}{\newline Downloads: 8105}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/diffr/index.html}{diffr}: Display Differences Between Two Files using Codediff Library}{\newline Downloads: 6577}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/neurobase/index.html}{neurobase}: Neuroconductor Base Package with Helper Functions for \newline nifti Objects}{\newline Downloads: 6113}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/spm12r/index.html}{spm12r}: Wrapper Functions for SPM (Statistical Parametric Mapping) \newline Version 12 from the Wellcome Trust Centre for Neuroimaging}{\newline Downloads: 4557}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/freesurfer/index.html}{freesurfer}: Wrapper Functions for Freesurfer}{\newline Downloads: 3119}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/papayar/index.html}{papayar}: View Medical Research Images using the Papaya \newline JavaScript Library}{\newline Downloads: 3013}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/kirby21.base/index.html}{kirby21.base}: Example Data from the Multi-Modal MRI \newline Reproducibility Resource}{\newline Downloads: 2551}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/kirby21.t1/index.html}{kirby21.t1}: Example T1 Structural Data from the Multi-Modal MRI \newline Reproducibility Resource}{\newline Downloads: 2025}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/gifti/index.html}{gifti}: Reads in Neuroimaging GIFTI Files with Geometry Information}{\newline Downloads: 1620}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/kirby21.fmri/index.html}{kirby21.fmri}: Example Functional Imaging Data from the Multi-Modal \newline MRI Reproducibility Resource}{\newline Downloads: 1590}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/gcite/index.html}{gcite}: Google Citation Parser}{\newline Downloads: 1516}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/cifti/index.html}{cifti}: Toolbox for Connectivity Informatics Technology Initiative \newline (CIFTI) Files}{\newline Downloads: 1235}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/neurohcp/index.html}{neurohcp}: Human Connectome Project Interface}{\newline Downloads: 1040}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/fedreporter/index.html}{fedreporter}: Interface to Federal RePORTER API}{\newline Downloads: 607}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/glassdoor/index.html}{glassdoor}: Interface to Glassdoor API}{\newline Downloads: 594}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/neurovault/index.html}{neurovault}: Neurovault Database API Access}{\newline Downloads: 243}{}{}{}
+\cventry{}{\href{http://cran.r-project.org/web/packages/stapler/index.html}{stapler}: Simultaneous Truth and Performance Level Estimation}{\newline Downloads: 114}{}{}{}
 
 % \cventry{CRAN}{\href{http://cran.r-project.org/web/packages/fslr/index.html}{fslr}: Wrapper functions for FSL (FMRIB Software Library) from \newline Functional MRI of the Brain (FMRIB)}{\newline Downloads: dl['fslr']}{}{}{}
 %

diff --git a/citations.bib b/citations.bib
@@ -1,6 +1,17 @@
+@Article{muschelli2017neuroconductor,
+  author = {John Muschelli and Adrian Gherman and Jean-Philippe Fortin and Brian Avants and Brandon Whitcher and Jonathan D Clayden and Brian S Caffo and Ciprian M Crainiceanu},
+  title = {Neuroconductor: an {R} platform for medical imaging analysis},
+  journal = {Biostatistics},
+  pages = {kxx068},
+  year = {2018},
+  doi = {10.1093/biostatistics/kxx068},
+  url = { + http://dx.doi.org/10.1093/biostatistics/kxx068},
+  eprint = {/oup/backfile/content_public/journal/biostatistics/pap/10.1093_biostatistics_kxx068/1/kxx068.pdf},
+}
+
 @Article{muschelli2016pitch,
   title = {{PItcHPERFeCT}: Primary Intracranial Hemorrhage Probability Estimation using Random Forests on {CT}},
-  journal = {NeuroImage: Clinical },
+  journal = {{NeuroImage}: Clinical },
   volume = {14},
   pages = {379 - 390},
   year = {2017},
@@ -10,14 +21,45 @@ @Article{muschelli2016pitch
   author = {John Muschelli and Elizabeth M. Sweeney and Natalie L. Ullman and Paul Vespa and Daniel F. Hanley and Ciprian M. Crainiceanu},
 }
 
+@Article{hanley2017thrombolytic,
+  title = {Thrombolytic removal of intraventricular haemorrhage in treatment of severe stroke: results of the randomised, multicentre, multiregion, placebo-controlled {CLEAR} {III} trial},
+  author = {Daniel F Hanley and Karen Lane and Nichol McBee and Wendy Ziai and Stanley Tuhrim and Kennedy R Lees and Jesse Dawson and Dheeraj Gandhi and Natalie Ullman and W Andrew Mould and Steven W Mayo and A David Mendelow and Barbara Gregson and Kenneth Butcher and Paul Vespa and David W Wright and Carlos S Kase and J Ricardo Carhuapoma and Penelope M Keyl and Marie Diener-West and John Muschelli and Joshua F Betz and Carol B Thompson and Elizabeth A Sugar and Gayane Yenokyan and Scott Janis and Sayona John and Sagi Harnof and George A Lopez and E Francois Aldrich and Mark R Harrigan and Safdar Ansari and Jack Jallo and Jean-Louis Caron and David LeDoux and Opeolu Adeoye and Mario Zuccarello and Harold P Adams and Michael Rosenblum and Richard E Thompson and Issam A Awad},
+  journal = {The Lancet},
+  volume = {389},
+  number = {10069},
+  pages = {603--611},
+  year = {2017},
+  publisher = {Elsevier},
+}
+
+@Article{kickingereder2017radiomic,
+  title = {Radiomic subtyping improves disease stratification beyond key molecular, clinical and standard imaging characteristics in patients with glioblastoma.},
+  journal = {{Neuro-Oncology}},
+  year = {2017},
+  author = {Philipp Kickingereder and Ulf Neuberger and David Bonekamp and Paula Piechotta and Michael Götz and Antje Wick and Martin Sill and Annekathrin Kratz and Russell Shinohara and David Jones and Alexander Radbruch and John Muschelli and Andreas Unterberg and Juergen Debus and Heinz-Peter Schlemmer and Christel Herold-Mende and Stefan Pfister and Andreas {von Deimling} and Wolfgang Wick and David Capper and Klaus Maier-Hein and Martin Bendszus},
+}
+
 @Article{maier2017isles,
-  title = {ISLES 2015-A public evaluation benchmark for ischemic stroke lesion segmentation from multispectral MRI},
-  author = {Oskar Maier and Bjoern H Menze and Janina                                                                                                                                    {von der Gablentz} and Levin H{\"a}ni and Mattias P Heinrich and Matthias Liebrand and Stefan Winzeck and Abdul Basit and Paul Bentley and Liang Chen and {others}},
+  author = {O. Maier and B.H. Menze and J. {von der Gablentz} and L. Häni and M.P. Heinrich and M. Liebrand and S. Winzeck and A. Basit and P. Bentley and L. Chen and D. Christiaens and F. Dutil and K. Egger and C. Feng and B. Glocker and M. Götz and T. Haeck and H.-L. Halme and M. Havaei and K.M. Iftekharuddin and P.-M. Jodoin and K. Kamnitsas and E. Kellner and A. Korvenoja and H. Larochelle and C. Ledig and J.-H. Lee and F. Maes and Q. Mahmood and K.H. Maier-Hein and R. McKinley and J. Muschelli and C. Pal and L. Pei and J.R. Rangarajan and S.M.S. Reza and D. Robben and D. Rueckert and E. Salli and P. Suetens and C.-W. Wang and M. Wilms and J.S. Kirschke and U.M. Krämer and T.F. Münte and P. Schramm and R. Wiest and H. Handels and M. Reyes},
+  title = {{ISLES} 2015 - A public evaluation benchmark for ischemic stroke lesion segmentation from multispectral {MRI}},
   journal = {Medical Image Analysis},
+  year = {2017},
   volume = {35},
-  pages = {250--269},
+  pages = {250-269},
+  doi = {10.1016/j.media.2016.07.009},
+  note = {cited By 14},
+  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84979950799&doi=10.1016%2fj.media.2016.07.009&partnerID=40&md5=15537a210adbbc102bcef75103bee7df},
+  document_type = {Article},
+  source = {Scopus},
+}
+
+@Article{smith2017feasibility,
+  title = {Feasibility of Coping Effectiveness Training for Caregivers of Children with Autism Spectrum Disorder: a Genetic Counseling Intervention},
+  author = {Christy Haakonsen Smith and Erin Turbitt and John Muschelli and Lori Leonard and Katie L Lewis and Brian Freedman and Michelle Muratori and Barbara B Biesecker},
+  journal = {Journal of genetic counseling},
+  pages = {1--11},
   year = {2017},
-  publisher = {Elsevier},
+  publisher = {Springer US},
 }
 
 @Article{bundy2016peds,
@@ -43,7 +85,7 @@ @Article{fortin2016removing
 
 @Article{hanley2016safety,
   title = {Safety and efficacy of minimally invasive surgery plus alteplase in intracerebral haemorrhage evacuation ({MISTIE}): a randomised, controlled, open-label, phase 2 trial},
-  author = {Daniel F Hanley and Richard E Thompson and John Muschelli and Michael Rosenblum and Nichol McBee and Karen Lane and Amanda J Bistran-Hall and Steven W Mayo and Penelope Keyl and Dheeraj Gandhi and {others}},
+  author = {Daniel F Hanley and Richard E Thompson and John Muschelli and Michael Rosenblum and Nichol McBee and Karen Lane and Amanda J Bistran-Hall and Steven W Mayo and Penelope Keyl and Dheeraj Gandhi and Tim C Morgan and Natalie Ullman and W Andrew Mould and J Ricardo Carhuapoma and Carlos Kase and Wendy Ziai and Carol B Thompson and Gayane Yenokyan and Emily Huang and William C Broaddus and R Scott Graham and E Francois Aldrich and Robert Dodd and Cristanne Wijman and Jean-Louis Caron and Judy Huang and Paul Camarata and A David Mendelow and Barbara Gregson and Scott Janis and Paul Vespa and Neil Martin and Issam Awad and Mario Zuccarello},
   journal = {The Lancet Neurology},
   volume = {15},
   number = {12},
@@ -52,17 +94,9 @@ @Article{hanley2016safety
   publisher = {Elsevier},
 }
 
-@Article{hanley2016thrombolytic,
-  title = {Thrombolytic removal of intraventricular haemorrhage in treating severe stroke: Results of the {CLEAR} {III} trial, a randomised, controlled trial},
-  author = {Daniel F Hanley and Karen Lane and Nichol McBee and Wendy Ziai and Stanley Tuhrim and Kennedy R Lees and Jesse Dawson and Deeraj Gandhi and Natalie Ullman and W Andrew Mould and {others}},
-  journal = {Lancet},
-  year = {2016},
-  publisher = {The Lancet Publishing Group},
-}
-
 @InProceedings{kickingereder2016large,
   title = {Large-scale radiomic profiling of glioblastoma identifies an imaging signature for predicting and stratifying antiangiogenic treatment response},
-  author = {P Kickingereder and M G{\"o}tz and J Muschelli and A Wick and U Neuberger and R Shinohara and A Radbruch and H Schlemmer and W Wick and M Bendszus and {others}},
+  author = {P Kickingereder and M Götz and J Muschelli and A Wick and U Neuberger and R Shinohara and A Radbruch and H Schlemmer and W Wick and M Bendszus and K Maier-Hein and D Bonekamp},
   booktitle = {R{\"o}Fo-Fortschritte auf dem Gebiet der R{\"o}ntgenstrahlen und der bildgebenden Verfahren},
   volume = {188},
   number = {S 01},
@@ -114,7 +148,7 @@ @Article{muschelli2015quantitative
 
 @Article{choe2015reproducibility,
   title = {Reproducibility and temporal structure in weekly resting-state fMRI over a period of 3.5 years},
-  author = {Ann S Choe and Craig K Jones and Suresh E Joel and John Muschelli and Visar Belegu and Brian S Caffo and Martin A Lindquist and Peter CM                                                                                                                                    {van Zijl} and James J Pekar},
+  author = {Ann S Choe and Craig K Jones and Suresh E Joel and John Muschelli and Visar Belegu and Brian S Caffo and Martin A Lindquist and Peter CM {van Zijl} and James J Pekar},
   journal = {PloS one},
   volume = {10},
   number = {10},

diff --git a/submitted.bib b/submitted.bib
@@ -1,12 +1,3 @@
-@Article{muschelli2017neuroconductor,
-  title = {Neuroconductor: An R Platform for Medical Imaging Analysis},
-  author = {John Muschelli and Jean-Philippe Fortin and Adrian Gherman and Brian Avants and Brandon Whitcher and Jonathan D. Clayden and Brian S. Caffo and Ciprian M. Crainiceanu},
-  journal = {Biostatistics},
-  pages = {Submitted},
-  year = {2017},
-  note={preprint on webpage at \url{http://works.bepress.com/john_muschelli/6/}}
- }
-
 @Article{haakonsen2017thesis,
   title = {Feasibility of Coping Effectiveness Training for Caregivers of Children with Autism Spectrum Disorder: A Genetic Counseling Intervention},
   author = {Christy Haakonsen Smith and Erin Turbitt and John Muschelli and Lori Leonard and Katie Lewis and Brian Freedman and Michelle Muratori and Barbara Biesecker},

diff --git a/teaching.tex b/teaching.tex
@@ -1,4 +1,4 @@
-\cventry{2016}{Co-instructor}{JHSPH}{Advanced Data Science}{}{
+\cventry{2016--present}{Co-instructor}{JHSPH}{Advanced Data Science}{}{
 Provides an intensive introduction to applied statistics and data analysis. Since both data analysis and methods development require substantial hands-on experience, focuses on hands-on data analysis. 
 }{}
 

diff --git a/working_groups.tex b/working_groups.tex
@@ -1,7 +1,7 @@
 \cventry{2014--Present}{Statistical and Applied Mathematical Sciences Institute (SAMSI) working group on Clinical Brain Imaging}{}{}{}{}
 \vspace{1em}
 
-\cventry{2012--Present}{Epidemiology and Biostatistics of Aging (EBA) Training Program Meeting}{Johns Hopkins University, Center on Aging and Health}{}{}{}
+\cventry{2012--2016}{Epidemiology and Biostatistics of Aging (EBA) Training Program Meeting}{Johns Hopkins University, Center on Aging and Health}{}{}{}
 \vspace{1em}