注意事項†
西暦年降順・著者順 (追加の場合は、それに従ってください。)
研究者にRを薦めると、「Rを使った論文とやらを見たことない、査読で落とされるのでは?」という質問をされます。S言語ですから、S-plusと変わらないのでは？と濁していますが、具体的な論文のリストがあると説得力があります。できればどのように使ったかもメモやソースコードの有無をお願いします。
「編集」画面からどんどん足していってください。
2014†
2013†
2012†
- Laurent, T., A. Ruiz-Gazen, and C. Thomas-Agnan, "GeoXp: An R Package for Exploratory Spatial Data Analysis", Journal of Statistical Software, vol. 47, no. 2, pp. 1?23, 4, 2012.
- Needham DM et al. Lung protective mechanical ventilation and two year survival in patients with acute lung injury: prospective cohort study. BMJ 2012;344:e2124. Cox回帰を使用。time-dependent covariateで解析したようです。propensity score analysisもおこなった。
- Shiihara T, Miyake T, Izumi S, Watanabe M, Kamayachi K, Kodama K, Nabetani M, Ikemiyagi M, Yamaguchi Y, Sawaura N. Serum and cerebrospinal fluid S100B, neuron-specific enolase, and total tau protein in acute encephalopathy with biphasic seizures and late reduced diffusion: a diagnostic validity. Pediatr Int. 2012;54:52-5.統計解析、ROC曲線など作図にRを用いてます
2011†
- Cebul RD, Love TE, Jain AK, Hebert CJ. Electronic health records and quality of diabetes care. N Engl J Med. 2011 Sep 1;365(9):825-33. Rのgee packパッケージを使用。
- Ducourau E, et al. Antibodies toward infliximab are associated with low infliximab concentration at treatment initiation and poor infliximab maintenance in rheumatic diseases. Arthritis Res Ther. 2011 Jun 27;13(3):R105.
- Keller T, et al. Serial Changes in Highly Sensitive Troponin I Assay and Early Diagnosis of Myocardial Infarction. JAMA 2011;306:2684-2693. ROC解析などを行っている論文。使用パッケージは不明。
- Kostis JB, Cabrera J, Cheng JQ, Cosgrove NM, Deng Y, Pressel SL, Davis BR. Association between chlorthalidone treatment of systolic hypertension and long-term survival. JAMA 2011;306:2588-93. 有名なSystolic Hypertension in the Elderly Program (SHEP) trialの22年フォローアップ。
- Toda H, Suzuki T, Sawahata H, Majima K, Kamitani Y, Hasegawa I. Simultaneous recording of ECoG and intracortical neuronal activity using a flexible multichannel electrode-mesh in visual cortex. Neuroimage 2011;54(1):203-12. 作表一般とaov, friedman.test, TukeyHSD。下処理はFree Pascal / Lazarusとこれもオープンソース。
2010†
- Annema JT, van Meerbeeck JP, Rintoul RC, et al. Mediastinoscopy vs endosonography for mediastinal nodal staging of lung cancer. JAMA, 2010;304(29):2245-2252. SPSS 17.0 と R 2.10.0 で統計解析していますが，使い分けは不明．Wilson スコア信頼区間を epiR で計算しています．
- Checkley W, West KP, Wise RA, et al. Maternal vitamin A supplementation and lung function in offspring. N Engl J Med 2010;362:1784-1794. Rのみでの分析はNEJMでは初めて？
- Chan PS, Krumholz HM, Spertus JA, et al. Automated external defibrillators and survival after in-hospital cardiac arrest. JAMA, 2010;304(19):2129-2136 SAS 9.2 と R 2.10.0 で分析．使い分けは不明．
- Cindy X Huang, Hocine Tighiouart, Srinivasan Beddhu, et al. Both low muscle mass and low fat are associated with higher all-cause mortality in hemodialysis patients. Kidney Int 2010;77,624–629. Cox比例ハザードモデルにrestricted cubic spline法を用いるのにDesign Libraryを使用しています。
- Cornwallis CK, West SA, Davies KE, Griffin AS. Promiscuity and the evolutionary transition to complex societies. Nature 446: 969-972. RではMCMCglmmパッケージを用い，系統種間比較，メタ解析を行っています．祖先形質推定にはBayesTraits（非R）を用いています．
- Johnson K, Scott J, Rughita B, et al. Association of sexual violence and human rights violations with physical and mental health in territories of the eastern Democratic Republic of the Congo. JAMA 2010;304:553-562. survey パッケージによる分析
- Kuhns DB, Gregory Alvord W, Heller T, et al. Residual NADPH oxidase and survival in chronic granulomatous disease. N Engl Med 2010;363:2600-10. SAS, S-Plus, Rを使って解析。どう使い分けたのかはよくわかりません。
- Lambert L, Brown K, Segal E, et al. Association between timeliness of reperfusion therapy and clinical outcomes in ST-elevation myocardial infaraction. JAMA 2010;303(21):2148-2155. SASとR(lme4, Matching)を使っています
- Mohammed AJ, AlAwaidy S, Bawikar S, et al. Fractional doses of inactivated poliovirus vaccine in Oman. N Engl J Med 2010;362:2351-2359. SASとRにより分析したとのことですが，Rで何をしたのかは不明
- Quinn JF, Raman R, Thomas RG, et al. Docosahexaenoic acid supplementation and cognitive decline in Alzheimer disease. JAMA, 2010;304(17):1903-1911. すべての統計処理をRでおこない，それをSASで検証したらしい。
- Saadoun D, Wechsler B, Desseaux K, Le Thi Huong D, Amoura Z, Resche-Rigon M, Cacoub P. Mortality in Behçet's disease. Arthritis Rheum 2010;62:2806-12.
- Shiihara T, Miyashita M, Yoshizumi M, Watanabe M, Yamada Y, Kato M. Peripheral lymphocyte subset and serum cytokine profiles of patients with West syndrome. Brain Dev. 2010;32:695-702. 統計処理、作図Rで行いました
- Solymosi, N., Wagner, S. E., Maroti-Agots, A., Allepuz, A.(2010):maps2WinBUGS: a QGIS plugin to facilitate data processing for Bayesian spatial modeling, Ecology, 33(6), 1093-1096.
- Thabut G, Christie JD, Kremers WK, et al. Survival differences following lung transplantation among US transplant centers. JAMA, 2010;304(1):53-60. Rのsurvival packageとcoxme packageを使っています
- 鑓田 亨(2010):RによるGISデータの利用について, NUCB journal of economics and information science 54(2), 241-248, 2010-03
2009†
- Carrasco, L., Colell, M., Calvo, M., Abello, M. T., Velasco, M., & Posada, S. (2009). Benefits of training/playing therapy in a group of captive lowland gorillas (gorilla gorilla gorilla). Animal Welfare, 18(1), 9-19.
- Cano-Serral G, Azlor E, Rodríguez-Sanz M, Pasarín MI, Martínez JM, Puigpinós R, Muntaner C, Borrell C. Health & Place. 2009;15(1) :186-192.
- Flachsbart F, Caliebe A, Kleindorp R, Blanché H, von Eller-Eberstein H, Nikolaus S, Schreiber S and Nebel A. Association of FOXO3A variation with human longevity confirmed in German centenarians. PNAS. 2009;106(8): 2700-2705.
- Gerharz LE, Kr�ger A, Klemm O. Applying indoor and outdoor modeling techniques to estimate individual exposure to PM2.5 from personal GPS profiles and diaries: a pilot study. Sci Total Environ. 2009;407(18):5184-93. （全ての計算処理にRを使用）
- Grossmann, E., Ohmann, J., Kagan, J., May, H. and Gregory, M.(2009):Mapping Ecological Systems with a Random Forest Model: Trade- offs between Errors and Bias, USGS GAP Bulletin, 17. randomForest パッケージ
- Katsuki T., Ailani D., Hiramoto M., Hiromi Y. Intra-axonal patterning: intrinsic compartmentalization of the axonal membrane in Drosophila neurons. Neuron 2009;64(2):188-199. （検定と画像解析に利用）
- Kamatani Y, Wattanapokayakit S, Ochi H, Kawaguchi T, Takahashi A, Hosono N, Kubo M, Tsunoda T, Kamatani N, Kumada H, Puseenam A, Sura T, Daigo Y, Chayama K, Chantratita W, Nakamura Y & Matsuda K. A genome-wide association study identifies variants in the HLA-DP locus associated with chronic hepatitis B in Asians. Nat Genet 2009;41(5):591-595. （Mantel-Haenszelをrmetaというパッケージで、ハプロタイプ解析をhaplo.statsというパッケージで行いました）
- Khatib H, Maltecca C, Monson RL, Schutzkus V, Rutledge JJ. Monoallelic maternal expression of STAT5A affects embryonic survival in cattle. BMC Genetics. 2009;10:13.
- Lin SM, Molan PC, Cursons RT. The invitro susceptibility of Campylobacter spp. to the antibacterial effect of manuka honey. Euroopean Journal of Clinical Microbiology & Infectious Diseases. 2009;28(4):339-344.
- Nakatani, T. and T. Teräsvirta (2009): Testing for Volatility Interactions in the Constant Conditional Correlation GARCH Model, Econometrics Journal, 12, 147-163. （関数optimでゴリゴリやってます。GARCH項の計算では、ループを使った逐次計算が不可欠なので、Cを使って高速化しています。）
- Newton-Cheh C. Common variants at ten loci influence QT interval duration in the QTGEN Study. Nature Genetics. 2009;41(4):399-406.
- 竹内 傑，渡邊將司，?井省三（2009）ジュニアサッカーチームのエリート選手はどのように選抜されたか．トレーニング科学 21: 289-296. （線形判別分析，決定木，Bootstrap法を使用）
- The NICE-SUGAR Study Investigators. Intensive versus Conventional Glucose Control in Critically Ill Patients. N Eng J Med, 360, 1283-1297. （生存分析など。S-Plus Ver 8.0, R Ver2.7で解析、検証をSAS 9.1で実施）
- Olcaydu D, Harutyunyan A, Jager R, Berg T, Gisslinger B, Pabinger I, Gisslinger H and Kralovics R. A common JAK2 haplotype confers susceptibility to myeloproliferative neoplasms. Nature Genetics, 2009;41(4): 450-454.
- 清水宏一(2009):精神疾患の入院・死亡リスクの評価−公的データベースを利用した相対リスク推定,日本保険医学会誌,107(1),1-17.
2008†
- Baron JA, Sandler RS, Bresalier RS, Lanas A, Morton DG, Riddell R, Iverson ER, Demets DL.:Cardiovascular events associated with rofecoxib: final analysis of the APPROVe trial, Lancet, 2008, 372(9651), p1756-64. http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(08)61490-7/fulltext (SAS9.1とR2.3の併用. Cox比例ハザードモデルなど)
- Buliung, R. N. and Remmel, T. K. (2008):Open source, spatial analysis, and activity-travel behaviour research: capabilities of the aspace package, Journal of Geographical Systems, Volume 10, Number 2, 要約,全文, aspace パッケージ.
- Caglar HB, Tishler RB, Othus M, Burke E, Li Y, Goguen L, Wirth LJ, Haddad RI, Norris CM, Court LE, Aninno DJ, Posner MR, Allen AM. Dose to larynx predicts for swallowing complications after intensity-modulated radiotherapy. Int J Radiat Oncol Biol Phys. 2008;72:1110-8. PMID: 18468812
- Farnsworth, Elizabeth J. and Ellison, Aaron M. Prey availability directly affects physiology, growth, nutrient allocation and scaling relationships among leaf traits in 10 carnivorous plant species. Journal of Ecology. 2008;96:213-221.
- Foulquier, A., Malard, F., Lefebure, T., Douady, C. J. and Gibert, J. :The imprint of Quaternary glaciers on the present-day distribution of the obligate groundwater amphipod Niphargus virei (Niphargidae) , Journal of Biogeography, Volume 35, Issue 3, Page 552-564, Mar 2008, doi: 10.1111/j.1365-2699.2007.01795.x using spdep
- Hengl, T., Bajat, B., Reuter, H.I., Blagojevic, D., 2008. Geostatistical modelling of topography using auxiliary maps. Computers & Geosciences, in press.
- Howden-Chapman P, Pierse N, Nicholls S, Gillespie-Bennett J, Viggers H, Cunningham M, Phipps R, Boulic M, Fj�llstr�m P, Free S, Chapman R, Lloyd B, Wickens K, Shields D, Baker M, Cunningham C, Woodward A, Bullen C, Crane J.(2008):Effects of improved home heating on asthma in community dwelling children: randomised controlled trial BMJという有名医学雑誌にNZからの報告です。lme4ライブラリを使ってgeneralized linear mixed-effects modelsを使って空気を汚さない暖房で喘息発作や受診が有意に減り学校を休むことが減ったという分析をしています(ポアソン)。全文読めると思います。
- Kreft, H., Jetz, W., Mutke, J., Kier, G. and Barthlott, W.: Global diversity of island floras from a macroecological perspective, Ecology Letters, Volume 11, Issue 2, Page 116-127, Feb 2008, doi: 10.1111/j.1461-0248.2007.01129. using spdep
- Laitinen, Jarmo, Rehell, Sakari and Oksanen, Jari. Community and species responses to water level fluctuations with reference to soil layers in different habitats of mid-boreal mire complexes. Plant Ecology. 2008; 194(1):17-36.
- Nakatani, T. and T. Teräsvirta (2008): Positivity Constraints on the Conditional Variances in the Family of Conditional Correlation GARCH Models, Finance Research Letters, 5, 88-95. （関数optimでゴリゴリやってます。）
- Yu D, Wei Y D, Wu C.:Modeling spatial dimensions of housing prices in Milwaukee, WI. Environment and Planning B: Planning and Design, 2007, v34(6), p1085-1102. using spdep & spgwr. PDF*1, MS-Word
- Zagmajster, M., Culver, D. C., Sket, B.:Species richness patterns of obligate subterranean beetles (Insecta: Coleoptera) in a global biodiversity hotspot ? effect of scale and sampling intensity, Diversity and Distributions, Volume 14, Issue 1, Page 95-105, Jan 2008, doi: 10.1111/j.1472-4642.2007.00423.x using spdep
- Zurriaga O, Vanaclocha H, Martinez-Beneito MA, Botella-Rocamora P.:Spatio-temporal evolution of female lung cancer mortality in a region of Spain, is it worth taking migration into account?, BMC Cancer. 2008 Jan 31;8:35. (R2WinBUGS で空間疫学)
- 清水宏一(2008):悪性新生物の相対死亡リスク―対数正規分布モデルによる生存分析,日本保険医学会誌,106(1),15-34.
- 竹澤邦夫(2008) RによるノンパラメトリックDVR法プログラム. システム農学, Vol.24, No.4, pp.263-269.
- 服部保・南山典子・松村俊和 (2008) 北限と上限の照葉樹林の種組成と種多様性の比較. 植生学会誌, 25, 25-35. (package veganでDCA:Detrended Correspondence Analysis)
2007†
- Årskölda E, Svenssona M, Gragea H et al. Environmental influences on exopolysaccharide formation in Lactobacillus reuteri ATCC 55730 International Journal of Food Microbiology 2007; 116: 159-67.
- Barendse W. The strike rate index: a new index for journal quality based on journal size and the h-index of citations. Biomedical Digital Libraries 2007; 4.
- Bylesjö M, Eriksson D, Sjödin A et al. Orthogonal projections to latent structures as a strategy for microarray data normalization. BMC Bioinformatics 2007; 8.
- Danchin, A., Fang, G. and Noria, S. (2007) The extant core bacterial proteome is an archive of the origin of life. Proteomics. 7(6):875-889. Note: Kuiper's test (CircStats package) and expactation maximisation method (Mclust package) were used in R.
- De Mey M, Maertens J, Lequeux GJ et al. Construction and model-based analysis of a promoter library for E. coli: an indispensable tool for metabolic engineering. BMC Biotechnology 2007; 7.
- Dormann, C. F., McPherson, J. M., . Arau´ jo, M. B., Bivand, R., Bolliger, J., Carl,G., Davies, R. G., Hirzel, A., Jetz, W., Kissling, W. D., Kuehn, I., Ohlemueller, R.,Peres-Neto, P. R., Bjo¨rn Reineking, Schroeder, B.,Schurr, F. M. and Wilson,R.:Methods to account for spatial autocorrelation in the analysis of species distributional data: a review, Ecography 30: 609-628, 2007 gee, geepack, spdep, ncf,MASS 各パッケージを使用。サンプルコードの掲載。
- Hochkirch, Axel and Adorf, Frauke. Effects of prescribed burning and wildfires on Orthoptera in Central European peat bogs. Environmental Conservation. 2007;34:225-35.
- Jochumsen, KM, Tan, Q, Hølund, B. (2007) Gene expression in epithelial ovarian cancer: a study of intratumor heterogeneity. Int J Gynecol Cancer.(Epub ahead of print). Note: Clustering (the clustering function hclust in the package stats), visualization and all calculations were done using R.
- Koichi Matsumura, Shigeki Matsunaga, and Nobuhiro Fusetani (2007) Phosphatidylcholine profile-mediated group recognition in catfish. J Exp Biol 210: 1992-1999. (PCA)
- Kristoffersen SM, Ravnum S, Tourasse NJ et al. Low concentrations of bile salts induce stress responses and reduce motility in Bacillus cereus ATCC 14570. Journal of Bacteriology 2007; 189: 5302-13.
- Liu R, Wang X, Chen GY et al. The prognostic role of a gene signature from tumorigenic breast-cancer cells. The New England Journal of Medicine 2007; 356: 217-26.
- Ma Q, Wyszynski DF, Farrell JJ et al. Fetal hemoglobin in sickle cell anemia: genetic determinants of response to hydroxyurea. The Pharmacogenomics Journal 2007; Epub ahead of print.
- Meyer, Michael, Beeh, Kai-Michael, Beier, Jutta, et al. Tolerability and pharmacokinetics of inhaled bimosiamose disodium in healthy males. British Journal of Clinical Pharmacology. 2007;63(4):451-8.
- Michalski, Stefan G. and Durka, Walter. Synchronous pulsed flowering: analysis of the flowering phenology in Juncus (Juncaceae). Annals of Botany. 2007; 100(6): 1271-85.
- Myoumoto A, Nakatani K, Koshimizu TA, Matsubara H, Adachi S, Tsujimoto G. Glucocorticoid-induced granzyme A expression can be used as a marker of glucocorticoid sensitivity for acute lymphoblastic leukemia therapy. J Hum Genet. 2007;52(4):328-33. Epub 2007 Feb 20.(Dunnetの多重比較を実施)
- Naderi A, Teschendorff AE, Barbosa-Morais NL et al. A gene-expression signature to predict survival in breast cancer across independent data sets. Oncogene 2007; 26: 1507-16.
- Nagaoka T, Hirata K. Reconstruction of paleodemographic characteristics from skeletal age at death distributions: Perspectives from Hitotsubashi, Japan. American Journal of Physical Anthropology 2007; 134: 301-311. (MLE with R 1.1.1 and the R function written by Frankenberg and Konigsberg 2006)
- Palmieri M, Schwind MA, Stevens MHH et al. Effects of the myosin ATPase inhibitor 2,3-butanedione monoxime on amyloplast kinetics and gravitropism of Arabidopsis hypocotyls Physiologia Plantarum 2007; 130: 613-26.
- Rezzonico E, Lariani S, Barretto C et al. Global transcriptome analysis of the heat shock response of Bifidobacterium longum. FEMS Microbiology Letters 2007; 271: 136-45.
- Robbins J, Aragaki AK, Kooperberg C, Watts N, Wactawski-Wende J, Jackson RD, LeBoff MS, Lewis CE, Chen Z, Stefanick ML, Cauley J. Factors associated with 5-year risk of hip fracture in postmenopausal women. JAMA. 2007;298:2389-98. SASとRを使用。RではpolsplineとROCRを使用。
- Rougemont J, Naef F. Dynamical signatures of cellular fluctuations and oscillator stability in peripheral circadian clocks. Molecular Systems Biology 2007; 3.
- Saulnier DMA, Molenaar D, de Vos WM et al. Identification of prebiotic fructooligosaccharide metabolism in Lactobacillus plantarum WCFS1 through microarrays. Appl Environ Microbiol 2007; 73: 1753-65.
- Séralini G-E, Cellier D, de Vendomois JS. New analysis of a rat feeding study with a genetically modified maize reveals signs of hepatorenal toxicity. Archives of Environmental Contamination and Toxicology 2007; 52: 596-602. using spdep for calucalting Moran'I
- Sundaresh S, Randall A, Unal B et al. From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis. Bioinformatics 2007; 23: 508-18.
- Tan, Q., Thomassen, M. and Kruse, T.A. (2007) Feature selection for predicting tumor metastases in microarray experiments using paired design. Cancer Informatics. 2:133-8. Note: Used packages: PAM, e1071, caTools, vsn in Bioconductor, pamr.
- Tao CY, Hoyt J, Feng Y. A support vector machine classifier for recognizing mitotic subphases using high-content screening data. Journal of Biomolecular Screening 2007; 12: 490-6.
- Ton J, D'Alessandro M, Jourdie V et al. Priming by airborne signals boosts direct and indirect resistance in maize. The Plant Journal 2007; 49: 16-26.
- Trosvik P, Skånseng B, Jakobsen KS et al. Multivariate analysis of complex DNA sequence electropherograms for high-throughput quantitative analysis of mixed microbial populations. Appl Environ Microbiol 2007; 73: 4975-83.
- von der Lippe, M. and Kowarik I. Long-distance dispersal of plants by vehicles as a driver of plant invasions. Conservation Biology. 2007. (OnlineEarly article).
- Wall T, Båth K, Britton RA et al. The early response to acid shock in Lactobacillus reuteri involves the ClpL chaperone and a putative cell wall-altering esterase. Appl Environ Microbiol 2007; 73: 3924-35.
- Ward MD, Hoff PD. Persistent patterns of international commerce. Journal of Peace Research 2007; 44: 157-75.
- Wiedermann, Magdalena M., Nordin, Annika, Gunnarsson, Urban, Nilsson, Mats B.and EEricson, Lars. Global change shifts vegetation and plant-parasite interactions in a boreal mire. Ecology. 2007; 88(2):454-64.
- Wright RW, Dunn WR, Amendola A et al. Risk of tearing the intact anterior cruciate ligament in the contralateral knee and rupturing the anterior cruciate ligament graft during the first 2 years after anterior cruciate ligament reconstruction: a prospective MOON cohort study. American Journal of Sports Medicine 2007; 35: 1131-4.
- 波江彰彦(2007):PLS回帰を用いた地域分析の試み. 地理学評論, 80(4), 178-191. PLS回帰入門を参考にして、 pls.pcr パッケージを利用。グローバルモランには、 R Book の谷村先生の論文を引用。
2006†
- Amat I, Castelo M, Desouhant E et al. The influence of temperature and host availability on the host exploitation strategies of sexual and asexual parasitic wasps of the same species. Oecologia 2006; 148: 153-61.
- Angiolillo, Dominick J., Fernandez-Ortiz, Antonio, Bernardo, Esther, et al. Contribution of gene sequence variations of the hepatic cytochrome P450 3A4 enzyme to variability in individual responsiveness to clopidogrel. Arteriosclerosis, Thrombosis, and Vascular Biology. 2006; 26:1895-900.
- Bacher CP, Guggiari M, Brors B et al. Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation. Nature Cell Biology 2006; 8: 293-9.
- Bruno VM, Kalachikov S, Subaran R et al. Control of the C. albicans cell wall damage response by transcriptional regulator Cas5. PLoS Pathogens 2006; 2: e21.
- Cankar K, Štebih D, Dreo T et al. Critical points of DNA quantification by real-time PCR--effects of DNA extraction method and sample matrix on quantification of genetically modified organisms. BMC Biotechnology 2006; 6.
- Clark RM, Wagler TN, Quijada P et al. A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nature Genetics 2006; 38: 594-7.
- Díaz-Uriarte,R. and Alvarez de Andrés, S. (2006) Gene selection and classification of microarray data using random forest. BMC Bioinformatics 7(3):http://www.biomedcentral.com/1471-2105/7/3. Note: Used packages randomForest for random forest, e1071 for SVM (Support Vector Machines), class for KNN (K nearest neighbor), PAM for shrunken centroids, and geSignatures for DLDA (Diagonal Linear Discriminant Analysis).
- Doran HC, Lockwood JR. Fitting value-added models in R. Journal of Educational and Behavioral Statistics 2006; 31: 205-30.
- Efrosini Setakis, Heide Stirnadel and David J. Balding (2006) Logistic regression protects agains population structure in genetic association studies. Genome Research 16:290-296.
- Gathmann A, Wirooks L, Hothorn LA et al. Impact of Bt maize pollen (MON810) on lepidopteran larvae living on accompanying weeds. Molecular Ecology 2006; 15: 2677-85.
- Gentile M, Yan T, Tiquia SM et al. Stability in a denitrifying fluidized bed reactor. Microbial Ecology 2006; 52: 311-21.
- Goggi AS, Caragea P, Lopez-Sanchez H et al. Statistical analysis of outcrossing between adjacent maize grain production fields. Field Crops Research 2006; 99: 147-57.
- Heylen K, Vanparys B, Wittebolle L, et al. (2006) Cultivation of denitrifying bacteria: optimization of isolation conditions and diversity study. Appl Environ Microbiol. 72(4):2637-43. Note: Used seao (simple evolutionary algorithms for optimization).
- Holleley CE, Dickman CR, Crowther MS et al. Size breeds success: multiple paternity, multivariate selection and male semelparity in a small marsupial, Antechinus stuartii. Molecular Ecology 2006; 15: 3439-48.
- Huguier M. Ischemic colitis. American Journal of Surgery 2006; 192: 679-84.
- Iijima, H., Shibuya, M., Saito, H., and Takahashi, K. 2006. The water relations of Picea jezoensis seedlings on fallen logs. Can. J. For. Res. 36: 664-670. 2元配置の分散分析でRを使っています。
- Iwakura K, Ito H, Kawano S, Okamura A, Kurotobi T, Date M, Inoue K, Fujii K. Chronic pre-treatment of statins is associated with the reduction of the no-reflow phenomenon in the patients with reperfused acute myocardial infarction. Eur Heart J. 2006 Mar;27(5):534-9 bootstrap法にRを使っています。
- Karel G.M. Moons, Rogier A.R.T. Donders, Theo Stijnen and Frank E. Harrell, Jr. (2006) Using the outcome for imputation of missing predictor values was preferred. Journal of Clinical Epidemiology 59(10):1092-1101.
- Kariv Y., Wang W., Senagore A.J. et al (2006) Multivariable analysis of factors associated with hospital readmission after intestinal surgery. Am J Surg 191, 364-371.
- Konstantinidis, K.T., Ramette, A. and Tiedje, J.M. (2006) Toward a more robust assessment of intraspecies diversity, using fewer genetic markers. Applied and Environmental Microbiology. 72(11):7286-93.
- Krabbe PFM. Valuation structures of health states revealed with singular value decomposition. Medical Decision Making 2006; 26: 30-7.
- Kudirkienė E, Žilinskas H, Šiugždaitė J. Microbial flora of the dog eyes. Veterinarija Ir Zootechnika 2006; 34: 18-21.
- Kulkarni N, Pierse N, Rushton L et al. Carbon in airway macrophages and lung function in children. The New England Journal of Medicine 2006; 355: 21-30.
- Kuo WP, Liu F, Trimarchi J et al. A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nature Biotechnology 2006; 24: 832-40.
- Lombardo, F., Obach, R.S. et al. A Hybrid Mixture Discriminant Analysis-Random Forest Computational Model for the Prediction of Volume of Distribution of Drugs in Human. Journal of Medicinal Chemistry 2006; 49: 2262-2267.
- MacDonald ML, Lamerdin J, Owens S et al. Identifying off-target effects and hidden phenotypes of drugs in human cells. Nature Chemical Biology 2006; 2: 329-37.
- Myers S, Grant RW, Lugn NE et al. Impact of home-based monitoring on the care of patients with congestive heart failure. Home Health Care Management & Practice 2006; 18: 444-51.
- Park, K.S., Nam, J.H. and Choi, J. (2006) The short vitamin D receptor is associated with increased risk for generalized aggressive periodontitis. J Clin Periodontol. 33(8):524-8. Note: Used for estimating the deviations of genotype distribution from Hardy–Weinberg equilibrium and degree of pairwise linkage disequilibria.
- Peters U, Cherian J, Kim JH et al. Probing cell-division phenotype space and Polo-like kinase function using small molecules. Nature Chemical Biology 2006; 2: 618-??
- Renda G, Tacconelli S, Capone ML et al. Celecoxib, ibuprofen, and the antiplatelet effect of aspirin in patients with osteoarthritis and ischemic heart disease. Clinical Pharmacology & Therapeutics 2006; 80: 264-94.
- Schauer N, Semel Y, Roessner U et al. Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nature Biotechnology 2006; 24: 447-54.
- States DJ, Omenn GS, Blackwell TW et al. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nature Biotechnology 2006; 24: 333-8.
- Tecon R, Wells M, van der Meer JR. (2006) A new green fluorescent protein-based bacterial biosensor for analysing phenanthrene fluxes. Environ Microbiol. 8(4):697-708. Note: Used the R algorithms quantiles and boot.ci.
- Toedling, J., Rhein, P., Ratei, R. et al. (2006) Automated in-silico detection of cell populations in flow cytometry readouts and its application to leukemia disease monitoring. BMC Bioinformatics. 7(282). http://www.biomedcentral.com/content/pdf/1471-2105-7-282. Note: "All computational methods were implemented in the statistical programming language R. Analyses were conducted using custom functions, which depend on released R packages. We used the SVM implementation of thepackage e1071. Our custom functions have been assembled into a new R-package, called cytomics, which is available from the authors upon request".
- Turcotte K, Loredo-Osti JC, Fortin P et al. Complex genetic control of susceptibility to Mycobacterium bovis (Bacille Calmette-Guérin) infection in wild-derived Mus spretus mice. Gene and Immunity 2006; 7: 684-7.
- Velasco S, Årskölda E, Paesea M et al. Environmental factors influencing growth of and exopolysaccharide formation by Pediococcus parvulus 2.6. International Journal of Food Microbiology 2006; 111: 252-8.
- Warren, B.R., Yuk, Hyun-Gyun and Schneider, K.R. (2006) Detection of Shigella sonnei in selected foods by flow-through immunocapture followed by real-time polymerase chain reaction of isolation on macconkey agar. Journal of Rapid Methods and Automation in Microbiology. 14(4):309-24. Note: "Bias-reduced logistic regression (BRLR) models were constructed using R to identify significant differences (P < 0.05) among the detection methods tested."
- Wassenaar TA, Mark AE. The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions. Journal of Computational Chemistry 2006; 27: 316-25.
- Wieland B, Sandberg M, Johannessen GS et al. Genetic variability of Campylobacter jejuni isolated from fresh and frozen broiler carcasses. Journal of Applied Microbiology 2006; 101: 1027-32.
- 可知悠子、前田基成、笹井惠子、後藤直子、守口善也、庄子雅保、廣山夏生、瀧井正人、石川俊男、小牧元 (2006) 摂食障害患者におけるアレキシサイミアの特徴. 心身医学, 46(3), 215-222.
- 谷村晋 (2006) 推定汚染源とその周辺住民の健康を評価する統計モデル. 放射線科学 Vol.49 No.4 pp.123-132. splancsパッケージのtribble()を紹介しています。
2005†
- Barrier A, Lemoine A, Boelle P-Y et al. Colon cancer prognosis prediction by gene expression profiling. Oncogene 2005; 24: 6155-64.
- Bontemps, C., Golfier, G., Gris-Liebe, C. (2005) Microarray-based detection and typing of the Rhizobium nodulation gene nodC: potential of DNA arrays to diagnose biological functions of interest. Appl Environ Microbiol. 71(12):8042-8. Note: "Distances computation (euclidean distance) and dendrogram reconstruction (complete linkage method) were made under the R software environment using the dist and hclust functions, respectively".
- Colombo, Sara, Soranzo, Nicole, Rotger, Margalida, et al. Influence of ABCB1, ABCC1, ABCC2, and ABCG2 haplotypes on the cellular exposure of nelfinavir in vivo. Pharmacogenetics & Genomics. 2005; 15(9):599-608.
- Dorn A, Zhao H, Granberg F, et al. (2005) Identification of specific cellular genes up-regulated late in adenovirus type 12 infection. J Virol. 79(4):2404-12. Note: Used for analyzing quantitated arrays.
- Elvidge, G.P., Price, T.S., Glenny, L. et al. (2005) Development and evaluation of real competitive PCR for high-throughput quantitative applications. Analytical Biochemistry. 339:231-41. Note: "To aid the analysis, we have created a public licence software package called TITAN (www.well.ox.ac.uk/~tprice/titan) that runs in the R statistical environment and on a variety of operating systems."
- Farrell-Gray CC & Gotelli NJ.(2005) Allometric exponents support a 3/4-power scaling law. Ecology 86(8): 2083-2087.
- Fukuyama S, Inaoka T, Matsumura Y, Yamauchi T, Natsuhara K, Kimura R and Ohtsuka R (2005) Anthropometry of 5-19 year old Tongan children with special interest in the high prevalence of obesity among adolescent girls. Annals of Human Biology, 32(6):714-723.
- Gomez-Rubio, V., Ferrandiz-Ferragud, J. and Lopez-Quilez, A. (2005). Detecting clusters of disease with R. Journal of Geographical Systems, 7:189-206.
- Hickey, E., Abruzzo, G., Bowman, J. et al.(2005) Caspofungin versus amphotericin B treatment of Aspergillus fumigatus in kidneys of chronically immunosuppressed infected mice. Therapy. 2(4): 615-21. The R environment was used for all calculations and the production of graphs. Note: "The built-in Trellis-style library (lattice/grid), the boot library, and the Modern Applied Statistics with S (MASS) library provided function commands in addition to the standard R system calls."
- Kashuba, Angela D.M., Tierney, Camlin, Downey, Gerald F., Acosta, Edward P., Vergis, Emanuel N., Klingman, Karin, Mellors, John W., Eshleman, Susan H., Scott, Trevor R. and Collier, Ann C. (2005)Combining fosamprenavir with lopinavir/ritonavir substantially reduces amprenavir and lopinavir exposure: ACTG protocol A5143 results. AIDS. 19(2):145-152.
- Keitt TH, Urban DL.(2005) Scale-specific inference using wavelets. Ecology: Vol. 86, No. 9, pp. 2497–2504. 詳しくないので良く分からないんですが、Haar-wavelett transform を使っているようです。
- Lopez, Camilo, Soto, Mauricio, Restrepo, Silvia, Piégu, Benoît, Cooke, Richard, Delseny, Michel, Tohme, Joe and Verdier, Valérie. Gene expression profile in response to Xanthomonas axonopodis pv. manihotis infection in cassava using a cDNA microarray. Plant Molocular Biology. 2005;57(3):393-410.
- Mamoru Satoh, Eri Haruta-Satoh, Akira Omori, Masamichi Oh-Ishi, Yoshio Kodera, Sen-Ichi Furudate, Tadakazu Maeda. Effect of thyroxine on abnormal pancreatic proteomes of the hypothyroid rdw rat. Proteomics. 2005 Mar;5(4):1113-24.
- Opgen-Rhein R, Fahrmeir L, Strimmer K. Inference of demographic history from genealogical trees using reversible jump Markov chain Monte Carlo. BMC Evolutionary Biology 2005, 5:6.
- Patel NS, Paris D, Mathura V, et al. Inflammatory cytokine levels correlate with amyloid load in transgenic mouse models of Alzheimer's disease. Journal of Neuroinflammation 2005; 2.
- Ryder, J.J., Webberley, K.M., Boots, M., and Knell, R.J. (2005) Measuring the transmission dynamics of a sexually transmitted disease. PNAS, in press (abstract).（R-2.0.1 for Macでglm()を使っています）
- Shichi D, Kikkawa EF, Ota M, Katsuyama Y, Kimura A, Matsumori A, Kulski JK, Naruse TK, Inoko H.(2005) The haplotype block, NFKBIL1-ATP6V1G2-BAT1-MICB-MICA, within the class III - class I boundary region of the human major histocompatibility complex may control susceptibility to hepatitis C virus-associated dilated cardiomyopathy. Tissue Antigens., 66: 200-8. パッケージ haplo.statsのEMアルゴリズムを用いたハプロタイプ解析、並びにgeneticsを用いた連鎖不平衡解析を行った。
- Silvestri, L. van Saene, H.K.F., Milanese, M. et al. (2005) Impact of selective decontamination of the digestive tract on fungal carriage and infection: systematic review of randomized controlled trials. Intensive Care Med. 31(7):898-910. Note: r-meta package was used.
- Skarpaas, O., K. Shea and J. M. Bullock (2005) Optimizing dispersal study design by Monte Carlo simulation. Journal of Applied Ecology, 42: 731-739.
- Takahashi, T. (2005) Social memory, social stress, and economic behaviors. Brain Res Bull. 67(5):398-402.
- Takahashi, T., Ikeda, K., Ishikawa, M. et al. (2005) Anxiety, reactivity, and social stress-induced cortisol elevation in humans. Neuroendocrinology Letters, 26(4): 269-272.
- Takahashi, T., Ikeda, K., Ishikawa, M. et al. (2005) Interpersonal trust and social stress-induced cortisol elevation. Neuroreport, 16(2): 197-199.
- Tan DS. Diversity-oriented synthesis: exploring the intersections between chemistry and biology. Nature Chemical Biology 2005; 1: 74-84.
- Tanaka KD & Ueda K (2005) Horsfield's hawk-cuckoo nestlings simulate multiple gapes for begging. Science 308: 653. 普通のGLM (binomial, Poisson)を使ってます．
- 阿部聖哉、梨本真、松木吏弓、竹内亨、石井孝 (2005) GISと分類木を用いた林床ササ被覆度の予測と地図化. 植生学会誌, 22(2): 103-111. (package rpart で CART) Proteomics. 2005 Mar;5(4):1113-24. Effect of thyroxine on abnormal pancreatic proteomes of the hypothyroid rdw rat.
- 河合 勝彦 (2005) 地理情報システムと経済学 フリーソフトウェアGeoTools-liteとＲによる地域経済分析, 46(3), 桃山学院大学総合研究所『経済経営論集』
- 戸坂凡展、吉羽要直 (2005) コピュラの金融実務での具体的な活用方法の解説、『金融研究』第24巻別冊第2号、115-162頁、2005年 要約 全文
2004†
- Bagley, S.J. and Orlovich, D.A. (2004) Genet size and distribution of Amanita muscaria in a suburban park, Dunedin, New Zealand. New Zealand Journal of Botany. 42:939-47.
- Bjornson, C.L., Klassen, T.P., Williamson, J. et al. (2004) A randomized trial of a single dose of oral dexamethasone for mild croup. The New England Journal of Medicine. 35(13):1306-13.
- Brown PE, Christensen OF, Clough HE, et al. (2004) Frequency and spatial distribution of environmental Campylobacter spp. Appl Environ Microbiol. 70(11):6501-11. Note: Used geoR package.
- Candice L. Bjornson et al. ;A Randomized Trial of a Single Dose of Oral Dexamethasone for Mild Croup. N Engl J Med 2004;3511306-1313(Stataと併用、使い分けは不明）
- Chiaretti, S., Li, X., Gentleman, R., et al. (2004) Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival. Blood. 103(7):2771-8.
- Coste, Alix T., Karababa, M., Ischer, F. et al.(2004) TAC1, transcriptional activator of CDR Genes, is a new transcription factor Involved in the regulation of Candida albicans ABC transporters CDR1 and CDR2. Eukaryotic Cell. 3(6): 1639-52.
- Cummings, Michael P. and Segal, Mark R.(2004) Few amino acid positions in rpoB are associated with most of the rifampin resistance in Mycobacterium tuberculosis. BMC Bioinformatics. 5(137) http://www.biomedcentral.com/1471-2105/5/137. Note: Analyses were done with rpart (recursive partitioning) using the rpart library.
- Fu, H. ,Umezaki, M., Nakamura, K., Chen, P., Chen, J., Shi, Hui-Jing, Takano, T. Political Science 867 Spatial Modeling Winter 2005. Using spdep.
- K. Mori, M. Hata, S. Neya and T. Hoshino : MD simulation of asymmetric phospholipid bilayers with ions and cholesterols. Chem-Bio Inform. J., 4, 15-26 (2004) パッケージ tripack、deldirを用いた生体膜のボロノイ分割、KernSmoothを用いたカーネル密度推定を行った
- Karababa, M., Coste, Alix T., Rognon, B. et al. (2004) Comparison of gene expression profiles of Candida albicans azole-resistant clinical isolates and laboratory strains exposed to drugs inducing multidrug transporters. Antimicrobial Agents and Chemotherapy. 48(8):3064-79. Note: "Experiments from each hybridization were normalized using a LOWESS analysis for print-tip variability and for slide-to-slide variability using the publicly available software from Lund University run in R."
- Lai HJ, Cheng Y, Cho H et al. Association between initial disease presentation, lung disease outcomes, and survival in patients with cyctic fibrosis. Am J epidemiol 2004; 159: 537-46.
- Mehtatalo, L.(2004) A longitudinal height-diameter model for Norway spruce in Finland. Canadian Journal of Forest Research, 34: 131-140.（nlmeパッケージを用いたnonlinear mixed-effect modelの回帰）
- Morris, R. J., Lewis, O. T. and Godfray, H. C. J. (2004) Experimental evidence for apparent competition in a tropical forest food web. Nature 428: 310-313.（一般化線形モデル）
- Muller, A., Lopez-Lozano, J.M., Bertrand, X. and Talon, D. Relationship between ceftriaxone use and resistance to third-generation cephalosporins among clinical strains of Enterobacter cloacae. Journal of Antimicrobial Chemotherapy. 2004;54(1):173-7.
- Peng, RD., LJ Welty, LJ., and A. McDermott.
The National Morbidity, Mortality, and Air Pollution Study Database in R.
Johns Hopkins University, Dept. of Biostatistics Working Papers - Johns Hopkins University, 2004.
- Regoes, Roland R., Wiuff, Camilla, Zappala, Renata M., Garner, Kim N., Baquero, Fernando and Levin, Bruce R. (2004) Pharmacodynamic functions: a multiparameter approach to the design of antibiotic treatment regimens. Antimicrobial Agents and Chemotherapy. 48(10):3670-3676.
- Schmoll et al. (2004) Paternak genetic effects on offspring fitness are context dependent within the extrapair mating system of a socially monogamous passerine. Evolution. Vol. 59, No. 3, pp. 645-657 (package MASSのglmmPQLでmultilevel logistic model)
- Susumu Tanimura and Tsutomu Mizota. A graphic tool for displaying regional specialization coefficients. Japanese Journal of Computer Science, Vol. 9, No. 1, pp. 5-11, December 2004.
- Susumu Tanimura and Tsutomu Mizota. Regional difference in specialization coefficients of physicians in Nagasaki, Japan. Acta Medica Nagasakiensia, Vol. 49, pp. 99-105, September 2004.
- Sys K, Boon N, and Verstraete W.(2004) Development and validation of evolutionary algorithm software as an optimization tool for biological and environmental applications. J Microbiol Methods. 57(3):309-22. Note: Used seao, seao.gui, tcltk R-library and TclTk.
- Takahashi, T.(2004) Cortisol levels and time-discounting of monetary gain in humans. Neuroreport,15(13):2145-7.
- Takahashi, T., Ikeda, K., Ishikawa, M. et al. (2004) Social stress-induced cortisol elevation acutely impairs social memory in humans. Neurosci Lett, 363(2):125-30.
- Wilson, S., Hamilton, M.A., Hamilton, G.C. et al. (2004) Statistical quantification of detachment rates and size distributions of cell clumps from wild-type (PAO1) and cell signaling mutant (JP1) Pseudomonas aeruginosa biofilms. Applied and Environmental Microbiology. 70(10): 5847-52.
2003†
- Buckley et al. (2003) Are invasives bigger? A global study of seed size variation in two invasive shrubs. Ecology 84: 1434-1440（全ての計算。nlmeパッケージを用いたmulti-level linea mixed effect model）
- Fisher DO, Blomberg SP, Owens IPF. Extrinsic versus intrinsic factors in the decline and extinction of Australian marsupials. Proc R Soc Lond B 2003; 270: 1801-8.
- García-Gil MR, Mikkonen M, Savolainen O. Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris. Molecular Ecology 2003; 12: 1195-206.
- Gunther EC, Stone DJ, Gerwien RW et al. Prediction of clinical drug efficacy by classification of drug-induced genomic expression profiles in vitro. PNAS 2003; 100: 9608-13.
- Kullisaar T, Songisepp E, Mikelsaar M et al. Antioxidative probiotic fermented goats' milk decreases oxidative stress-mediated atherogenicity in human subjects. British Journal of Nutrition 2003; 90: 449-56.
- Lobry, J.R. and Chessel, D. (2003) Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria. J. Appl. Genet. 44(2):235-61. Note: ade4 package was used.
- Sentchilo V, Zehnder AJB, van der Meer JR. Charaterization of two alternative promoters for integrase expression in the clc genomic island of Pseudomonas sp. strain B13. Molecular Microbiology 2003; 49: 93-104.
- T. Sakaguchi and S. Mase, On the threshold method for marked spatial point processes, J. Japan Statist. Soc., 33-1, 23-37 (2003) パッケージ RandomFileds を用いた確率場シミュレーションを行なった
- 谷村晋. 空間疫学アプローチは疾病対策にどのように役に立つか. 日本熱帯医学会雑誌, Vol. 31, No. 3, pp. 237-241, December 2003.
2002†
- Bernstein, C., Heizmann, A. and Desouhant, E. (2002) Intraspecific competition between healthy and parasitised hosts in a host–parasitoid system: consequences for life-history traits. Ecological Entomology. 27(4): 415–423. Note: Used R for maximum-likelihood procedure.
- Guitton J, Grand F, Magat L, et al. (2002) Continuous flow isotope ratio mass spectrometry for the measurement of nanomole amounts of (13)CO(2) by a reverse isotope dilution method. J Mass Spectrom. 37(1):108-14. Note: R was used for the determination of polynomials.
- Nakazawa, M., T. Yamauchi, M. Tanaka, D. Ishimori, T. Furusawa, T. Midorikawa and R. Ohtsuka (2002) Community health assessment by urine dipstick screening in relation to the variety of lifestyles in Solomon Islands. People and Culture in Oceania, 18: 35-44.
- Rao, J., Seligson, D., Visapaa, H. et al. (2002) Tissue microarray analysis of cytoskeletal actin-associated biomarkers gelsolin and E-cadherin in urothelial carcinoma. Cancer. 95(6): 1247-57. Note: All analyses (student t test, analysis of variance (ANOVA), and the nonparametric Kruskal-Wallis tests, multivariate logistic regression , Kaplan-Meier curves, the log rank test, the Cox proportional hazards model) were performed with R.
2001†
- Bardow A, Nyvadb B, Nauntofte B. Relationships between medication intake, complaints of dry mouth, salivary flow rate and composition, and the rate of tooth demineralization in situ Archives of Oral Biology 2001; 46: 413-23.
2000†
- Bivand, R. Integrating GRASS 5.0 and R: GIS and modern statistics Computers & Geosciences, 2000, 26, 1043–1052.
1996†
- Ross Ihaka and Robert Gentleman (1996) R: A Language for Data Analysis and Graphics. Journal of computational and graphical statistics 5: 299-314. Rを使った論文ではなく、Rそのものの論文ですが、Rを使った時に引用できるはずです。
コメント†
- 自作関数 --
- Rを使った学術論文が山ほど出てくる昨今、もうこのページの役目は終わったのでは。現在はトップページの「主な内容」にこのページがリンクされていますが、そろそろトップページから除外してもよいのでは。 --
- ここでいう「学術論文」とはレフリーつきの学術雑誌に掲載れたもののみを含み、その他の大学で出されている紀要や研究報告書は含まないのでしょうか？ --
- 「Rを使った論文とやらを見たことない、査読で落とされるのでは？」に対する回答としてこのページがあると冒頭にあります。個人的には、「説得力のある学術誌を記入すべき」と思っています。 --
- 論文のリストが増えてきたので、年次別にするとか、分野別にしたらどうでしょうか？ -- ぼやき
- 年次別，かつ，著者アルファベット順にしてみました（言い出しっぺの原則というのはご存じない？） --
- Morris et al. (2004) moved from the category 2003 to 2004. -- Sam
- Added a few references in 2007, 2006, 2003, 2001 -- Sam
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