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Items: 1 to 50 of 236

1.

Genomic analysis of benign prostatic hyperplasia implicates cellular re-landscaping in disease pathogenesis.

Middleton LW, Shen Z, Varma S, Pollack AS, Gong X, Zhu S, Zhu C, Foley JW, Vennam S, Sweeney RT, Tu K, Biscocho J, Eminaga O, Nolley R, Tibshirani R, Brooks JD, West RB, Pollack JR.

JCI Insight. 2019 May 16;5. pii: 129749. doi: 10.1172/jci.insight.129749.

2.

Shaping of infant B cell receptor repertoires by environmental factors and infectious disease.

Nielsen SCA, Roskin KM, Jackson KJL, Joshi SA, Nejad P, Lee JY, Wagar LE, Pham TD, Hoh RA, Nguyen KD, Tsunemoto HY, Patel SB, Tibshirani R, Ley C, Davis MM, Parsonnet J, Boyd SD.

Sci Transl Med. 2019 Feb 27;11(481). pii: eaat2004. doi: 10.1126/scitranslmed.aat2004.

PMID:
30814336
3.

Reply to J. Wang et al.

Kurtz DM, Scherer F, Jin MC, Soo J, Craig AFM, Esfahani MS, Chabon JJ, Stehr H, Liu CL, Tibshirani R, Maeda LS, Gupta NK, Khodadoust MS, Advani RH, Newman AM, Dührsen U, Hüttmann A, Meignan M, Casasnovas O, Westin JR, Roschewski M, Wilson WH, Gaidano G, Rossi D, Diehn M, Alizadeh AA.

J Clin Oncol. 2019 Mar 20;37(9):755-757. doi: 10.1200/JCO.18.01907. Epub 2019 Feb 12. No abstract available.

PMID:
30753108
4.

Proliferation tracing with single-cell mass cytometry optimizes generation of stem cell memory-like T cells.

Good Z, Borges L, Vivanco Gonzalez N, Sahaf B, Samusik N, Tibshirani R, Nolan GP, Bendall SC.

Nat Biotechnol. 2019 Mar;37(3):259-266. doi: 10.1038/s41587-019-0033-2. Epub 2019 Feb 11.

PMID:
30742126
5.

High-dimensional longitudinal classification with the multinomial fused lasso.

Adhikari S, Lecci F, Becker JT, Junker BW, Kuller LH, Lopez OL, Tibshirani RJ.

Stat Med. 2019 May 30;38(12):2184-2205. doi: 10.1002/sim.8100. Epub 2019 Jan 30.

PMID:
30701586
6.

Collaborative efforts to forecast seasonal influenza in the United States, 2015-2016.

McGowan CJ, Biggerstaff M, Johansson M, Apfeldorf KM, Ben-Nun M, Brooks L, Convertino M, Erraguntla M, Farrow DC, Freeze J, Ghosh S, Hyun S, Kandula S, Lega J, Liu Y, Michaud N, Morita H, Niemi J, Ramakrishnan N, Ray EL, Reich NG, Riley P, Shaman J, Tibshirani R, Vespignani A, Zhang Q, Reed C; Influenza Forecasting Working Group.

Sci Rep. 2019 Jan 24;9(1):683. doi: 10.1038/s41598-018-36361-9.

7.

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy.

Ghaemi MS, DiGiulio DB, Contrepois K, Callahan B, Ngo TTM, Lee-McMullen B, Lehallier B, Robaczewska A, Mcilwain D, Rosenberg-Hasson Y, Wong RJ, Quaintance C, Culos A, Stanley N, Tanada A, Tsai A, Gaudilliere D, Ganio E, Han X, Ando K, McNeil L, Tingle M, Wise P, Maric I, Sirota M, Wyss-Coray T, Winn VD, Druzin ML, Gibbs R, Darmstadt GL, Lewis DB, Partovi Nia V, Agard B, Tibshirani R, Nolan G, Snyder MP, Relman DA, Quake SR, Shaw GM, Stevenson DK, Angst MS, Gaudilliere B, Aghaeepour N.

Bioinformatics. 2019 Jan 1;35(1):95-103. doi: 10.1093/bioinformatics/bty537.

8.

Found In Translation: a machine learning model for mouse-to-human inference.

Normand R, Du W, Briller M, Gaujoux R, Starosvetsky E, Ziv-Kenet A, Shalev-Malul G, Tibshirani RJ, Shen-Orr SS.

Nat Methods. 2018 Dec;15(12):1067-1073. doi: 10.1038/s41592-018-0214-9. Epub 2018 Nov 26.

PMID:
30478323
9.

Analyzing excess risk from matched designs with double controls: author's response.

Redelmeier DA, Tibshirani RJ.

J Clin Epidemiol. 2019 Mar;107:127-128. doi: 10.1016/j.jclinepi.2018.11.009. Epub 2018 Nov 16. No abstract available.

PMID:
30453039
10.

Log-ratio lasso: Scalable, sparse estimation for log-ratio models.

Bates S, Tibshirani R.

Biometrics. 2018 Nov 2. doi: 10.1111/biom.12995. [Epub ahead of print]

PMID:
30387139
11.

Genomic Feature Selection by Coverage Design Optimization.

Reid S, Newman AM, Diehn M, Alizadeh AA, Tibshirani R.

J Appl Stat. 2018;45(14):2658-2676. doi: 10.1080/02664763.2018.1432577. Epub 2018 Feb 7.

12.

Multicenter Study Using Desorption-Electrospray-Ionization-Mass-Spectrometry Imaging for Breast-Cancer Diagnosis.

Porcari AM, Zhang J, Garza KY, Rodrigues-Peres RM, Lin JQ, Young JH, Tibshirani R, Nagi C, Paiva GR, Carter SA, Sarian LO, Eberlin MN, Eberlin LS.

Anal Chem. 2018 Oct 2;90(19):11324-11332. doi: 10.1021/acs.analchem.8b01961. Epub 2018 Sep 18.

PMID:
30170496
13.

Post-Selection Inference for 1-Penalized Likelihood Models.

Taylor J, Tibshirani R.

Can J Stat. 2018 Mar;46(1):41-61. doi: 10.1002/cjs.11313. Epub 2017 Mar 6.

14.

Circulating Tumor DNA Measurements As Early Outcome Predictors in Diffuse Large B-Cell Lymphoma.

Kurtz DM, Scherer F, Jin MC, Soo J, Craig AFM, Esfahani MS, Chabon JJ, Stehr H, Liu CL, Tibshirani R, Maeda LS, Gupta NK, Khodadoust MS, Advani RH, Levy R, Newman AM, Dührsen U, Hüttmann A, Meignan M, Casasnovas RO, Westin JR, Roschewski M, Wilson WH, Gaidano G, Rossi D, Diehn M, Alizadeh AA.

J Clin Oncol. 2018 Oct 1;36(28):2845-2853. doi: 10.1200/JCO.2018.78.5246. Epub 2018 Aug 20.

PMID:
30125215
15.

Nonmechanistic forecasts of seasonal influenza with iterative one-week-ahead distributions.

Brooks LC, Farrow DC, Hyun S, Tibshirani RJ, Rosenfeld R.

PLoS Comput Biol. 2018 Jun 15;14(6):e1006134. doi: 10.1371/journal.pcbi.1006134. eCollection 2018 Jun.

16.

Reply to Vickers: Pharmacogenetics and progression to neovascular age-related macular degeneration-Evidence supporting practice change.

Vavvas DG, Small KW, Awh C, Zanke BW, Tibshirani RJ, Kustra R.

Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):E5640-E5641. doi: 10.1073/pnas.1804781115. Epub 2018 Jun 7. No abstract available.

17.

Noninvasive blood tests for fetal development predict gestational age and preterm delivery.

Ngo TTM, Moufarrej MN, Rasmussen MH, Camunas-Soler J, Pan W, Okamoto J, Neff NF, Liu K, Wong RJ, Downes K, Tibshirani R, Shaw GM, Skotte L, Stevenson DK, Biggio JR, Elovitz MA, Melbye M, Quake SR.

Science. 2018 Jun 8;360(6393):1133-1136. doi: 10.1126/science.aar3819.

PMID:
29880692
18.

Distinguishing malignant from benign microscopic skin lesions using desorption electrospray ionization mass spectrometry imaging.

Margulis K, Chiou AS, Aasi SZ, Tibshirani RJ, Tang JY, Zare RN.

Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):6347-6352. doi: 10.1073/pnas.1803733115. Epub 2018 Jun 4.

19.

DRUG-NEM: Optimizing drug combinations using single-cell perturbation response to account for intratumoral heterogeneity.

Anchang B, Davis KL, Fienberg HG, Williamson BD, Bendall SC, Karacosta LG, Tibshirani R, Nolan GP, Plevritis SK.

Proc Natl Acad Sci U S A. 2018 May 1;115(18):E4294-E4303. doi: 10.1073/pnas.1711365115. Epub 2018 Apr 13.

20.

Some methods for heterogeneous treatment effect estimation in high dimensions.

Powers S, Qian J, Jung K, Schuler A, Shah NH, Hastie T, Tibshirani R.

Stat Med. 2018 May 20;37(11):1767-1787. doi: 10.1002/sim.7623. Epub 2018 Mar 6.

21.

Results from the second year of a collaborative effort to forecast influenza seasons in the United States.

Biggerstaff M, Johansson M, Alper D, Brooks LC, Chakraborty P, Farrow DC, Hyun S, Kandula S, McGowan C, Ramakrishnan N, Rosenfeld R, Shaman J, Tibshirani R, Tibshirani RJ, Vespignani A, Yang W, Zhang Q, Reed C.

Epidemics. 2018 Sep;24:26-33. doi: 10.1016/j.epidem.2018.02.003. Epub 2018 Feb 24.

22.

Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse.

Good Z, Sarno J, Jager A, Samusik N, Aghaeepour N, Simonds EF, White L, Lacayo NJ, Fantl WJ, Fazio G, Gaipa G, Biondi A, Tibshirani R, Bendall SC, Nolan GP, Davis KL.

Nat Med. 2018 May;24(4):474-483. doi: 10.1038/nm.4505. Epub 2018 Mar 5.

23.

Methods for analyzing matched designs with double controls: excess risk is easily estimated and misinterpreted when evaluating traffic deaths.

Redelmeier DA, Tibshirani RJ.

J Clin Epidemiol. 2018 Jun;98:117-122. doi: 10.1016/j.jclinepi.2018.02.005. Epub 2018 Feb 13.

PMID:
29452220
24.

CFH and ARMS2 genetic risk determines progression to neovascular age-related macular degeneration after antioxidant and zinc supplementation.

Vavvas DG, Small KW, Awh CC, Zanke BW, Tibshirani RJ, Kustra R.

Proc Natl Acad Sci U S A. 2018 Jan 23;115(4):E696-E704. doi: 10.1073/pnas.1718059115. Epub 2018 Jan 8.

25.

Food allergy and omics.

Dhondalay GK, Rael E, Acharya S, Zhang W, Sampath V, Galli SJ, Tibshirani R, Boyd SD, Maecker H, Nadeau KC, Andorf S.

J Allergy Clin Immunol. 2018 Jan;141(1):20-29. doi: 10.1016/j.jaci.2017.11.007. Review.

PMID:
29307411
26.

Nuclear penalized multinomial regression with an application to predicting at bat outcomes in baseball.

Powers S, Hastie T, Tibshirani R.

Stat Modelling. 2018;18(5-6):388-410. doi: 10.1177/1471082X18777669. Epub 2018 Jun 11.

27.

A proteomic clock of human pregnancy.

Aghaeepour N, Lehallier B, Baca Q, Ganio EA, Wong RJ, Ghaemi MS, Culos A, El-Sayed YY, Blumenfeld YJ, Druzin ML, Winn VD, Gibbs RS, Tibshirani R, Shaw GM, Stevenson DK, Gaudilliere B, Angst MS.

Am J Obstet Gynecol. 2018 Mar;218(3):347.e1-347.e14. doi: 10.1016/j.ajog.2017.12.208. Epub 2017 Dec 24.

PMID:
29277631
28.

KLHL6 Is Preferentially Expressed in Germinal Center-Derived B-Cell Lymphomas.

Kunder CA, Roncador G, Advani RH, Gualco G, Bacchi CE, Sabile JM, Lossos IS, Nie K, Tibshirani RJ, Green MR, Alizadeh AA, Natkunam Y.

Am J Clin Pathol. 2017 Nov 20;148(6):465-476. doi: 10.1093/ajcp/aqx099.

29.

Big data modeling to predict platelet usage and minimize wastage in a tertiary care system.

Guan L, Tian X, Gombar S, Zemek AJ, Krishnan G, Scott R, Narasimhan B, Tibshirani RJ, Pham TD.

Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):11368-11373. doi: 10.1073/pnas.1714097114. Epub 2017 Oct 9.

30.

Data Shared Lasso: A Novel Tool to Discover Uplift.

Gross SM, Tibshirani R.

Comput Stat Data Anal. 2016 Sep;101:226-235. doi: 10.1016/j.csda.2016.02.015. Epub 2016 Mar 12.

31.

An immune clock of human pregnancy.

Aghaeepour N, Ganio EA, Mcilwain D, Tsai AS, Tingle M, Van Gassen S, Gaudilliere DK, Baca Q, McNeil L, Okada R, Ghaemi MS, Furman D, Wong RJ, Winn VD, Druzin ML, El-Sayed YY, Quaintance C, Gibbs R, Darmstadt GL, Shaw GM, Stevenson DK, Tibshirani R, Nolan GP, Lewis DB, Angst MS, Gaudilliere B.

Sci Immunol. 2017 Sep 1;2(15). pii: eaan2946. doi: 10.1126/sciimmunol.aan2946.

32.

Corrigendum: Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells.

Xu J, Carter AC, Gendrel AV, Attia M, Loftus J, Greenleaf WJ, Tibshirani R, Heard E, Chang HY.

Nat Genet. 2017 May 26;49(6):970. doi: 10.1038/ng0617-970a. No abstract available.

PMID:
28546577
33.

Metabolic Markers and Statistical Prediction of Serous Ovarian Cancer Aggressiveness by Ambient Ionization Mass Spectrometry Imaging.

Sans M, Gharpure K, Tibshirani R, Zhang J, Liang L, Liu J, Young JH, Dood RL, Sood AK, Eberlin LS.

Cancer Res. 2017 Jun 1;77(11):2903-2913. doi: 10.1158/0008-5472.CAN-16-3044. Epub 2017 Apr 17.

34.

Diagnosis of prostate cancer by desorption electrospray ionization mass spectrometric imaging of small metabolites and lipids.

Banerjee S, Zare RN, Tibshirani RJ, Kunder CA, Nolley R, Fan R, Brooks JD, Sonn GA.

Proc Natl Acad Sci U S A. 2017 Mar 28;114(13):3334-3339. doi: 10.1073/pnas.1700677114. Epub 2017 Mar 14.

35.

A human judgment approach to epidemiological forecasting.

Farrow DC, Brooks LC, Hyun S, Tibshirani RJ, Burke DS, Rosenfeld R.

PLoS Comput Biol. 2017 Mar 10;13(3):e1005248. doi: 10.1371/journal.pcbi.1005248. eCollection 2017 Mar.

36.

Chemical Space Mimicry for Drug Discovery.

Yuan W, Jiang D, Nambiar DK, Liew LP, Hay MP, Bloomstein J, Lu P, Turner B, Le QT, Tibshirani R, Khatri P, Moloney MG, Koong AC.

J Chem Inf Model. 2017 Apr 24;57(4):875-882. doi: 10.1021/acs.jcim.6b00754. Epub 2017 Apr 3.

37.

Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells.

Xu J, Carter AC, Gendrel AV, Attia M, Loftus J, Greenleaf WJ, Tibshirani R, Heard E, Chang HY.

Nat Genet. 2017 Mar;49(3):377-386. doi: 10.1038/ng.3769. Epub 2017 Jan 23. Erratum in: Nat Genet. 2017 May 26;49(6):970.

38.

Cardiolipins Are Biomarkers of Mitochondria-Rich Thyroid Oncocytic Tumors.

Zhang J, Yu W, Ryu SW, Lin J, Buentello G, Tibshirani R, Suliburk J, Eberlin LS.

Cancer Res. 2016 Nov 15;76(22):6588-6597. doi: 10.1158/0008-5472.CAN-16-1545. Epub 2016 Sep 22.

39.

High-dimensional regression adjustments in randomized experiments.

Wager S, Du W, Taylor J, Tibshirani RJ.

Proc Natl Acad Sci U S A. 2016 Nov 8;113(45):12673-12678. doi: 10.1073/pnas.1614732113. Epub 2016 Oct 25.

40.

Long-term course of patients with primary ocular adnexal MALT lymphoma: a large single-institution cohort study.

Desai A, Joag MG, Lekakis L, Chapman JR, Vega F, Tibshirani R, Tse D, Markoe A, Lossos IS.

Blood. 2017 Jan 19;129(3):324-332. doi: 10.1182/blood-2016-05-714584. Epub 2016 Oct 27.

41.

Pancreatic Cancer Surgical Resection Margins: Molecular Assessment by Mass Spectrometry Imaging.

Eberlin LS, Margulis K, Planell-Mendez I, Zare RN, Tibshirani R, Longacre TA, Jalali M, Norton JA, Poultsides GA.

PLoS Med. 2016 Aug 30;13(8):e1002108. doi: 10.1371/journal.pmed.1002108. eCollection 2016 Aug.

42.

A simple method for analyzing matched designs with double controls: McNemar's test can be extended.

Redelmeier DA, Tibshirani RJ.

J Clin Epidemiol. 2017 Jan;81:51-55.e2. doi: 10.1016/j.jclinepi.2016.08.006. Epub 2016 Aug 24.

PMID:
27565976
43.

Pathophysiological significance and therapeutic targeting of germinal center kinase in diffuse large B-cell lymphoma.

Matthews JM, Bhatt S, Patricelli MP, Nomanbhoy TK, Jiang X, Natkunam Y, Gentles AJ, Martinez E, Zhu D, Chapman JR, Cortizas E, Shyam R, Chinichian S, Advani R, Tan L, Zhang J, Choi HG, Tibshirani R, Buhrlage SJ, Gratzinger D, Verdun R, Gray NS, Lossos IS.

Blood. 2016 Jul 14;128(2):239-48. doi: 10.1182/blood-2016-02-696856. Epub 2016 May 5.

44.

Successful immunotherapy induces previously unidentified allergen-specific CD4+ T-cell subsets.

Ryan JF, Hovde R, Glanville J, Lyu SC, Ji X, Gupta S, Tibshirani RJ, Jay DC, Boyd SD, Chinthrajah RS, Davis MM, Galli SJ, Maecker HT, Nadeau KC.

Proc Natl Acad Sci U S A. 2016 Mar 1;113(9):E1286-95. doi: 10.1073/pnas.1520180113. Epub 2016 Jan 25.

45.

CUSTOMIZED TRAINING WITH AN APPLICATION TO MASS SPECTROMETRIC IMAGING OF CANCER TISSUE.

Powers S, Hastie T, Tibshirani R.

Ann Appl Stat. 2015 Dec;9(4):1709-1725. doi: 10.1214/15-AOAS866. Epub 2016 Jan 28.

46.

Sparse regression and marginal testing using cluster prototypes.

Reid S, Tibshirani R.

Biostatistics. 2016 Apr;17(2):364-76. doi: 10.1093/biostatistics/kxv049. Epub 2015 Nov 27.

47.

The Radiogenomic Risk Score: Construction of a Prognostic Quantitative, Noninvasive Image-based Molecular Assay for Renal Cell Carcinoma.

Jamshidi N, Jonasch E, Zapala M, Korn RL, Aganovic L, Zhao H, Tumkur Sitaram R, Tibshirani RJ, Banerjee S, Brooks JD, Ljungberg B, Kuo MD.

Radiology. 2015 Oct;277(1):114-23. doi: 10.1148/radiol.2015150800. Epub 2015 Aug 19.

PMID:
26402495
48.

Flexible Modeling of Epidemics with an Empirical Bayes Framework.

Brooks LC, Farrow DC, Hyun S, Tibshirani RJ, Rosenfeld R.

PLoS Comput Biol. 2015 Aug 28;11(8):e1004382. doi: 10.1371/journal.pcbi.1004382. eCollection 2015 Aug.

49.

Regularization Paths for Conditional Logistic Regression: The clogitL1 Package.

Reid S, Tibshirani R.

J Stat Softw. 2014 Jul;58(12). pii: 12.

50.

QnAs with Robert Tibshirani.

Tibshirani R, Ahmed F.

Proc Natl Acad Sci U S A. 2015 Jun 23;112(25):7621. doi: 10.1073/pnas.1509016112. No abstract available.

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