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Reproducibility of Methods to Detect Differentially Expressed Genes from Single-Cell RNA Sequencing.

Mou T, Deng W, Gu F, Pawitan Y, Vu TN.

Front Genet. 2020 Jan 17;10:1331. doi: 10.3389/fgene.2019.01331. eCollection 2019.


Disease trajectories and mortality among women diagnosed with breast cancer.

Yang H, Pawitan Y, He W, Eriksson L, Holowko N, Hall P, Czene K.

Breast Cancer Res. 2019 Aug 16;21(1):95. doi: 10.1186/s13058-019-1181-5.


Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data.

Deng W, Mou T, Kalari KR, Niu N, Wang L, Pawitan Y, Vu TN.

Bioinformatics. 2020 Feb 1;36(3):805-812. doi: 10.1093/bioinformatics/btz640.


Antibiotics use and risk of amyotrophic lateral sclerosis in Sweden.

Sun J, Zhan Y, Mariosa D, Larsson H, Almqvist C, Ingre C, Zagai U, Pawitan Y, Fang F.

Eur J Neurol. 2019 Nov;26(11):1355-1361. doi: 10.1111/ene.13986. Epub 2019 Jun 7.


Cell-level somatic mutation detection from single-cell RNA sequencing.

Vu TN, Nguyen HN, Calza S, Kalari KR, Wang L, Pawitan Y.

Bioinformatics. 2019 Nov 1;35(22):4679-4687. doi: 10.1093/bioinformatics/btz288.


On the relationship between the heritability and the attributable fraction.

Dahlqwist E, Magnusson PKE, Pawitan Y, Sjölander A.

Hum Genet. 2019 Apr;138(4):425-435. doi: 10.1007/s00439-019-02006-8. Epub 2019 Apr 2.


CREDO: Highly confident disease-relevant A-to-I RNA-editing discovery in breast cancer.

Hwang W, Calza S, Silvestri M, Pawitan Y, Lee Y.

Sci Rep. 2019 Mar 25;9(1):5064. doi: 10.1038/s41598-019-41294-y.


A fast detection of fusion genes from paired-end RNA-seq data.

Vu TN, Deng W, Trac QT, Calza S, Hwang W, Pawitan Y.

BMC Genomics. 2018 Nov 1;19(1):786. doi: 10.1186/s12864-018-5156-1.


Likelihood-based inference for bounds of causal parameters.

Lee W, Sjölander A, Larsson A, Pawitan Y.

Stat Med. 2018 Dec 30;37(30):4695-4706. doi: 10.1002/sim.7949. Epub 2018 Aug 28.


Accumulation of potential driver genes with genomic alterations predicts survival of high-risk neuroblastoma patients.

Suo C, Deng W, Vu TN, Li M, Shi L, Pawitan Y.

Biol Direct. 2018 Jul 16;13(1):14. doi: 10.1186/s13062-018-0218-5.


RPASE: Individual-based allele-specific expression detection without prior knowledge of haplotype phase.

Wang M, Uebbing S, Pawitan Y, Scofield DG.

Mol Ecol Resour. 2018 Nov;18(6):1247-1262. doi: 10.1111/1755-0998.12909. Epub 2018 Jun 20.


Isoform-level gene expression patterns in single-cell RNA-sequencing data.

Vu TN, Wills QF, Kalari KR, Niu N, Wang L, Pawitan Y, Rantalainen M.

Bioinformatics. 2018 Jul 15;34(14):2392-2400. doi: 10.1093/bioinformatics/bty100.


A Selection Operator for Summary Association Statistics Reveals Allelic Heterogeneity of Complex Traits.

Ning Z, Lee Y, Joshi PK, Wilson JF, Pawitan Y, Shen X.

Am J Hum Genet. 2017 Dec 7;101(6):903-912. doi: 10.1016/j.ajhg.2017.09.027.


Heritable Variation, With Little or No Maternal Effect, Accounts for Recurrence Risk to Autism Spectrum Disorder in Sweden.

Yip BHK, Bai D, Mahjani B, Klei L, Pawitan Y, Hultman CM, Grice DE, Roeder K, Buxbaum JD, Devlin B, Reichenberg A, Sandin S.

Biol Psychiatry. 2018 Apr 1;83(7):589-597. doi: 10.1016/j.biopsych.2017.09.007. Epub 2017 Sep 21.


Generalized survival models for correlated time-to-event data.

Liu XR, Pawitan Y, Clements MS.

Stat Med. 2017 Dec 20;36(29):4743-4762. doi: 10.1002/sim.7451. Epub 2017 Sep 14.


Regression standardization and attributable fraction estimation with between-within frailty models for clustered survival data.

Dahlqwist E, Pawitan Y, Sjölander A.

Stat Methods Med Res. 2019 Feb;28(2):462-485. doi: 10.1177/0962280217727558. Epub 2017 Sep 13.


A clinical model for identifying the short-term risk of breast cancer.

Eriksson M, Czene K, Pawitan Y, Leifland K, Darabi H, Hall P.

Breast Cancer Res. 2017 Mar 14;19(1):29. doi: 10.1186/s13058-017-0820-y.


Patterns of acute inflammatory symptoms prior to cancer diagnosis.

Setiawan A, Yin L, Auer G, Czene K, Smedby KE, Pawitan Y.

Sci Rep. 2017 Mar 6;7(1):67. doi: 10.1038/s41598-017-00133-8.


The ABC model of prostate cancer: A conceptual framework for the design and interpretation of prognostic studies.

Pettersson A, Gerke T, Fall K, Pawitan Y, Holmberg L, Giovannucci EL, Kantoff PW, Adami HO, Rider JR, Mucci LA; Transdisciplinary Prostate Cancer Partnership (ToPCaP).

Cancer. 2017 May 1;123(9):1490-1496. doi: 10.1002/cncr.30582. Epub 2017 Feb 2. Review.


Comprehensive landscape of subtype-specific coding and non-coding RNA transcripts in breast cancer.

Vu TN, Pramana S, Calza S, Suo C, Lee D, Pawitan Y.

Oncotarget. 2016 Oct 18;7(42):68851-68863. doi: 10.18632/oncotarget.11998.


Parametric and penalized generalized survival models.

Liu XR, Pawitan Y, Clements M.

Stat Methods Med Res. 2018 May;27(5):1531-1546. doi: 10.1177/0962280216664760. Epub 2016 Sep 1.


Multidimensional Normalization to Minimize Plate Effects of Suspension Bead Array Data.

Hong MG, Lee W, Nilsson P, Pawitan Y, Schwenk JM.

J Proteome Res. 2016 Oct 7;15(10):3473-3480. Epub 2016 Sep 12.


ABO blood group and risk of cancer: A register-based cohort study of 1.6 million blood donors.

Vasan SK, Hwang J, Rostgaard K, Nyrén O, Ullum H, Pedersen OBV, Erikstrup C, Melbye M, Hjalgrim H, Pawitan Y, Edgren G.

Cancer Epidemiol. 2016 Oct;44:40-43. doi: 10.1016/j.canep.2016.06.005. Epub 2016 Jul 25.


A Critical Look at Entropy-Based Gene-Gene Interaction Measures.

Lee W, Sjölander A, Pawitan Y.

Genet Epidemiol. 2016 Jul;40(5):416-24. doi: 10.1002/gepi.21974. Epub 2016 May 27.


Beta-Poisson model for single-cell RNA-seq data analyses.

Vu TN, Wills QF, Kalari KR, Niu N, Wang L, Rantalainen M, Pawitan Y.

Bioinformatics. 2016 Jul 15;32(14):2128-35. doi: 10.1093/bioinformatics/btw202. Epub 2016 Apr 19.


Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease.

Allen GI, Amoroso N, Anghel C, Balagurusamy V, Bare CJ, Beaton D, Bellotti R, Bennett DA, Boehme KL, Boutros PC, Caberlotto L, Caloian C, Campbell F, Chaibub Neto E, Chang YC, Chen B, Chen CY, Chien TY, Clark T, Das S, Davatzikos C, Deng J, Dillenberger D, Dobson RJ, Dong Q, Doshi J, Duma D, Errico R, Erus G, Everett E, Fardo DW, Friend SH, Fröhlich H, Gan J, St George-Hyslop P, Ghosh SS, Glaab E, Green RC, Guan Y, Hong MY, Huang C, Hwang J, Ibrahim J, Inglese P, Iyappan A, Jiang Q, Katsumata Y, Kauwe JS, Klein A, Kong D, Krause R, Lalonde E, Lauria M, Lee E, Lin X, Liu Z, Livingstone J, Logsdon BA, Lovestone S, Ma TW, Malhotra A, Mangravite LM, Maxwell TJ, Merrill E, Nagorski J, Namasivayam A, Narayan M, Naz M, Newhouse SJ, Norman TC, Nurtdinov RN, Oyang YJ, Pawitan Y, Peng S, Peters MA, Piccolo SR, Praveen P, Priami C, Sabelnykova VY, Senger P, Shen X, Simmons A, Sotiras A, Stolovitzky G, Tangaro S, Tateo A, Tung YA, Tustison NJ, Varol E, Vradenburg G, Weiner MW, Xiao G, Xie L, Xie Y, Xu J, Yang H, Zhan X, Zhou Y, Zhu F, Zhu H, Zhu S; Alzheimer's Disease Neuroimaging Initiative.

Alzheimers Dement. 2016 Jun;12(6):645-53. doi: 10.1016/j.jalz.2016.02.006. Epub 2016 Apr 11.


Model-based estimation of the attributable fraction for cross-sectional, case-control and cohort studies using the R package AF.

Dahlqwist E, Zetterqvist J, Pawitan Y, Sjölander A.

Eur J Epidemiol. 2016 Jun;31(6):575-82. doi: 10.1007/s10654-016-0137-7. Epub 2016 Mar 18.


Nonparametric estimation of the rediscovery rate.

Lee D, Ganna A, Pawitan Y, Lee W.

Stat Med. 2016 Aug 15;35(18):3203-12. doi: 10.1002/sim.6915. Epub 2016 Feb 22.


One CNV Discordance in NRXN1 Observed Upon Genome-wide Screening in 38 Pairs of Adult Healthy Monozygotic Twins.

Magnusson PK, Lee D, Chen X, Szatkiewicz J, Pramana S, Teo S, Sullivan PF, Feuk L, Pawitan Y.

Twin Res Hum Genet. 2016 Apr;19(2):97-103. doi: 10.1017/thg.2016.5. Epub 2016 Feb 22.


Improving the Prediction of Prostate Cancer Overall Survival by Supplementing Readily Available Clinical Data with Gene Expression Levels of IGFBP3 and F3 in Formalin-Fixed Paraffin Embedded Core Needle Biopsy Material.

Peng Z, Andersson K, Lindholm J, Dethlefsen O, Pramana S, Pawitan Y, Nistér M, Nilsson S, Li C.

PLoS One. 2016 Jan 5;11(1):e0145545. doi: 10.1371/journal.pone.0145545. eCollection 2016.


Doubly robust methods for handling confounding by cluster.

Zetterqvist J, Vansteelandt S, Pawitan Y, Sjölander A.

Biostatistics. 2016 Apr;17(2):264-76. doi: 10.1093/biostatistics/kxv041. Epub 2015 Oct 26.


Likelihood ratio and score burden tests for detecting disease-associated rare variants.

Lee W, Lee D, Pawitan Y.

Stat Appl Genet Mol Biol. 2015 Nov;14(5):481-95. doi: 10.1515/sagmb-2014-0089.


Gene-based meta-analysis of genome-wide association studies implicates new loci involved in obesity.

Hägg S, Ganna A, Van Der Laan SW, Esko T, Pers TH, Locke AE, Berndt SI, Justice AE, Kahali B, Siemelink MA, Pasterkamp G; GIANT Consortium, Strachan DP, Speliotes EK, North KE, Loos RJ, Hirschhorn JN, Pawitan Y, Ingelsson E.

Hum Mol Genet. 2015 Dec 1;24(23):6849-60. doi: 10.1093/hmg/ddv379. Epub 2015 Sep 16.


Identifying and Assessing Interesting Subgroups in a Heterogeneous Population.

Lee W, Alexeyenko A, Pernemalm M, Guegan J, Dessen P, Lazar V, Lehtiö J, Pawitan Y.

Biomed Res Int. 2015;2015:462549. doi: 10.1155/2015/462549. Epub 2015 Aug 3.


Sparse estimation of gene-gene interactions in prediction models.

Lee S, Pawitan Y, Ingelsson E, Lee Y.

Stat Methods Med Res. 2017 Oct;26(5):2319-2332. doi: 10.1177/0962280215597261. Epub 2015 Aug 11.


A simplified interventional mapping system (SIMS) for the selection of combinations of targeted treatments in non-small cell lung cancer.

Lazar V, Rubin E, Depil S, Pawitan Y, Martini JF, Gomez-Navarro J, Yver A, Kan Z, Dry JR, Kehren J, Validire P, Rodon J, Vielh P, Ducreux M, Galbraith S, Lehnert M, Onn A, Berger R, Pierotti MA, Porgador A, Pramesh CS, Ye DW, Carvalho AL, Batist G, Le Chevalier T, Morice P, Besse B, Vassal G, Mortlock A, Hansson J, Berindan-Neagoe I, Dann R, Haspel J, Irimie A, Laderman S, Nechushtan H, Al Omari AS, Haywood T, Bresson C, Soo KC, Osman I, Mata H, Lee JJ, Jhaveri K, Meurice G, Palmer G, Lacroix L, Koscielny S, Eterovic KA, Blay JY, Buller R, Eggermont A, Schilsky RL, Mendelsohn J, Soria JC, Rothenberg M, Scoazec JY, Hong WK, Kurzrock R.

Oncotarget. 2015 Jun 10;6(16):14139-52.


Molecular differences in transition zone and peripheral zone prostate tumors.

Sinnott JA, Rider JR, Carlsson J, Gerke T, Tyekucheva S, Penney KL, Sesso HD, Loda M, Fall K, Stampfer MJ, Mucci LA, Pawitan Y, Andersson SO, Andrén O.

Carcinogenesis. 2015 Jun;36(6):632-8. doi: 10.1093/carcin/bgv051. Epub 2015 Apr 13.


Integration of somatic mutation, expression and functional data reveals potential driver genes predictive of breast cancer survival.

Suo C, Hrydziuszko O, Lee D, Pramana S, Saputra D, Joshi H, Calza S, Pawitan Y.

Bioinformatics. 2015 Aug 15;31(16):2607-13. doi: 10.1093/bioinformatics/btv164. Epub 2015 Mar 24.


Distinct effects of anti-inflammatory and anti-thrombotic drugs on cancer characteristics at diagnosis.

Pawitan Y, Yin L, Setiawan A, Auer G, Smedby KE, Czene K.

Eur J Cancer. 2015 Apr;51(6):751-7. doi: 10.1016/j.ejca.2015.02.004. Epub 2015 Feb 25.


VEGF-A Expression Correlates with TP53 Mutations in Non-Small Cell Lung Cancer: Implications for Antiangiogenesis Therapy.

Schwaederlé M, Lazar V, Validire P, Hansson J, Lacroix L, Soria JC, Pawitan Y, Kurzrock R.

Cancer Res. 2015 Apr 1;75(7):1187-90. doi: 10.1158/0008-5472.CAN-14-2305. Epub 2015 Feb 11.


Operator dependent choice of prostate cancer biopsy has limited impact on a gene signature analysis for the highly expressed genes IGFBP3 and F3 in prostate cancer epithelial cells.

Peng Z, Andersson K, Lindholm J, Bodin I, Pramana S, Pawitan Y, Nistér M, Nilsson S, Li C.

PLoS One. 2014 Oct 8;9(10):e109610. doi: 10.1371/journal.pone.0109610. eCollection 2014.


Rediscovery rate estimation for assessing the validation of significant findings in high-throughput studies.

Ganna A, Lee D, Ingelsson E, Pawitan Y.

Brief Bioinform. 2015 Jul;16(4):563-75. doi: 10.1093/bib/bbu033. Epub 2014 Sep 24.


Bounds on sufficient-cause interaction.

Sjölander A, Lee W, Källberg H, Pawitan Y.

Eur J Epidemiol. 2014 Nov;29(11):813-20. doi: 10.1007/s10654-014-9953-9. Epub 2014 Sep 24.


Most genetic risk for autism resides with common variation.

Gaugler T, Klei L, Sanders SJ, Bodea CA, Goldberg AP, Lee AB, Mahajan M, Manaa D, Pawitan Y, Reichert J, Ripke S, Sandin S, Sklar P, Svantesson O, Reichenberg A, Hultman CM, Devlin B, Roeder K, Buxbaum JD.

Nat Genet. 2014 Aug;46(8):881-5. doi: 10.1038/ng.3039. Epub 2014 Jul 20.


Aspirin intake and breast cancer survival - a nation-wide study using prospectively recorded data in Sweden.

Holmes MD, Olsson H, Pawitan Y, Holm J, Lundholm C, Andersson TM, Adami HO, Askling J, Smedby KE.

BMC Cancer. 2014 Jun 2;14:391. doi: 10.1186/1471-2407-14-391.


Affinity proteomics reveals elevated muscle proteins in plasma of children with cerebral malaria.

Bachmann J, Burté F, Pramana S, Conte I, Brown BJ, Orimadegun AE, Ajetunmobi WA, Afolabi NK, Akinkunmi F, Omokhodion S, Akinbami FO, Shokunbi WA, Kampf C, Pawitan Y, Uhlén M, Sodeinde O, Schwenk JM, Wahlgren M, Fernandez-Reyes D, Nilsson P.

PLoS Pathog. 2014 Apr 17;10(4):e1004038. doi: 10.1371/journal.ppat.1004038. eCollection 2014 Apr.


Bounds on causal interactions for binary outcomes.

Sjölander A, Lee W, Källberg H, Pawitan Y.

Biometrics. 2014 Sep;70(3):500-5. doi: 10.1111/biom.12166. Epub 2014 Mar 12.


An expression signature at diagnosis to estimate prostate cancer patients' overall survival.

Peng Z, Skoog L, Hellborg H, Jonstam G, Wingmo IL, Hjälm-Eriksson M, Harmenberg U, Cedermark GC, Andersson K, Ahrlund-Richter L, Pramana S, Pawitan Y, Nistér M, Nilsson S, Li C.

Prostate Cancer Prostatic Dis. 2014 Mar;17(1):81-90. doi: 10.1038/pcan.2013.57. Epub 2014 Jan 7.


Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data.

Suo C, Calza S, Salim A, Pawitan Y.

Bioinformatics. 2014 Feb 15;30(4):506-13. doi: 10.1093/bioinformatics/btt704. Epub 2013 Dec 3.


Integrated molecular portrait of non-small cell lung cancers.

Lazar V, Suo C, Orear C, van den Oord J, Balogh Z, Guegan J, Job B, Meurice G, Ripoche H, Calza S, Hasmats J, Lundeberg J, Lacroix L, Vielh P, Dufour F, Lehtiö J, Napieralski R, Eggermont A, Schmitt M, Cadranel J, Besse B, Girard P, Blackhall F, Validire P, Soria JC, Dessen P, Hansson J, Pawitan Y.

BMC Med Genomics. 2013 Dec 3;6:53. doi: 10.1186/1755-8794-6-53.

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