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Items: 1 to 50 of 76

1.

Points of Significance: Machine learning: a primer.

Bzdok D, Krzywinski M, Altman N.

Nat Methods. 2017 Nov 30;14(12):1119-1120. doi: 10.1038/nmeth.4526. No abstract available.

PMID:
29664466
2.

A collaborative filtering-based approach to biomedical knowledge discovery.

Lever J, Gakkhar S, Gottlieb M, Rashnavadi T, Lin S, Siu C, Smith M, Jones MR, Krzywinski M, Jones SJM, Wren J.

Bioinformatics. 2018 Feb 15;34(4):652-659. doi: 10.1093/bioinformatics/btx613.

PMID:
29028901
3.

Enhancing knowledge discovery from cancer genomics data with Galaxy.

Albuquerque MA, Grande BM, Ritch EJ, Pararajalingam P, Jessa S, Krzywinski M, Grewal JK, Shah SP, Boutros PC, Morin RD.

Gigascience. 2017 May 1;6(5):1-13. doi: 10.1093/gigascience/gix015.

4.

SnapShot: Epigenomic Assays.

Krzywinski M, Hirst M.

Cell. 2016 Nov 17;167(5):1430-1430.e1. doi: 10.1016/j.cell.2016.11.015.

5.

An Epigenomic Approach to Improving Response to Neoadjuvant Cisplatin Chemotherapy in Bladder Cancer.

Xylinas E, Hassler MR, Zhuang D, Krzywinski M, Erdem Z, Robinson BD, Elemento O, Clozel T, Shariat SF.

Biomolecules. 2016 Sep 2;6(3). pii: E37. doi: 10.3390/biom6030037.

6.

Analyzing outliers: influential or nuisance?

Altman N, Krzywinski M.

Nat Methods. 2016 Apr;13(4):281-2. No abstract available.

PMID:
27482566
7.

Neural circuit diagrams.

Hunnicutt BJ, Krzywinski M.

Nat Methods. 2016 Mar;13(3):189. No abstract available.

PMID:
27347585
8.

Visualizing Clonal Evolution in Cancer.

Krzywinski M.

Mol Cell. 2016 Jun 2;62(5):652-6. doi: 10.1016/j.molcel.2016.05.025. Review.

9.

Points of View: Pathways.

Hunnicutt BJ, Krzywinski M.

Nat Methods. 2016 Jan;13(1):5. No abstract available.

PMID:
27110623
10.

Study Design for Sequencing Studies.

Honaas LA, Altman NS, Krzywinski M.

Methods Mol Biol. 2016;1418:39-66. doi: 10.1007/978-1-4939-3578-9_3.

PMID:
27008009
11.

Multiple linear regression.

Krzywinski M, Altman N.

Nat Methods. 2015 Dec;12(12):1103-4. No abstract available.

PMID:
26962577
12.

Simple linear regression.

Altman N, Krzywinski M.

Nat Methods. 2015 Nov;12(11):999-1000. No abstract available.

PMID:
26824102
13.

Association, correlation and causation.

Altman N, Krzywinski M.

Nat Methods. 2015 Oct;12(10):899-900. No abstract available.

PMID:
26688882
14.

Points of Significance. Bayesian networks.

Puga JL, Krzywinski M, Altman N.

Nat Methods. 2015 Sep;12(9):799-800. No abstract available.

PMID:
26554085
15.

POINTS OF VIEW: Unentangling complex plots.

McInerny G, Krzywinski M.

Nat Methods. 2015 Jul;12(7):591. No abstract available.

PMID:
26339708
16.

Sampling distributions and the bootstrap.

Kulesa A, Krzywinski M, Blainey P, Altman N.

Nat Methods. 2015 Jun;12(6):477-8. No abstract available.

17.

POINTS OF SIGNIFICANCE: Bayesian statistics.

López Puga J, Krzywinski M, Altman N.

Nat Methods. 2015 May;12(5):377-8. No abstract available.

PMID:
26120626
18.

Points of significance: Bayes' theorem.

López Puga J, Krzywinski M, Altman N.

Nat Methods. 2015 Apr;12(4):277-8. No abstract available.

PMID:
26005726
19.

Split plot design.

Altman N, Krzywinski M.

Nat Methods. 2015 Mar;12(3):165-6. No abstract available.

PMID:
25879095
20.

Comprehensive miRNA sequence analysis reveals survival differences in diffuse large B-cell lymphoma patients.

Lim EL, Trinh DL, Scott DW, Chu A, Krzywinski M, Zhao Y, Robertson AG, Mungall AJ, Schein J, Boyle M, Mottok A, Ennishi D, Johnson NA, Steidl C, Connors JM, Morin RD, Gascoyne RD, Marra MA.

Genome Biol. 2015 Jan 29;16:18. doi: 10.1186/s13059-014-0568-y.

21.

Points of significance: Sources of variation.

Altman N, Krzywinski M.

Nat Methods. 2015 Jan;12(1):5-6. No abstract available.

PMID:
25699313
22.

The Release 6 reference sequence of the Drosophila melanogaster genome.

Hoskins RA, Carlson JW, Wan KH, Park S, Mendez I, Galle SE, Booth BW, Pfeiffer BD, George RA, Svirskas R, Krzywinski M, Schein J, Accardo MC, Damia E, Messina G, Méndez-Lago M, de Pablos B, Demakova OV, Andreyeva EN, Boldyreva LV, Marra M, Carvalho AB, Dimitri P, Villasante A, Zhimulev IF, Rubin GM, Karpen GH, Celniker SE.

Genome Res. 2015 Mar;25(3):445-58. doi: 10.1101/gr.185579.114. Epub 2015 Jan 14.

23.

Points of significance: two-factor designs.

Krzywinski M, Altman N.

Nat Methods. 2014 Dec;11(12):1187-8. No abstract available.

PMID:
25584374
24.

Points of significance: nested designs. For studies with hierarchical noise sources, use a nested analysis of variance approach.

Krzywinski M, Altman N, Blainey P.

Nat Methods. 2014 Oct;11(10):977-8. No abstract available.

PMID:
25392877
25.

Points of significance: replication.

Blainey P, Krzywinski M, Altman N.

Nat Methods. 2014 Sep;11(9):879-80. No abstract available.

PMID:
25317452
26.

Understanding the sequence requirements of protein families: insights from the BioVis 2013 contests.

Ray WC, Rumpf RW, Sullivan B, Callahan N, Magliery T, Machiraju R, Wong B, Krzywinski M, Bartlett CW.

BMC Proc. 2014 Aug 28;8(Suppl 2 Proceedings of the 3rd Annual Symposium on Biologica):S1. doi: 10.1186/1753-6561-8-S2-S1. eCollection 2014.

27.

Points of significance: Analysis of variance and blocking.

Krzywinski M, Altman N.

Nat Methods. 2014 Jul;11(7):699-700. No abstract available.

PMID:
25110779
28.

Points of view: designing comparative experiments.

Krzywinski M, Altman N.

Nat Methods. 2014 Jun;11(6):597-8. No abstract available.

PMID:
25019145
29.

Impact of ERBB2 mutations on in vitro sensitivity of bladder cancer to lapatinib.

de Martino M, Zhuang D, Klatte T, Rieken M, Rouprêt M, Xylinas E, Clozel T, Krzywinski M, Elemento O, Shariat SF.

Cancer Biol Ther. 2014 Sep;15(9):1239-47. doi: 10.4161/cbt.29687. Epub 2014 Jul 14.

30.

Points of significance: Nonparametric tests.

Krzywinski M, Altman N.

Nat Methods. 2014 May;11(5):467-8. doi: 10.1038/nmeth.2937. No abstract available.

PMID:
24820360
31.

Points of significance: Comparing samples—part I.

Krzywinski M, Altman N.

Nat Methods. 2014 Mar;11(3):215-6. No abstract available.

PMID:
24724163
32.

Visualizing samples with box plots.

Krzywinski M, Altman N.

Nat Methods. 2014 Feb;11(2):119-20. No abstract available.

PMID:
24645192
33.

Significance, P values and t-tests.

Krzywinski M, Altman N.

Nat Methods. 2013 Nov;10(11):1041-2. No abstract available.

PMID:
24344377
34.

Reply to: "against storytelling of scientific results".

Krzywinski M, Cairo A.

Nat Methods. 2013 Nov;10(11):1046. doi: 10.1038/nmeth.2700. No abstract available.

PMID:
24173379
35.

Points of significance: error bars.

Krzywinski M, Altman N.

Nat Methods. 2013 Oct;10(10):921-2. doi: 10.1038/nmeth.2659. No abstract available.

PMID:
24161969
36.

Points of significance: Importance of being uncertain.

Krzywinski M, Altman N.

Nat Methods. 2013 Sep;10(9):809-10. No abstract available.

PMID:
24143821
37.

The anatomy of successful computational biology software.

Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M, Li H, Nekrutenko A, Robinson J, Rasband W, Taylor J, Trapnell C.

Nat Biotechnol. 2013 Oct;31(10):894-7. doi: 10.1038/nbt.2721. No abstract available.

38.

Points of view: Storytelling.

Krzywinski M, Cairo A.

Nat Methods. 2013 Aug;10(8):687. No abstract available.

PMID:
24058975
39.

Multidimensional data.

Krzywinski M, Savig E.

Nat Methods. 2013 Jul;10(7):595. No abstract available.

PMID:
23967480
40.

Points of view: plotting symbols.

Krzywinski M, Wong B.

Nat Methods. 2013 Jun;10(6):451. No abstract available.

PMID:
23866328
41.

Points of view: Elements of visual style.

Krzywinski M.

Nat Methods. 2013 May;10(5):371. No abstract available.

PMID:
23762902
42.

Points of view: Labels and callouts.

Krzywinski M.

Nat Methods. 2013 Apr;10(4):275. No abstract available.

PMID:
23653918
43.

The genetic landscape of high-risk neuroblastoma.

Pugh TJ, Morozova O, Attiyeh EF, Asgharzadeh S, Wei JS, Auclair D, Carter SL, Cibulskis K, Hanna M, Kiezun A, Kim J, Lawrence MS, Lichenstein L, McKenna A, Pedamallu CS, Ramos AH, Shefler E, Sivachenko A, Sougnez C, Stewart C, Ally A, Birol I, Chiu R, Corbett RD, Hirst M, Jackman SD, Kamoh B, Khodabakshi AH, Krzywinski M, Lo A, Moore RA, Mungall KL, Qian J, Tam A, Thiessen N, Zhao Y, Cole KA, Diamond M, Diskin SJ, Mosse YP, Wood AC, Ji L, Sposto R, Badgett T, London WB, Moyer Y, Gastier-Foster JM, Smith MA, Guidry Auvil JM, Gerhard DS, Hogarty MD, Jones SJ, Lander ES, Gabriel SB, Getz G, Seeger RC, Khan J, Marra MA, Meyerson M, Maris JM.

Nat Genet. 2013 Mar;45(3):279-84. doi: 10.1038/ng.2529. Epub 2013 Jan 20.

44.

MKNK1 is a YB-1 target gene responsible for imparting trastuzumab resistance and can be blocked by RSK inhibition.

Astanehe A, Finkbeiner MR, Krzywinski M, Fotovati A, Dhillon J, Berquin IM, Mills GB, Marra MA, Dunn SE.

Oncogene. 2012 Oct 11;31(41):4434-46. doi: 10.1038/onc.2011.617. Epub 2012 Jan 16.

PMID:
22249268
45.

Hive plots--rational approach to visualizing networks.

Krzywinski M, Birol I, Jones SJ, Marra MA.

Brief Bioinform. 2012 Sep;13(5):627-44. doi: 10.1093/bib/bbr069. Epub 2011 Dec 9.

PMID:
22155641
46.

Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma.

Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M, Strauss J, Barnes R, Watson P, Allen-Vercoe E, Moore RA, Holt RA.

Genome Res. 2012 Feb;22(2):299-306. doi: 10.1101/gr.126516.111. Epub 2011 Oct 18.

47.

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma.

Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA.

Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351.

48.

Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts.

D'Souza CA, Kronstad JW, Taylor G, Warren R, Yuen M, Hu G, Jung WH, Sham A, Kidd SE, Tangen K, Lee N, Zeilmaker T, Sawkins J, McVicker G, Shah S, Gnerre S, Griggs A, Zeng Q, Bartlett K, Li W, Wang X, Heitman J, Stajich JE, Fraser JA, Meyer W, Carter D, Schein J, Krzywinski M, Kwon-Chung KJ, Varma A, Wang J, Brunham R, Fyfe M, Ouellette BF, Siddiqui A, Marra M, Jones S, Holt R, Birren BW, Galagan JE, Cuomo CA.

MBio. 2011 Feb 8;2(1):e00342-10. doi: 10.1128/mBio.00342-10. Print 2011.

49.

Fast diploidization in close mesopolyploid relatives of Arabidopsis.

Mandáková T, Joly S, Krzywinski M, Mummenhoff K, Lysak MA.

Plant Cell. 2010 Jul;22(7):2277-90. doi: 10.1105/tpc.110.074526. Epub 2010 Jul 16.

50.

PICS: probabilistic inference for ChIP-seq.

Zhang X, Robertson G, Krzywinski M, Ning K, Droit A, Jones S, Gottardo R.

Biometrics. 2011 Mar;67(1):151-63. doi: 10.1111/j.1541-0420.2010.01441.x.

PMID:
20528864

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