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Items: 1 to 50 of 69

1.

Saturating Splines and Feature Selection.

Boyd N, Hastie T, Boyd S, Recht B, Jordan MI.

J Mach Learn Res. 2018 Apr;18. pii: 197.

2.

Deep generative modeling for single-cell transcriptomics.

Lopez R, Regier J, Cole MB, Jordan MI, Yosef N.

Nat Methods. 2018 Dec;15(12):1053-1058. doi: 10.1038/s41592-018-0229-2. Epub 2018 Nov 30.

3.

Transferable Representation Learning with Deep Adaptation Networks.

Long M, Cao Y, Cao Z, Wang J, Jordan MI.

IEEE Trans Pattern Anal Mach Intell. 2018 Sep 5. doi: 10.1109/TPAMI.2018.2868685. [Epub ahead of print]

PMID:
30188813
4.

A variational perspective on accelerated methods in optimization.

Wibisono A, Wilson AC, Jordan MI.

Proc Natl Acad Sci U S A. 2016 Nov 22;113(47):E7351-E7358. Epub 2016 Nov 9.

5.

A Marked Poisson Process Driven Latent Shape Model for 3D Segmentation of Reflectance Confocal Microscopy Image Stacks of Human Skin.

Ghanta S, Jordan MI, Kose K, Brooks DH, Rajadhyaksha M, Dy JG.

IEEE Trans Image Process. 2017 Jan;26(1):172-184. doi: 10.1109/TIP.2016.2615291. Epub 2016 Oct 5.

6.

Combinatorial Clustering and the Beta Negative Binomial Process.

Broderick T, Mackey L, Paisley J, Jordan MI.

IEEE Trans Pattern Anal Mach Intell. 2015 Feb;37(2):290-306. doi: 10.1109/TPAMI.2014.2318721.

PMID:
26353242
7.

Nested Hierarchical Dirichlet Processes.

Paisley J, Wang C, Blei DM, Jordan MI.

IEEE Trans Pattern Anal Mach Intell. 2015 Feb;37(2):256-70. doi: 10.1109/TPAMI.2014.2318728.

PMID:
26353240
8.

Machine learning: Trends, perspectives, and prospects.

Jordan MI, Mitchell TM.

Science. 2015 Jul 17;349(6245):255-60. doi: 10.1126/science.aaa8415. Review.

PMID:
26185243
9.

Iterative Discovery of Multiple AlternativeClustering Views.

Donglin Niu, Dy JG, Jordan MI.

IEEE Trans Pattern Anal Mach Intell. 2014 Jul;36(7):1340-53. doi: 10.1109/TPAMI.2013.180.

PMID:
26353307
10.

SMaSH: a benchmarking toolkit for human genome variant calling.

Talwalkar A, Liptrap J, Newcomb J, Hartl C, Terhorst J, Curtis K, Bresler M, Song YS, Jordan MI, Patterson D.

Bioinformatics. 2014 Oct;30(19):2787-95. doi: 10.1093/bioinformatics/btu345. Epub 2014 Jun 3.

11.

Molecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: recurrence of tyrosine aminotransferase activity in the Iα subfamily.

Muratore KE, Engelhardt BE, Srouji JR, Jordan MI, Brenner SE, Kirsch JF.

Proteins. 2013 Sep;81(9):1593-609. doi: 10.1002/prot.24318. Epub 2013 Jun 17.

12.

Computational and statistical tradeoffs via convex relaxation.

Chandrasekaran V, Jordan MI.

Proc Natl Acad Sci U S A. 2013 Mar 26;110(13):E1181-90. doi: 10.1073/pnas.1302293110. Epub 2013 Mar 11.

13.

Evolutionary inference via the Poisson Indel Process.

Bouchard-Côté A, Jordan MI.

Proc Natl Acad Sci U S A. 2013 Jan 22;110(4):1160-6. doi: 10.1073/pnas.1220450110. Epub 2012 Dec 28.

14.

Phylogenetic inference via sequential Monte Carlo.

Bouchard-Côté A, Sankararaman S, Jordan MI.

Syst Biol. 2012 Jul;61(4):579-93. doi: 10.1093/sysbio/syr131. Epub 2012 Jan 4.

15.

Nonparametric combinatorial sequence models.

Wauthier FL, Jordan MI, Jojic N.

J Comput Biol. 2011 Nov;18(11):1649-60. doi: 10.1089/cmb.2011.0175. Epub 2011 Nov 2.

PMID:
22047543
16.

Genome-scale phylogenetic function annotation of large and diverse protein families.

Engelhardt BE, Jordan MI, Srouji JR, Brenner SE.

Genome Res. 2011 Nov;21(11):1969-80. doi: 10.1101/gr.104687.109. Epub 2011 Jul 22.

17.

Learning Low-Dimensional Signal Models: A Bayesian approach based on incomplete measurements.

Carin L, Baraniuk RG, Cevher V, Dunson D, Jordan MI, Sapiro G, Wakin MB.

IEEE Signal Process Mag. 2011 Mar 1;28(2). doi: 10.1109/MSP.2010.939733. No abstract available.

18.

Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model.

Ting D, Wang G, Shapovalov M, Mitra R, Jordan MI, Dunbrack RL Jr.

PLoS Comput Biol. 2010 Apr 29;6(4):e1000763. doi: 10.1371/journal.pcbi.1000763.

19.

Feature space resampling for protein conformational search.

Blum B, Jordan MI, Baker D.

Proteins. 2010 May 1;78(6):1583-93. doi: 10.1002/prot.22677.

20.

Active site prediction using evolutionary and structural information.

Sankararaman S, Sha F, Kirsch JF, Jordan MI, Sjölander K.

Bioinformatics. 2010 Mar 1;26(5):617-24. doi: 10.1093/bioinformatics/btq008. Epub 2010 Jan 14.

21.

Convex and semi-nonnegative matrix factorizations.

Ding C, Li T, Jordan MI.

IEEE Trans Pattern Anal Mach Intell. 2010 Jan;32(1):45-55. doi: 10.1109/TPAMI.2008.277.

PMID:
19926898
22.

Genomic privacy and limits of individual detection in a pool.

Sankararaman S, Obozinski G, Jordan MI, Halperin E.

Nat Genet. 2009 Sep;41(9):965-7. doi: 10.1038/ng.436. Epub 2009 Aug 23.

PMID:
19701190
23.

Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data.

Yin J, Jordan MI, Song YS.

Bioinformatics. 2009 Jun 15;25(12):i231-9. doi: 10.1093/bioinformatics/btp229.

24.

Phylogenetic molecular function annotation.

Engelhardt BE, Jordan MI, Repo ST, Brenner SE.

J Phys Conf Ser. 2009;180(1):12024.

25.

Association mapping and significance estimation via the coalescent.

Kimmel G, Karp RM, Jordan MI, Halperin E.

Am J Hum Genet. 2008 Dec;83(6):675-83. doi: 10.1016/j.ajhg.2008.10.017. Epub 2008 Nov 20.

26.

A dual receptor crosstalk model of G-protein-coupled signal transduction.

Flaherty P, Radhakrishnan ML, Dinh T, Rebres RA, Roach TI, Jordan MI, Arkin AP.

PLoS Comput Biol. 2008 Sep 26;4(9):e1000185. doi: 10.1371/journal.pcbi.1000185.

27.

Consistent probabilistic outputs for protein function prediction.

Obozinski G, Lanckriet G, Grant C, Jordan MI, Noble WS.

Genome Biol. 2008;9 Suppl 1:S6. doi: 10.1186/gb-2008-9-s1-s6. Epub 2008 Jun 27.

28.

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.

Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP.

Genome Biol. 2008;9 Suppl 1:S2. doi: 10.1186/gb-2008-9-s1-s2. Epub 2008 Jun 27.

29.

On the inference of ancestries in admixed populations.

Sankararaman S, Kimmel G, Halperin E, Jordan MI.

Genome Res. 2008 Apr;18(4):668-75. doi: 10.1101/gr.072751.107. Epub 2008 Mar 18.

30.

A randomization test for controlling population stratification in whole-genome association studies.

Kimmel G, Jordan MI, Halperin E, Shamir R, Karp RM.

Am J Hum Genet. 2007 Nov;81(5):895-905. Epub 2007 Sep 12.

31.

Bayesian haplotype inference via the Dirichlet process.

Xing EP, Jordan MI, Sharan R.

J Comput Biol. 2007 Apr;14(3):267-84.

PMID:
17563311
32.
33.

LOGOS: a modular Bayesian model for de novo motif detection.

Xing EP, Wu W, Jordan MI, Karp RM.

Proc IEEE Comput Soc Bioinform Conf. 2003;2:266-76.

PMID:
16452802
34.

Protein molecular function prediction by Bayesian phylogenomics.

Engelhardt BE, Jordan MI, Muratore KE, Brenner SE.

PLoS Comput Biol. 2005 Oct;1(5):e45. Epub 2005 Oct 7.

35.

Genome-wide requirements for resistance to functionally distinct DNA-damaging agents.

Lee W, St Onge RP, Proctor M, Flaherty P, Jordan MI, Arkin AP, Davis RW, Nislow C, Giaever G.

PLoS Genet. 2005 Aug;1(2):e24. Epub 2005 Aug 19.

36.

A latent variable model for chemogenomic profiling.

Flaherty P, Giaever G, Kumm J, Jordan MI, Arkin AP.

Bioinformatics. 2005 Aug 1;21(15):3286-93. Epub 2005 May 26.

PMID:
15919724
37.

Subtree power analysis and species selection for comparative genomics.

McAuliffe JD, Jordan MI, Pachter L.

Proc Natl Acad Sci U S A. 2005 May 31;102(22):7900-5. Epub 2005 May 23.

38.

Lessons from Escherichia coli genes similarly regulated in response to nitrogen and sulfur limitation.

Gyaneshwar P, Paliy O, McAuliffe J, Jones A, Jordan MI, Kustu S.

Proc Natl Acad Sci U S A. 2005 Mar 1;102(9):3453-8. Epub 2005 Feb 16.

39.

Robust sparse hyperplane classifiers: application to uncertain molecular profiling data.

Bhattacharyya C, Grate LR, Jordan MI, El Ghaoui L, Mian IS.

J Comput Biol. 2004;11(6):1073-89.

PMID:
15662199
40.

Sulfur and nitrogen limitation in Escherichia coli K-12: specific homeostatic responses.

Gyaneshwar P, Paliy O, McAuliffe J, Popham DL, Jordan MI, Kustu S.

J Bacteriol. 2005 Feb;187(3):1074-90.

41.

Logos: a modular bayesian model for de novo motif detection.

Xing EP, Wu W, Jordan MI, Karp RM.

J Bioinform Comput Biol. 2004 Mar;2(1):127-54.

PMID:
15272436
42.

A statistical framework for genomic data fusion.

Lanckriet GR, De Bie T, Cristianini N, Jordan MI, Noble WS.

Bioinformatics. 2004 Nov 1;20(16):2626-35. Epub 2004 May 6.

PMID:
15130933
43.

Kernel-based data fusion and its application to protein function prediction in yeast.

Lanckriet GR, Deng M, Cristianini N, Jordan MI, Noble WS.

Pac Symp Biocomput. 2004:300-11.

44.

Multiple-sequence functional annotation and the generalized hidden Markov phylogeny.

McAuliffe JD, Pachter L, Jordan MI.

Bioinformatics. 2004 Aug 12;20(12):1850-60. Epub 2004 Feb 26.

PMID:
14988105
45.

Chemogenomic profiling: identifying the functional interactions of small molecules in yeast.

Giaever G, Flaherty P, Kumm J, Proctor M, Nislow C, Jaramillo DF, Chu AM, Jordan MI, Arkin AP, Davis RW.

Proc Natl Acad Sci U S A. 2004 Jan 20;101(3):793-8. Epub 2004 Jan 12.

46.

Toward a protein profile of Escherichia coli: comparison to its transcription profile.

Corbin RW, Paliy O, Yang F, Shabanowitz J, Platt M, Lyons CE Jr, Root K, McAuliffe J, Jordan MI, Kustu S, Soupene E, Hunt DF.

Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9232-7. Epub 2003 Jul 23.

47.

Integrated analysis of transcript profiling and protein sequence data.

Grate LR, Bhattacharyya C, Jordan MI, Mian IS.

Mech Ageing Dev. 2003 Jan;124(1):109-14.

PMID:
12618013
48.

Optimal feedback control as a theory of motor coordination.

Todorov E, Jordan MI.

Nat Neurosci. 2002 Nov;5(11):1226-35.

PMID:
12404008
49.

Sensorimotor adaptation of speech I: Compensation and adaptation.

Houde JF, Jordan MI.

J Speech Lang Hear Res. 2002 Apr;45(2):295-310.

PMID:
12003512
50.

Asymptotic convergence rate of the EM algorithm for gaussian mixtures

Ma J, Xu L, Jordan MI.

Neural Comput. 2000 Dec;12(12):2881-907.

PMID:
11112259

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