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Items: 39


Revisiting the tumorigenesis timeline with a data-driven generative model.

Lahouel K, Younes L, Danilova L, Giardiello FM, Hruban RH, Groopman J, Kinzler KW, Vogelstein B, Geman D, Tomasetti C.

Proc Natl Acad Sci U S A. 2020 Jan 14;117(2):857-864. doi: 10.1073/pnas.1914589117. Epub 2019 Dec 27.


Robust determination of differential abundance in shotgun proteomics using nonparametric statistics.

Slama P, Hoopmann MR, Moritz RL, Geman D.

Mol Omics. 2018 Dec 3;14(6):424-436. doi: 10.1039/c8mo00077h.


Digitizing omics profiles by divergence from a baseline.

Dinalankara W, Ke Q, Xu Y, Ji L, Pagane N, Lien A, Matam T, Fertig EJ, Price ND, Younes L, Marchionni L, Geman D.

Proc Natl Acad Sci U S A. 2018 May 1;115(18):4545-4552. doi: 10.1073/pnas.1721628115. Epub 2018 Apr 16.


Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer.

Afsari B, Guo T, Considine M, Florea L, Kagohara LT, Stein-O'Brien GL, Kelley D, Flam E, Zambo KD, Ha PK, Geman D, Ochs MF, Califano JA, Gaykalova DA, Favorov AV, Fertig EJ.

Bioinformatics. 2018 Jun 1;34(11):1859-1867. doi: 10.1093/bioinformatics/bty004.


High resolution time-course mapping of early transcriptomic, molecular and cellular phenotypes in Huntington's disease CAG knock-in mice across multiple genetic backgrounds.

Ament SA, Pearl JR, Grindeland A, St Claire J, Earls JC, Kovalenko M, Gillis T, Mysore J, Gusella JF, Lee JM, Kwak S, Howland D, Lee MY, Baxter D, Scherler K, Wang K, Geman D, Carroll JB, MacDonald ME, Carlson G, Wheeler VC, Price ND, Hood LE.

Hum Mol Genet. 2017 Mar 1;26(5):913-922. doi: 10.1093/hmg/ddx006.


Opinion: Science in the age of selfies.

Geman D, Geman S.

Proc Natl Acad Sci U S A. 2016 Aug 23;113(34):9384-7. doi: 10.1073/pnas.1609793113. No abstract available.


Visual Turing test for computer vision systems.

Geman D, Geman S, Hallonquist N, Younes L.

Proc Natl Acad Sci U S A. 2015 Mar 24;112(12):3618-23. doi: 10.1073/pnas.1422953112. Epub 2015 Mar 9.


Learning dysregulated pathways in cancers from differential variability analysis.

Afsari B, Geman D, Fertig EJ.

Cancer Inform. 2014 Oct 23;13(Suppl 5):61-7. doi: 10.4137/CIN.S14066. eCollection 2014. Review.


An argument for mechanism-based statistical inference in cancer.

Geman D, Ochs M, Price ND, Tomasetti C, Younes L.

Hum Genet. 2015 May;134(5):479-95. doi: 10.1007/s00439-014-1501-x. Epub 2014 Nov 9. Review.


Measuring the effect of inter-study variability on estimating prediction error.

Ma S, Sung J, Magis AT, Wang Y, Geman D, Price ND.

PLoS One. 2014 Oct 17;9(10):e110840. doi: 10.1371/journal.pone.0110840. eCollection 2014.


switchBox: an R package for k-Top Scoring Pairs classifier development.

Afsari B, Fertig EJ, Geman D, Marchionni L.

Bioinformatics. 2015 Jan 15;31(2):273-4. doi: 10.1093/bioinformatics/btu622. Epub 2014 Sep 26.


Identification of direction in gene networks from expression and methylation.

Simcha DM, Younes L, Aryee MJ, Geman D.

BMC Syst Biol. 2013 Nov 1;7:118. doi: 10.1186/1752-0509-7-118.


Multi-study integration of brain cancer transcriptomes reveals organ-level molecular signatures.

Sung J, Kim PJ, Ma S, Funk CC, Magis AT, Wang Y, Hood L, Geman D, Price ND.

PLoS Comput Biol. 2013;9(7):e1003148. doi: 10.1371/journal.pcbi.1003148. Epub 2013 Jul 25.


A simple and reproducible breast cancer prognostic test.

Marchionni L, Afsari B, Geman D, Leek JT.

BMC Genomics. 2013 May 17;14:336. doi: 10.1186/1471-2164-14-336.


The limits of de novo DNA motif discovery.

Simcha D, Price ND, Geman D.

PLoS One. 2012;7(11):e47836. doi: 10.1371/journal.pone.0047836. Epub 2012 Nov 7.


Computational medicine: translating models to clinical care.

Winslow RL, Trayanova N, Geman D, Miller MI.

Sci Transl Med. 2012 Oct 31;4(158):158rv11. doi: 10.1126/scitranslmed.3003528.


Learning multivariate distributions by competitive assembly of marginals.

Sánchez-Vega F, Younes L, Geman D.

IEEE Trans Pattern Anal Mach Intell. 2013 Feb;35(2):398-410.


Comparing machines and humans on a visual categorization test.

Fleuret F, Li T, Dubout C, Wampler EK, Yantis S, Geman D.

Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17621-5. doi: 10.1073/pnas.1109168108. Epub 2011 Oct 17.


Identification of family-determining residues in PHD fingers.

Slama P, Geman D.

Nucleic Acids Res. 2011 Mar;39(5):1666-79. doi: 10.1093/nar/gkq947. Epub 2010 Nov 8.


A comprehensive statistical model for cell signaling.

Yörük E, Ochs MF, Geman D, Younes L.

IEEE/ACM Trans Comput Biol Bioinform. 2011 May-Jun;8(3):592-606. doi: 10.1109/TCBB.2010.87.


Tackling the widespread and critical impact of batch effects in high-throughput data.

Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly K, Irizarry RA.

Nat Rev Genet. 2010 Oct;11(10):733-9. doi: 10.1038/nrg2825. Epub 2010 Sep 14. Review.


Identifying tightly regulated and variably expressed networks by Differential Rank Conservation (DIRAC).

Eddy JA, Hood L, Price ND, Geman D.

PLoS Comput Biol. 2010 May 27;6(5):e1000792. doi: 10.1371/journal.pcbi.1000792.


Relative expression analysis for molecular cancer diagnosis and prognosis.

Eddy JA, Sung J, Geman D, Price ND.

Technol Cancer Res Treat. 2010 Apr;9(2):149-59. Review.


Relative expression analysis for identifying perturbed pathways.

Eddy JA, Geman D, Price ND.

Conf Proc IEEE Eng Med Biol Soc. 2009;2009:5456-9. doi: 10.1109/IEMBS.2009.5334063.


Two-transcript gene expression classifiers in the diagnosis and prognosis of human diseases.

Edelman LB, Toia G, Geman D, Zhang W, Price ND.

BMC Genomics. 2009 Dec 5;10:583. doi: 10.1186/1471-2164-10-583.


Real-world image annotation and retrieval: an introduction to the special section.

Wang JZ, Geman D, Luo J, Gray RM.

IEEE Trans Pattern Anal Mach Intell. 2008 Nov;30(11):1873-6. No abstract available.


The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations.

Lin X, Afsari B, Marchionni L, Cope L, Parmigiani G, Naiman D, Geman D.

BMC Bioinformatics. 2009 Aug 20;10:256. doi: 10.1186/1471-2105-10-256.


A statistical framework for image category search from a mental picture.

Ferecatu M, Geman D.

IEEE Trans Pattern Anal Mach Intell. 2009 Jun;31(6):1087-101. doi: 10.1109/TPAMI.2008.259.


Merging microarray data from separate breast cancer studies provides a robust prognostic test.

Xu L, Tan AC, Winslow RL, Geman D.

BMC Bioinformatics. 2008 Feb 27;9:125. doi: 10.1186/1471-2105-9-125.


Discovering robust protein biomarkers for disease from relative expression reversals in 2-D DIGE data.

Anderson TJ, Tchernyshyov I, Diez R, Cole RN, Geman D, Dang CV, Winslow RL.

Proteomics. 2007 Apr;7(8):1197-207.


Classifying gene expression profiles from pairwise mRNA comparisons.

Geman D, d'Avignon C, Naiman DQ, Winslow RL.

Stat Appl Genet Mol Biol. 2004;3:Article19. Epub 2004 Aug 30.


Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data.

Xu L, Tan AC, Naiman DQ, Geman D, Winslow RL.

Bioinformatics. 2005 Oct 15;21(20):3905-11. Epub 2005 Aug 30.


Simple decision rules for classifying human cancers from gene expression profiles.

Tan AC, Naiman DQ, Xu L, Winslow RL, Geman D.

Bioinformatics. 2005 Oct 15;21(20):3896-904. Epub 2005 Aug 16.


A coarse-to-fine strategy for multiclass shape detection.

Amit Y, Geman D, Fan X.

IEEE Trans Pattern Anal Mach Intell. 2004 Dec;26(12):1606-21.


A computational model for visual selection.

Amit Y, Geman D.

Neural Comput. 1999 Oct 1;11(7):1691-715.


Nonlinear image recovery with half-quadratic regularization.

Geman D, Yang C.

IEEE Trans Image Process. 1995;4(7):932-46.


Stochastic relaxation, gibbs distributions, and the bayesian restoration of images.

Geman S, Geman D.

IEEE Trans Pattern Anal Mach Intell. 1984 Jun;6(6):721-41.


Bayes smoothing algorithms for segmentation of binary images modeled by markov random fields.

Derin H, Elliott H, Cristi R, Geman D.

IEEE Trans Pattern Anal Mach Intell. 1984 Jun;6(6):707-20.


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