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Items: 1 to 50 of 60

1.

Visual Exploration of Neural Document Embedding in Information Retrieval: Semantics and Feature Selection.

Ji X, Shen HW, Ritter A, Machiraju R, Yen PY.

IEEE Trans Vis Comput Graph. 2019 Jun;25(6):2181-2192. doi: 10.1109/TVCG.2019.2903946. Epub 2019 Mar 15.

PMID:
30892213
3.

Semantic workflows for benchmark challenges: Enhancing comparability, reusability and reproducibility.

Srivastava A, Adusumilli R, Boyce H, Garijo D, Ratnakar V, Mayani R, Yu T, Machiraju R, Gil Y, Mallick P.

Pac Symp Biocomput. 2019;24:208-219.

4.

Imitating Pathologist Based Assessment With Interpretable and Context Based Neural Network Modeling of Histology Images.

Srivastava A, Kulkarni C, Huang K, Parwani A, Mallick P, Machiraju R.

Biomed Inform Insights. 2018 Oct 31;10:1178222618807481. doi: 10.1177/1178222618807481. eCollection 2018.

5.

Integrative cancer patient stratification via subspace merging.

Ding H, Sharpnack M, Wang C, Huang K, Machiraju R.

Bioinformatics. 2019 May 15;35(10):1653-1659. doi: 10.1093/bioinformatics/bty866.

PMID:
30329022
6.

Proteogenomic Analysis of Surgically Resected Lung Adenocarcinoma.

Sharpnack MF, Ranbaduge N, Srivastava A, Cerciello F, Codreanu SG, Liebler DC, Mascaux C, Miles WO, Morris R, McDermott JE, Sharpnack JL, Amann J, Maher CA, Machiraju R, Wysocki VH, Govindan R, Mallick P, Coombes KR, Huang K, Carbone DP.

J Thorac Oncol. 2018 Oct;13(10):1519-1529. doi: 10.1016/j.jtho.2018.06.025. Epub 2018 Jul 11.

PMID:
30017829
7.

annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq.

Tang X, Srivastava A, Liu H, Machiraju R, Huang K, Leone G.

Bioinformatics. 2018 Aug 15;34(16):2879. doi: 10.1093/bioinformatics/bty226. No abstract available.

8.

Visualizing Article Similarities via Sparsified Article Network and Map Projection for Systematic Reviews.

Ji X, Machiraju R, Ritter A, Yen PY.

Stud Health Technol Inform. 2017;245:422-426.

PMID:
29295129
9.

Building trans-omics evidence: using imaging and 'omics' to characterize cancer profiles.

Srivastava A, Kulkarni C, Mallick P, Huang K, Machiraju R.

Pac Symp Biocomput. 2018;23:377-387.

10.

Predictive models for pressure ulcers from intensive care unit electronic health records using Bayesian networks.

Kaewprag P, Newton C, Vermillion B, Hyun S, Huang K, Machiraju R.

BMC Med Inform Decis Mak. 2017 Jul 5;17(Suppl 2):65. doi: 10.1186/s12911-017-0471-z.

11.

Are there differences in the mental health status of adolescents in Puducherry?

Deb S, Sathyanarayanan P, Machiraju R, Thomas S, McGirr K.

Asian J Psychiatr. 2017 Jun;27:32-39. doi: 10.1016/j.ajp.2017.02.011. Epub 2017 Feb 17.

PMID:
28558893
12.

Analysis of live cell images: Methods, tools and opportunities.

Nketia TA, Sailem H, Rohde G, Machiraju R, Rittscher J.

Methods. 2017 Feb 15;115:65-79. doi: 10.1016/j.ymeth.2017.02.007. Epub 2017 Feb 27. Review.

PMID:
28242295
13.

annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq.

Tang X, Srivastava A, Liu H, Machiraju R, Huang K, Leone G.

Bioinformatics. 2017 May 15;33(10):1570-1571. doi: 10.1093/bioinformatics/btx016. Erratum in: Bioinformatics. 2018 Aug 15;34(16):2879.

14.

Identification of recurrent combinatorial patterns of chromatin modifications at promoters across various tissue types.

Meng N, Machiraju R, Huang K.

BMC Bioinformatics. 2016 Dec 23;17(Suppl 17):534. doi: 10.1186/s12859-016-1346-5.

15.

E2f8 mediates tumor suppression in postnatal liver development.

Kent LN, Rakijas JB, Pandit SK, Westendorp B, Chen HZ, Huntington JT, Tang X, Bae S, Srivastava A, Senapati S, Koivisto C, Martin CK, Cuitino MC, Perez M, Clouse JM, Chokshi V, Shinde N, Kladney R, Sun D, Perez-Castro A, Matondo RB, Nantasanti S, Mokry M, Huang K, Machiraju R, Fernandez S, Rosol TJ, Coppola V, Pohar KS, Pipas JM, Schmidt CR, de Bruin A, Leone G.

J Clin Invest. 2016 Aug 1;126(8):2955-69. doi: 10.1172/JCI85506. Epub 2016 Jul 25.

16.

Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes.

Wang J, Xia S, Arand B, Zhu H, Machiraju R, Huang K, Ji H, Qian J.

PLoS Comput Biol. 2016 Apr 21;12(4):e1004892. doi: 10.1371/journal.pcbi.1004892. eCollection 2016 Apr.

17.

Identify Critical Genes in Development with Consistent H3K4me2 Patterns across Multiple Tissues.

Meng N, Machiraju R, Huang K.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Sep-Oct;12(5):1104-11.

PMID:
26734704
18.

GRAPHIE: graph based histology image explorer.

Ding H, Wang C, Huang K, Machiraju R.

BMC Bioinformatics. 2015;16 Suppl 11:S10. doi: 10.1186/1471-2105-16-S11-S10. Epub 2015 Aug 13.

19.

Predictive Modeling for Pressure Ulcers from Intensive Care Unit Electronic Health Records.

Kaewprag P, Newton C, Vermillion B, Hyun S, Huang K, Machiraju R.

AMIA Jt Summits Transl Sci Proc. 2015 Mar 25;2015:82-6. eCollection 2015.

20.

Redeployment of Myc and E2f1-3 drives Rb-deficient cell cycles.

Liu H, Tang X, Srivastava A, Pécot T, Daniel P, Hemmelgarn B, Reyes S, Fackler N, Bajwa A, Kladney R, Koivisto C, Chen Z, Wang Q, Huang K, Machiraju R, Sáenz-Robles MT, Cantalupo P, Pipas JM, Leone G.

Nat Cell Biol. 2015 Aug;17(8):1036-48. doi: 10.1038/ncb3210. Epub 2015 Jul 20.

21.

Actin grips: circular actin-rich cytoskeletal structures that mediate the wrapping of polymeric microfibers by endothelial cells.

Jones D, Park D, Anghelina M, Pécot T, Machiraju R, Xue R, Lannutti JJ, Thomas J, Cole SL, Moldovan L, Moldovan NI.

Biomaterials. 2015 Jun;52:395-406. doi: 10.1016/j.biomaterials.2015.02.034. Epub 2015 Mar 18.

22.

Examining the Distribution, Modularity, and Community Structure in Article Networks for Systematic Reviews.

Ji X, Machiraju R, Ritter A, Yen PY.

AMIA Annu Symp Proc. 2015 Nov 5;2015:1927-36. eCollection 2015.

23.

An integrative analysis of regional gene expression profiles in the human brain.

Myers EM, Bartlett CW, Machiraju R, Bohland JW.

Methods. 2015 Feb;73:54-70. doi: 10.1016/j.ymeth.2014.12.010. Epub 2014 Dec 15.

PMID:
25524419
24.

2013 IEEE Scientific Visualization Contest winner: Observing genomics and phenotypical patterns in the developing mouse brain.

Li Q, Zachmann G, Feng D, Huang K, Machiraju R.

IEEE Comput Graph Appl. 2014 Sep-Oct;34(5):88-97. No abstract available.

PMID:
25379583
25.

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.

26.

Effectively processing medical term queries on the UMLS Metathesaurus by layered dynamic programming.

Ren K, Lai AM, Mukhopadhyay A, Machiraju R, Huang K, Xiang Y.

BMC Med Genomics. 2014;7 Suppl 1:S11. doi: 10.1186/1755-8794-7-S1-S11. Epub 2014 May 8.

27.

iGPSe: a visual analytic system for integrative genomic based cancer patient stratification.

Ding H, Wang C, Huang K, Machiraju R.

BMC Bioinformatics. 2014 Jul 10;15:203. doi: 10.1186/1471-2105-15-203.

28.

Breast cancer patient stratification using a molecular regularized consensus clustering method.

Wang C, Machiraju R, Huang K.

Methods. 2014 Jun 1;67(3):304-12. doi: 10.1016/j.ymeth.2014.03.005. Epub 2014 Mar 18.

29.

Gene × smoking interactions on human brain gene expression: finding common mechanisms in adolescents and adults.

Wolock SL, Yates A, Petrill SA, Bohland JW, Blair C, Li N, Machiraju R, Huang K, Bartlett CW.

J Child Psychol Psychiatry. 2013 Oct;54(10):1109-19. doi: 10.1111/jcpp.12119. Epub 2013 Aug 2.

30.

Identifying survival associated morphological features of triple negative breast cancer using multiple datasets.

Wang C, Pécot T, Zynger DL, Machiraju R, Shapiro CL, Huang K.

J Am Med Inform Assoc. 2013 Jul-Aug;20(4):680-7. doi: 10.1136/amiajnl-2012-001538. Epub 2013 Apr 12.

31.

Identify condition-specific gene co-expression networks.

Kalluru V, Machiraju R, Huang K.

Int J Comput Biol Drug Des. 2013;6(1-2):50-9. doi: 10.1504/IJCBDD.2013.052201. Epub 2013 Feb 21.

PMID:
23428473
32.

Canonical and atypical E2Fs regulate the mammalian endocycle.

Chen HZ, Ouseph MM, Li J, Pécot T, Chokshi V, Kent L, Bae S, Byrne M, Duran C, Comstock G, Trikha P, Mair M, Senapati S, Martin CK, Gandhi S, Wilson N, Liu B, Huang YW, Thompson JC, Raman S, Singh S, Leone M, Machiraju R, Huang K, Mo X, Fernandez S, Kalaszczynska I, Wolgemuth DJ, Sicinski P, Huang T, Jin V, Leone G.

Nat Cell Biol. 2012 Nov;14(11):1192-202. doi: 10.1038/ncb2595. Epub 2012 Oct 14.

33.

A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data.

Han Z, Tian L, Pécot T, Huang T, Machiraju R, Huang K.

BMC Bioinformatics. 2012 Mar 13;13 Suppl 2:S2. doi: 10.1186/1471-2105-13-S2-S2.

34.

Atypical E2F repressors and activators coordinate placental development.

Ouseph MM, Li J, Chen HZ, Pécot T, Wenzel P, Thompson JC, Comstock G, Chokshi V, Byrne M, Forde B, Chong JL, Huang K, Machiraju R, de Bruin A, Leone G.

Dev Cell. 2012 Apr 17;22(4):849-62. doi: 10.1016/j.devcel.2012.01.013.

35.

Message from the paper chairs and guest editors. Conference proceedings.

van Ham F, Machiraju R, Mueller K, Scheuermann G, Weaver C.

IEEE Trans Vis Comput Graph. 2011 Dec;17(12):x-xi. No abstract available.

PMID:
22106451
36.

The feasibility of hybrid automatic segmentation of axillary lymph nodes from a 3-D sonogram.

Sammet S, Evans KD, Irfanoglu MO, Strapp A, Machiraju R.

Ultrasound Med Biol. 2011 Dec;37(12):2075-85. doi: 10.1016/j.ultrasmedbio.2011.09.002. Epub 2011 Oct 26.

PMID:
22033128
37.

Non-parametric population analysis of cellular phenotypes.

Singh S, Janoos F, Pécot T, Caserta E, Huang K, Rittscher J, Leone G, Machiraju R.

Med Image Comput Comput Assist Interv. 2011;14(Pt 2):343-51.

38.

Susceptibility distortion correction for echo planar images with non-uniform B-spline grid sampling: a diffusion tensor image study.

Irfanoglu MO, Walker L, Sammet S, Pierpaoli C, Machiraju R.

Med Image Comput Comput Assist Interv. 2011;14(Pt 2):174-81.

PMID:
21995027
39.

State-space models of mental processes from fMRI.

Janoos F, Singh S, Machiraju R, Wells WM, Mórocz IA.

Inf Process Med Imaging. 2011;22:588-99.

40.

Identifying nuclear phenotypes using semi-supervised metric learning.

Singh S, Janoos F, Pécot T, Caserta E, Leone G, Rittscher J, Machiraju R.

Inf Process Med Imaging. 2011;22:398-410.

41.

Tocotrienol vitamin E protects against preclinical canine ischemic stroke by inducing arteriogenesis.

Rink C, Christoforidis G, Khanna S, Peterson L, Patel Y, Khanna S, Abduljalil A, Irfanoglu O, Machiraju R, Bergdall VK, Sen CK.

J Cereb Blood Flow Metab. 2011 Nov;31(11):2218-30. doi: 10.1038/jcbfm.2011.85. Epub 2011 Jun 15.

42.

Spatio-temporal models of mental processes from fMRI.

Janoos F, Machiraju R, Singh S, Morocz IÁ.

Neuroimage. 2011 Jul 15;57(2):362-77. doi: 10.1016/j.neuroimage.2011.03.047. Epub 2011 Mar 24.

PMID:
21440069
43.

IEEE Visualization Conference and IEEE Information Visualization Conference proceedings 2010. Preface.

Fekete JD, van Ham F, Machiraju R, Möller T, Pfister H.

IEEE Trans Vis Comput Graph. 2010 Nov-Dec;16(6):xi-xiii. No abstract available.

PMID:
21077279
44.

Unsupervised learning of brain states from fMRI data.

Janoos F, Machiraju R, Sammet S, Knopp MV, Mórocz IA.

Med Image Comput Comput Assist Interv. 2010;13(Pt 2):201-8.

PMID:
20879316
45.

Guest editors' introduction: special section on volume graphics and point-based graphics.

Hege HC, Laidlaw DH, Machiraju R.

IEEE Trans Vis Comput Graph. 2010 Jul-Aug;16(4):531-2. No abstract available.

PMID:
20578285
46.

Two-Point Correlation as a Feature for Histology Images: Feature Space Structure and Correlation Updating.

Cooper L, Saltz J, Machiraju R, Huang K.

Conf Comput Vis Pattern Recognit Workshops. 2010:79-86.

47.

ANISOTROPIC PLATE DIFFUSION FILTERING FOR DETECTION OF CELL MEMBRANES IN 3D MICROSCOPY IMAGES.

Mosaliganti K, Janoos F, Gelas A, Noche R, Obholzer N, Machiraju R, Megason SG.

Proc IEEE Int Symp Biomed Imaging. 2010:588-591.

48.

Diffusion tensor field registration in the presence of uncertainty.

Irfanoglu MO, Koay CG, Pajevic S, Machiraju R, Basser PJ.

Med Image Comput Comput Assist Interv. 2009;12(Pt 1):181-9.

PMID:
20425986
49.

Visualizing particle/flow structure interactions in the small bronchial tubes.

Soni B, Thompson D, Machiraju R.

IEEE Trans Vis Comput Graph. 2008 Nov-Dec;14(6):1412-9. doi: 10.1109/TVCG.2008.183.

PMID:
18988991
50.

Automatic deformable diffusion tensor registration for fiber population analysis.

Irfanoglu MO, Machiraju R, Sammet S, Pierpaoli C, Knopp MV.

Med Image Comput Comput Assist Interv. 2008;11(Pt 2):1014-22.

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