About Us

You are here

Raghu Machiraju

  • Professor, SBS-Biomedical Informatics
  • IntDir of Data Analyt Collabor, Discovery Themes Admin
  • Professor, Computer Science & Engineering
  • 779 Dreese Laboratories
    2015 Neil Ave
    Columbus, OH 43210
  • 614-292-6730

Journal Articles

2015

  • Myers,Emma,M; Bartlett,Christopher,W; Machiraju,Raghu; Bohland,Jason,W, 2015, "An integrative analysis of regional gene expression profiles in the human brain." METHODS 73, 54 - 70.
  • Ding H, Wang C, Huang K, Machiraju R., 2015, "GRAPHIE: graph based histology image explorer." . BMC Bioinformatics. 2015 Suppl 11, no. S10, 1186 -
  • Jones,Desiree; Park,Doyoung; Anghelina,Mirela; Pecot,Thierry; Machiraju,Raghu; Xue,Ruipeng; Lannutti,John,J; Thomas,Jessica; Cole,Sara,L; Moldovan,Leni; Moldovan,Nicanor,I, 2015, "Actin grips: Circular actin-rich cytoskeletal structures that mediate the wrapping of polymeric microfibers by endothelial cells." BIOMATERIALS 52, 395 - 406.
  • 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 M, Cantalupo M, Pipas J, and Leone G., 2015, "Redeployment of Myc and E2f1–3 drives Rb-deficient cell cycles.." Nat Cell Biol 17, no. 8, 1036 - 48.

2014

  • Chao Wang, Raghu Machiraju, and Kun Huang, 2014, "Breast cancer patient stratification using a molecular regularized consensus clustering method." Methods 3, 304–312 -
  • Li Q, Zachmann G, David F, Huang K, Machiraju R, 2014, "Observing Genomics and Phenotypical Patterns in the Developing Mouse Brain." IEEE Computer Graphics and Applications 4, 88 - 97.
  • Zhang,L; Deng,Q; Machiraju,R; Rangarajan,A; Thompson,D; Walters,D,K; Shen,H-W, 2014, "Boosting Techniques for Physics-Based Vortex Detection." COMPUTER GRAPHICS FORUM 33, no. 1, 282 - 293.
  • Yates,A; Webb,A; Sharpnack,M; Chamberlin,H; Huang,K; Machiraju,R, 2014, "Visualizing Multidimensional Data with Glyph SPLOMs." COMPUTER GRAPHICS FORUM 33, no. 3, 301 - 310.
  • Wang,Chao; Machiraju,Raghu; Huang,Kun, 2014, "Breast cancer patient stratification using a molecular regularized consensus clustering method." METHODS 67, no. 3, 304 - 312.
  • Ding,Hao; Wang,Chao; Huang,Kun; Machiraju,Raghu, 2014, "iGPSe: A visual analytic system for integrative genomic based cancer patient stratification." BMC BIOINFORMATICS 15, 203 -

2013

  • Wolock,Samuel,L; Yates,Andrew; Petrill,Stephen,A; Bohland,Jason,W; Blair,Clancy; Li,Ning; Machiraju,Raghu; Huang,Kun; Bartlett,Christopher,W, 2013, "Gene X smoking interactions on human brain gene expression: finding common mechanisms in adolescents and adults." JOURNAL OF CHILD PSYCHOLOGY AND PSYCHIATRY 54, no. 10, 1109 - 1119.
  • Kalluru V, Machiraju R, Huang K., 2013, "Identify condition-specific gene co-expression networks.." Int J Comput Biol Drug Design 6, no. 1-2, 50 - 59.
  • Kalluru,Vikram; Machiraju,Raghu; Huang,Kun, 2013, "Identify condition-specific gene co-expression networks.." International journal of computational biology and drug design 6, no. 1-2, 50 - 59.

2012

  • Ouseph,Madhu,M; Li,Jing; Chen,Hui-Zi; Pecot,Thierry; Wenzel,Pamela; Thompson,John,C; Comstock,Grant; Chokshi,Veda; Byrne,Morgan; Forde,Braxton; Chong,Jean-Leon; Huang,Kun; Machiraju,Raghu; de Bruin,Alain; Leone,Gustavo, 2012, "Atypical E2F Repressors and Activators Coordinate Placental Development." DEVELOPMENTAL CELL 22, no. 4, 849 - 862.
  • 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., 2012, Canonical and atypical E2Fs regulate the mammalian endocycle.. Nature Cell Biology 14, no. 11, 1192 - 202.

2011

  • Singh,Shantanu; Janoos,Firdaus; Pécot,Thierry; Caserta,Enrico; Leone,Gustavo; Rittscher,Jens; Machiraju,Raghu, 2011, "Identifying nuclear phenotypes using semi-supervised metric learning.." Information processing in medical imaging : proceedings of the ... conference 22, 398 - 410.
  • Kasmai,N; Thompson,D; Luke,E; Jankun-Kelly,M; Machiraju,R, 2011, "Feature-based adaptive mesh refinement for wingtip vortices." INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS 66, no. 10, 1274 - 1294.
  • Rink,Cameron; Christoforidis,Greg; Khanna,Savita; Peterson,Laura; Patel,Yojan; Khanna,Suchin; Abduljalil,Amir; Irfanoglu,Okan; Machiraju,Raghu; Bergdall,Valerie,K; Sen,Chandan,K, 2011, "Tocotrienol vitamin E protects against preclinical canine ischemic stroke by inducing arteriogenesis." JOURNAL OF CEREBRAL BLOOD FLOW AND METABOLISM 31, no. 11, 2218 - 2230.
  • Singh,Shantanu; Janoos,Firdaus; Pécot,Thierry; Caserta,Enrico; Huang,Kun; Rittscher,Jens; Leone,Gustavo; Machiraju,Raghu, 2011, "Non-parametric population analysis of cellular phenotypes.." Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention 14, 343 - 351.
  • Sammet,Steffen; Evans,Kevin,D; Irfanoglu,M,Okan; Strapp,Ashley; Machiraju,Raghu, 2011, "THE FEASIBILITY OF HYBRID AUTOMATIC SEGMENTATION OF AXILLARY LYMPH NODES FROM A 3-D SONOGRAM." ULTRASOUND IN MEDICINE AND BIOLOGY 37, no. 12, 2075 - 2085.
  • Janoos,Firdaus; Singh,Shantanu; Machiraju,Raghu; Wells,William,M; Mórocz,Istvan,A, 2011, "State-space models of mental processes from fMRI.." Information processing in medical imaging : proceedings of the ... conference 22, 588 - 599.
  • Janoos,Firdaus; Machiraju,Raghu; Singh,Shantanu; Morocz,Istvan,Akos, 2011, "Spatio-temporal models of mental processes from fMRI." NEUROIMAGE 57, no. 2, 362 - 377.

2010

  • Janoos,F; Machiraju,R; Sammet,S; Knopp,M,V; Mórocz,I,A, 2010, "Unsupervised learning of brain states from fMRI data.." Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention 13, 201 - 208.

2009

  • Irfanoglu,Mustafa,Okan; Koay,Cheng,Guan; Pajevic,Sinisa; Machiraju,Raghu; Basser,Peter,J, 2009, "Diffusion tensor field registration in the presence of uncertainty.." Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention 12, 181 - 189.

2008

  • Mosaliganti,Kishore; Pan,Tony; Ridgway,Randall; Sharp,Richard; Cooper,Lee; Gulacy,Alex; Sharma,Ashish; Irfanoglu,Okan; Machiraju,Raghu; Kurc,Tahsin; de Bruin,Alain; Wenzel,Pamela; Leone,Gustavo; Saltz,Joel; Huang,Kun, 2008, "An imaging workflow for characterizing phenotypical change in large histological mouse model datasets." JOURNAL OF BIOMEDICAL INFORMATICS 41, no. 6, 863 - 873.
  • Soni,Bela; Thompson,David; Machiraju,Raghu, 2008, "Visualizing Particle/Flow Structure Interactions in the Small Bronchial Tubes." IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 14, no. 6, 1412 - 1419.
  • Irfanoglu,M,O; Machiraju,R; Sammet,S; Pierpaoli,C; Knopp,M,V, 2008, "Automatic deformable diffusion tensor registration for fiber population analysis.." Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention 11, 1014 - 1022.

2007

  • Mosaliganti,Kishore; Janoos,Firdaus; Sharp,Richard; Ridgway,Randall; Machiraju,Raghu; Huang,Kun; Wenzel,Pamela; deBruin,Alain; Leone,Gustavo; Saltz,Joel, 2007, "Detection and visualization of surface-pockets to enable phenotyping studies." IEEE TRANSACTIONS ON MEDICAL IMAGING 26, no. 9, 1283 - 1290.
  • Sharp,Richard,P; Ridgway,Randall; Mosaliganti,Kishore; Wenzel,Pamela; Pan,Tony; de Bruin,Alain; Machiraju,Raghu; Huang,Kun; Leone,Gustavo; Saltz,Joel,H, 2007, "Volume rendering phenotype differences in mouse placenta microscopy data." COMPUTING IN SCIENCE & ENGINEERING 9, no. 1, 38 - 47.
  • Sharp,Richard; Adams,Jacob; Machiraju,Raghu; Lee,Robert; Crane,Robert, 2007, "Physics-based subsurface visualization of human tissue." IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 13, no. 3, 620 - 629.
  • Wenzel,Pamela,L; Wu,Lizhao; de Bruin,Alain; Chong,Jean-Leon; Chen,Wen-Yi; Dureska,Geoffrey; Sites,Emily; Pan,Tony; Sharma,Ashish; Huang,Kun; Ridgway,Randall; Mosaliganti,Kishore; Sharp,Richard; Machiraju,Raghu; Saltz,Joel; Yamamoto,Hideyuki; Cross,James,C; Robinson,Michael,L; Leone,Gustavo, 2007, "Rb is critical in a mammalian tissue stem cell population." GENES & DEVELOPMENT 21, no. 1, 85 - 97.

2006

  • Sharp,Richard; Machiraju,Raghu, 2006, "Accelerating subsurface scattering using Cholesky factorization." VISUAL COMPUTER 22, no. 8, 541 - 549.
  • Mosaliganti,Kishore; Jia,Guang; Heverhagen,Johannes; Machiraju,Raghu; Saltz,Joel; Knopp,Michael, 2006, "Preventing signal degradation during elastic matching of noisy DCE-MR eye images.." Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention 9, 832 - 839.

2005

  • Craciun,G; Jiang,M; Thompson,D; Machiraju,R, 2005, "Spatial domain wavelet design for feature preservation in computational data sets." IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 11, no. 2, 149 - 159.

2002

  • Thompson,D,S; Nair,J,S; Venkata,S,SD; Machiraju,R,K; Jiang,M; Craciun,G, 2002, "Physics-based feature mining for large data exploration." COMPUTING IN SCIENCE & ENGINEERING 4, no. 4, 22 - 30.

Unknown

  • Myers EM, Bartlett CW, Machiraju R, Bohland JW, "An integrative analysis of regional gene expression profiles in the human brain." Methods

Papers in Proceedings

2015

  • Ayan Biswas, David Thompson, Wenbin He, Qi Deng, Chun-Ming Chen, Han-Wei Shen, Raghu Machiraju, and Anand Rangarajan "An Uncertainty-Driven Approach to Vortex Analysis Using Oracle Consensus and Spatial Proximity." in Pacific Visualization 2015. Hangzhou, (4 2015). 23 - 31.

2014

  • Wang C, Machiraju R, Huang K "Cancer Patient Integrative Stratification via a Two-step Consensus Clustering of Molecular Expression and Clinical Attributes.." in 2014 AMIA (American Medical Informatics Association) Summit on Translational Bioinformatics,. San Francisco, (4 2014). 2 -

2013

  • Park D-Y, Jones D, Moldovan N, Machiraju R, Pécot T "Robust Detection and Visualization of 
Cytoskeletal Structures in Fibrillar Scaffolds from 3-Dimensional Confocal Images." in IEEE Symposium 
on Biological Data Visualization (BioVis) 2013,. Atlanta, (10 2013). 25 - 32.

2012

  • Han,Zhi; Tian,Lu; Pecot,Thierry; Huang,Tim; Machiraju,Raghu; Huang,Kun "A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data." JOURNAL: "BMC BIOINFORMATICS." in 1st Annual Meeting of the Great Lakes Bioinformatics (GLBIO). (3 2012). S2 -
  • Pecot,Thierry; Singh,Shantanu; Caserta,Enrico; Huang,Kun; Machiraju,Raghu; Leone,Gustavo "NON PARAMETRIC CELL NUCLEI SEGMENTATION BASED ON A TRACKING OVER DEPTH FROM 3D FLUORESCENCE CONFOCAL IMAGES." in 9th IEEE International Symposium on Biomedical Imaging (ISBI) - From Nano to Macro. NEW YORK, (1 2012). 170 - 173.

2011

  • Singh,Shantanu; Janoos,Firdaus; Pecot,Thierry; Caserta,Enrico; Huang,Kun; Rittscher,Jens; Leone,Gustavo; Machiraju,Raghu "Non-parametric Population Analysis of Cellular Phenotypes." in 14th International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI 2011). BERLIN, (9 2011). 343 - 351.
  • Janoos,Firdaus; Singh,Shantanu; Machiraju,Raghu; Wells,William,M; Morocz,Istvan,A "State-Space Models of Mental Processes from fMRI." in 22nd International Conference on Information Processing in Medical Imaging (IPMI). BERLIN, (7 2011). 588 - 599.
  • Irfanoglu,M,O; Walker,L; Sammet,S; Pierpaoli,C; Machiraju,R "Susceptibility Distortion Correction for Echo Planar Images with Non-uniform B-Spline Grid Sampling: A Diffusion Tensor Image Study." in 14th International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI 2011). BERLIN, (9 2011). 174 - 181.
  • Singh,Shantanu; Janoos,Firdaus; Pecot,Thierry; Caserta,Enrico; Leone,Gustavo; Rittscher,Jens; Machiraju,Raghu "Identifying Nuclear Phenotypes Using Semi-supervised Metric Learning." in 22nd International Conference on Information Processing in Medical Imaging (IPMI). BERLIN, (1 2011). 398 - 410.

2010

  • Janoos,Firdaus; Machiraju,Raghu; Sammet,Steffen; Knopp,Michael,V; Warfield,Simon,K; Morocz,Istvan,Akos "Measuring Effects of Latency in Brain Activity with FMRI." in 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro. NEW YORK, (1 2010). 1141 - 1144.
  • Sammet,S; Irfanoglu,O; Koch,R; Schmalbrock,P; Choi,S; Machiraju,R; Yuh,W; Knopp,M "Diffusion Tensor Imaging and Fibertracking at 7T." JOURNAL: "AMERICAN JOURNAL OF ROENTGENOLOGY." in 110th Annual Meeting of the American-Roentgen-Ray-Society. (5 2010). 16 - 23.
  • Janoos F, Irfanoglu O, Afacan O, Machiraju R, Warfield S, Wald L, Morocz I "Brain State Identification from fMRI Using Unsupervised Learning." in Proceedings of Human Brain Mapping. (1 2010).
  • Janoos,Firdaus; Machiraju,Raghu; Morocz,Istvan,A "Decoding brain states from fMRI data." JOURNAL: "INTERNATIONAL JOURNAL OF PSYCHOPHYSIOLOGY." in 15th World Congress of Psychophysiology. (9 2010). 322 - 323.
  • Mosaliganti K, Janoos F, Gelas A, Noche R, Obholzer N, Machiraju R, Megason S "Anisotropic Plate Diffusion Filtering for Detection of Cell Membranes in 3D Microscopy Images." in The IEEE International Symposium on Biomedical Imaging (ISBI) 2010. Rotterdam, (4 2010). 1 - 7.
  • Irfanoglu M, Koay G, Basser P, Machiraju R "Diffusion Tensor Field Registration in the Presence of Uncertainty." in Medical Image Computing and Computer Assisted Intervention Conference (MICCAI) 2009. (1 2010).
  • F.Janoos, R. Machiraju, S. Sammet, M.V. Knopp and I.A. Morocz "Unsupervised Learning of Brain States from fMRI Data." in 3th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) Conference, 2010. BERLIN, (1 2010). 201 - 208.
  • Singh S, Raman S, Caserta E, Leone G, Ostrowski M, Rittscher J, Machiraju R "Analysis of Spatial Variation of Nuclear Morphology in Tissue Microenviroments." in International Symposium on Biological Imaging, Rotterdam, The Netherlands, April 2010 (to appear).. (1 2010).
  • Singh,S; Raman,S; Caserta,E; Leone,G; Ostrowski,M; Rittscher,J; Machiraju,R "ANALYSIS OF SPATIAL VARIATION OF NUCLEAR MORPHOLOGY IN TISSUE MICROENVIRONMENTS." in 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro. NEW YORK, (1 2010). 1293 - 1296.

2009

  • Janoos,Firdaus; Mosaliganti,Kishore; Xu,Xiaoyin; Machiraju,Raghu; Huang,Kun; Wong,Stephen,TC "Robust 3D reconstruction and identification of dendritic spines from optical microscopy imaging." JOURNAL: "MEDICAL IMAGE ANALYSIS." in 1st International Workshop on Microscopy Image Analysis with Applications to Biology. (2 2009). 167 - 179.
  • Janoos,Firdaus; Nouanesengsy,Boonthanome; Machiraju,Raghu; Shen,Han,Wei; Sammet,Steffen; Knopp,Michael; Morocz,Istvan,A "Visual Analysis of Brain Activity from fMRI Data." JOURNAL: "COMPUTER GRAPHICS FORUM." in 11th Eurographics/IEEE VGTC Symposium on Visualization (EuroVis 09). (6 2009). 903 - 910.

2005

  • Sharp,R; Machiraju,R "A simplified model for inhomogeneous subsurface scattering." in 4th International Workshop on Volume Graphics. AIRE-LA-VILLE, (1 2005). 63 - ?.

2004

  • Lee,J,H; Moghaddam,B; Pfister,H; Machiraju,R "Finding optimal views for 3D face shape modeling." in 6th IEEE International Conference on Automatic Face and Gesture Recognition. Seoul, (1 2004). 80 - 88.

2003

  • Kim,Y; Machiraju,R; Thompson,D "Rough surface modeling using surface growth." in International Conference on Shape Modeling International (SMI 2003). Seoul, (1 2003). 1 - 8.
  • Moghaddam,B; Lee,J; Pfister,H; Machiraju,R "Model-based 3D face capture with shape-from-silhouettes." in IEEE International Workshop on Analysis and Modeling of Faces and Gestures (AMFG 2003). Seoul, (1 2003). 1 - 8.

2002

  • Polapally,N,K; Machiraju,R; Panda,D "Feature estimation for efficient streaming." in 7th Symposium on Volume Visualization and Graphics. Atlanta, (1 2002). 34 - 40.
  • Jiang,M; Machiraju,R; Thompson,D "Geometric verification of swirling features in flow fields." in IEEE Visualization 2002 Eurovis Conference. Barcelona, (1 2002). 15 - 22.

2001

  • Machiraju,R; Fowler,J,E; Thompson,D; Soni,B; Schroeder,W "EVITA - Efficient visualization and interrogation of tera-scale data." in Workshop on Mining Scientific Datasets. DORDRECHT, (1 2001). 257 - 279.
  • Tenginakai,S; Lee,J; Machiraju,R "Salient iso-surface detection with model-independent statistical signatures." in IEEE Visualization Conference. NEW YORK, (1 2001). 231 - 238.
  • Scoggins,R; Machiraju,R; Moorhead,R,J "Approximate shading for the re-illumination of synthetic images." in IEEE Visualization Conference. NEW YORK, (1 2001). 379 - 386.

1998

  • Machiraju,R; Zhu,Z,F; Fry,B; Moorhead,R "Structure-significant representation of structured datasets." JOURNAL: "IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS." in 8th Annual IEEE Conference on Visualization. (4 1998). 117 - 132.