Publications and Manuscripts
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- Oh, Jung Hun; Thor, Maria ; Olsson, Caroline ; Skokic, Viktor; Jörnsten, Rebecka; Alsadius, David; Pettersson, Niclas; Steineck, Gunnar; Deasy, Joseph (2016). A Factor Analysis Approach for Clustering Patient Reported Outcomes. To appear in Methods of Information in Medicine
- Kling, T., Johansson, P., Sanchez, J., Marinescu, V.M., Jörnsten, , Nelander, S. (2015) Efficient exploration of pan-cancer networks by generalized covariance selection and interactive web content Nuclear Acids Research 43(15), e98, 2015 gkv413
- Barren\"as, F., Bruhn, S., Jörnsten , Langston, M., C., Nester, C., Rogers, G., Wang, H., Zhao, Y., and Benson, M. (2014) DNA methylation controls transcription factor binding in allergen-challenged CD4+ cells. PLoS Genetics, January 2014, 10(1), e1004059.
- The Cancer Genome Atlas Research Network; Authors: Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM; Published as collaborators Nelander S, Johansson, P, Jörnsten R, Kling T, Sanchez J, (2013) The Cancer Genome Atlas Pan-Cancer analysis project. Nature Genetics, 2013 Sep 26;45(10):1113-20. doi: 10.1038/ng.2764.
- Moreau, M.P., Bruse, S.E., Jörnsten, , Liu, Y., Brzustowicz, L.M. (2013) Chronological Changes in MicroRNA Expression in the Developing Human Brain. \\ PLoS One 8(4): e60480. doi:10.1371/journal.pone.0060480.
- Gerlee, P., Schmidt, L., Monsefi, N., Kling, T., Jörnsten, , Nelander, S. (2012) Searching for Synergies: Matrix Algebraic Approaches for Efficient Pair Screening\\ PLoS One 8(7): e68598. doi:10.1371/journal.pone.0068598.
- Vickhoff, B., Malmgren, H., {\AA}ström, R., Nyberg, G., Ekström, S.R., Engvall, M., Snygg, J., Nilsson, M., Jörnsten, (2013) Music structure determines heart rate variability of singers. Frontiers in Psychology 2013; 4: 334: Auditory and Cognitive Neuroscience, 09 July 2013, doi.org/10.3389/fpsyg.2013.00334
- Jauhiainen, A., Nerman, O., Michailidis, G., Jörnsten, (2012) Transcriptional and metabolic data integration and modeling for pathway identification. Biostatistics, doi: 10.1093/biostatistics/kxs016.
- Barren\"as, F., Couto Alves, A., Chavali, S., Coin, L, Jarvelin, M-R., Jörnsten, , Langston, M.A., Ramasamy, A., Rogers, G., Wang H., Benson, M. (2011) Highly interconnected complex disease genes are enriched for disease-associated polymorphisms. Genome Biology 2012, 13(46), doi:10.1186/gb-2012-13-6-r46
- Jörnsten, , Abenius, T., Kling T., Schmidt, L., Johansson, E., Nordling, T., Nordlander, B., Sander, C., Gennemark, P., Funa, K., Nilsson, B., Lindahl, L., Nelander, S. (2011) Network modeling of the transcriptional effects of copy number aberrations in glioblastoma. Molecular Systems Biology 7: 486 doi:10.1038/msb.2011.17}
- Abel, F., Dalevi, D., Nethander, M., Jörnsten, , De Preter K., Vermulen, J., Stallings, R., Kogner, R., Maris, J., Nilsson, S. (2011) A 6-gene signature identifies four molecular subgroups of neuroblastoma. Cancer Cell Int. 11(1):9
- Rodriguez-Saona, C.R., Polavarapu, S., Barry J.D., Pol, D., Jörnsten, , Oudemans, P.V., Liburd, O.E. (2010) Color preference, seasonality, spatial distribution and species composition of thrips (Thysanoptera: Thripidae) in northern highbush blueberries. Crop Protection, 29(11):133-1340, Nov 2010
- Jornsten, R., Abenius, T., Kling T., Schmidt, L., Johansson, E., Nordling, T., Nordlander, B., Sander, C., Gennemark, P., Funa, K., Nilsson, B., Lindahl, L., Nelander, S. (2011) Network modeling of the transcriptional effects of copy number aberrations in glioblastoma. Molecular Systems Biology 7: 486 doi:10.1038/msb.2011.17
- Asp, E., Jornsten, R., Nilsson, D., Jauhianen, A., Nerman, O., Sunnerhagen, P. (2011) Impact of oxidative stress and the MAP kinase Sty1 on mRNA stability in S.Pombe. Under revision.
- Jauhianen, A., Nerman, O., Michailidis, G., Jornsten, R. (2011) Transcriptional and metabolic data integration and modeling for pathway identification. Under revision for Biostatistics.
- Abenius, T., Jornsten, R., Schmidth, L., Nelander, S. (2011) System scale network modeling using EPoC. Proceedings of the 11th ICSB, Advances in Experimental Medicine and Biology, Springer series (ICSB), Volume 736, Part 5, 617-643, DOI: 10.1007.978-1-4419-7210-1-37
- Abel, F., Dalevi, D., Nethander, M., Jornsten, R. , De Preter K., Vermulen, J., Stallings, R., Kogner, R., Maris, J., Nilsson, S. (2011) A 6-gene signature identifies four molecular subgroups of neuroblastoma. Cancer Cell Int. 11(1):9
- Rodriguez-Saona, C.R., Polavarapu, S., Barry J.D., Pol, D., Jornsten, R., Oudemans, P.V., Liburd, O.E. (2010) Color preference, seasonality, spatial distribution and species composition of thrips (Thysanoptera: Thripidae) in northern highbush blueberries. Crop Protection, 29(11):133-1340, Nov 2010
- Jornsten, R. (2009) Simultaneous Model Selection via Rate-Distortion Theory, With Applications to Cluster and Significance Analysis of Gene Expression Data Journal of Computational and Graphical Statistics. September 1, 2009, 18(3): 613-639. doi:10.1198/jcgs.2009.07043.
- Jornsten, R. (2009) MIXT, mixture modeling with profile transformations. Technical report.
- Jornsten, R. and Keles, S. (2008) MIXL, Multi-level mixture modeling, with application to the analysis of multi-factor gene expression studies. Biostatistics 9(3): 540-554.
- Jornsten, R., Wang, H-Y., and Ouyang, M. (2007) A Meta-data based method for DNA microarray imputation. BMC Bioinformatics 8(109):doi:10.1186/1471-2105-8-109
- Goff, L.A., Hart, R., Jornsten, R., and Keles, S. (2007) Bioinformatic analysis of neural stem cell differentiation. Journal of Biomolecular Techniques 18:205-212
- Lakshmipathy, U., Love, B., Goff, L., Jornsten, R., Graichen, R., Hart, R.P., Chesnut, J.D (2007) Micro RNA expression pattern of undifferentiated and differentiated human embryonic stem cells. Stem Cells and Development 16:1-14
- Lopez-Pintado, S., and Jornsten, R. (2006) Functional analysis via extensions of the Band Depth. IMS Lecture Series, Volume 54, ed. R. Liu et al, p. 103-120
- Charych, E., Akum, B., Goldberg, J.S., Jornsten, R.J., Rongo, C., and Firestein, B.L. (2006) Activity-Independent Regulation of Dendrite Patterning by Postsynaptic Density Protein PSD-95. The Journal of Neuroscience, October 4, 2006, 26(40):10164-10176;
- Chen, M., Lucas, K.G., Akum, B.F., Balsingam, G., Stawicki, T.M., Provost, J.M., Riefler, G.M., Jornsten, R.J., and Firestein, B.L. (2005) Novel Role for Snapin in Dendrite Patterning: Interaction with Cypin. Molecular Biology of the Cell, Vol. 16, Issue 11, 5103-5114, November 2005.
- Jornsten, R. , Wang H-Y., Welsh, W.J., and Ouyang, M. (2005) DNA microarray data imputation and significance analysis of differential expression. Bioinformatics 2005 21(22):4155-4161
- Jornsten, R. DDclust: Clustering and Classification based on the L1 data depth. Journal of Multivariate Analysis Volume 90, Issue 1, July 2004, p. 67-89
- Jornsten, R., and Yu, B. (2004) Simultaneous clustering and subset selection via MDL. Advances in Minimum Description Length: Theory and Applications, MIT press. P.Grunwald, IJ Myung, M. Pitt Editors. p295-322.
- Jornsten, R., and Yu, B. (2004) Compressing Genomic and Proteomic Array Images for Statistical Analysis. Invited book chapter Genomic Signal Processing and Statistics. E.R. Dougherty, I. Shmulevich, J. Chen, Z.J. Wang Editors. p341-366
- PClust: clustering based on Pvalues Technical report Joint work with Jun Li and Regina Liu
- Pan, J.Z., Jornsten, R. , and Hart, R.P. (2004) Screening anti-inflammatory compounds in injured spinal cord with microarrays: A comparison of bioinformatics analysis approaches. Physiol. Genomics, 17:201-214.
- Freeman, W., Gaal, G., and Jornsten, R. (2003) A neurobiological theory of meaning in perception. Part 3. Multiple cortical areas synchronize without loss of local autonomy. International Journal of Bifurcation & Chaos, 13(10), 2845-2856
- Jornsten, R. , and Yu, B. (2003) Simultaneous gene clustering and subset selection for sample classification via MDL. Bioinformatics, 2003, 19: 1100-1109.
- Jornsten, R., Yu, B., Wang, W., and Ramachandran, K. (2003) Microarray image compression: SLOCO and the effects of information loss. EURASIP Signal Processing Journal, Special issue on genomic signal processing, (2003), 83/4, 859-869
- Jornsten, R., Vardi, Y., Zhang, C-H., (2002) A Robust Clustering Method and Visualization Tool Based on Data Depth. Statistical data analysis based on the L1norm and related methods. Y. Dodge editor. p. 353-366
- Jornsten, R., Vardi, Y., Zhang, C-H., (2002) On the bit-plane compression of Microarray images. Statistical Data Analysis based on the L1-norm and Related methods. Y. Dodge editor. p415-425
- Jornsten, R., and Yu, B., (2002) Multiterminal estimation - extensions and a geometric intepretation Peer-reviewed extended abstract for IEEE ISIT 2002, Lausanne, p24-29
- Comprestimation: Microarray images in abundance, Proc. of Conference on Information Science and Systems, Princeton, 2000
- Insensitivity of Adaptive Quantization to Model Estimation in Wavelet Subband Coding
Rebecka Jornsten and Bin Yu
Technical report, UC Berkeley, Department of Statistics- Data compression and Its Statistical Implications, with applications to the analysis of Microarray images UC Berkeley, PhD thesis, Dec 2001