Melissa S. Cline, Ph.D. - Publications

2000 University of California, Santa Cruz, Santa Cruz, CA, United States 
Computer Science, Biostatistics Biology, Molecular Biology

45 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Cai B, Li B, Kiga N, Thusberg J, Bergquist T, Chen YC, Niknafs N, Carter H, Tokheim C, Beleva-Guthrie V, Douville C, Bhattacharya R, Grace Yeo HT, Fan J, Sengupta S, ... ... Cline M, et al. Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges. Human Mutation. PMID 28544481 DOI: 10.1002/Humu.23265  0.84
2015 Karchin R, Cline MS. Human genetics special issue on computational molecular medicine. Human Genetics. 134: 455-7. PMID 25805167 DOI: 10.1007/S00439-015-1545-6  0.84
2015 Goldman M, Craft B, Swatloski T, Cline M, Morozova O, Diekhans M, Haussler D, Zhu J. The UCSC Cancer Genomics Browser: update 2015. Nucleic Acids Research. 43: D812-7. PMID 25392408 DOI: 10.1093/Nar/Gku1073  0.84
2015 Zhu J, Craft B, Goldman M, Cline M, Diekhans M, Haussler D. Abstract B1-07: Using the UCSC Xena Platform to integrate, visualize, and analyze your own data in the context of large external genomic datasets Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-B1-07  0.44
2014 Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, ... ... Cline MS, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 515: 355-64. PMID 25409824 DOI: 10.1038/Nature13992  0.84
2014 Wilks C, Cline MS, Weiler E, Diehkans M, Craft B, Martin C, Murphy D, Pierce H, Black J, Nelson D, Litzinger B, Hatton T, Maltbie L, Ainsworth M, Allen P, et al. The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data. Database : the Journal of Biological Databases and Curation. 2014. PMID 25267794 DOI: 10.1093/Database/Bau093  0.84
2014 Paz I, Kosti I, Ares M, Cline M, Mandel-Gutfreund Y. RBPmap: a web server for mapping binding sites of RNA-binding proteins. Nucleic Acids Research. 42: W361-7. PMID 24829458 DOI: 10.1093/Nar/Gku406  0.84
2014 Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hinrichs AS, Learned K, Lee BT, et al. The UCSC Genome Browser database: 2014 update. Nucleic Acids Research. 42: D764-70. PMID 24270787 DOI: 10.1093/Nar/Gkt1168  0.84
2013 Cline MS, Craft B, Swatloski T, Goldman M, Ma S, Haussler D, Zhu J. Exploring TCGA Pan-Cancer data at the UCSC Cancer Genomics Browser. Scientific Reports. 3: 2652. PMID 24084870 DOI: 10.1038/Srep02652  0.84
2013 Hall MP, Nagel RJ, Fagg WS, Shiue L, Cline MS, Perriman RJ, Donohue JP, Ares M. Quaking and PTB control overlapping splicing regulatory networks during muscle cell differentiation. Rna (New York, N.Y.). 19: 627-38. PMID 23525800 DOI: 10.1261/Rna.038422.113  0.84
2013 Pistoni M, Shiue L, Cline MS, Bortolanza S, Neguembor MV, Xynos A, Ares M, Gabellini D. Rbfox1 downregulation and altered calpain 3 splicing by FRG1 in a mouse model of Facioscapulohumeral muscular dystrophy (FSHD). Plos Genetics. 9: e1003186. PMID 23300487 DOI: 10.1371/Journal.Pgen.1003186  0.84
2013 Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Raney BJ, Pohl A, Malladi VS, Li CH, Lee BT, ... ... Cline MS, et al. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Research. 41: D64-9. PMID 23155063 DOI: 10.1093/Nar/Gks1048  0.84
2013 Goldman M, Craft B, Swatloski T, Ellrott K, Cline M, Diekhans M, Ma S, Wilks C, Stuart J, Haussler D, Zhu J. The UCSC Cancer Genomics Browser: update 2013. Nucleic Acids Research. 41: D949-54. PMID 23109555 DOI: 10.1093/Nar/Gks1008  0.84
2012 Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, ... ... Cline MS, et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology. 13: 418. PMID 22889292 DOI: 10.1186/Gb-2012-13-8-418  0.84
2012 Charizanis K, Lee KY, Batra R, Goodwin M, Zhang C, Yuan Y, Shiue L, Cline M, Scotti MM, Xia G, Kumar A, Ashizawa T, Clark HB, Kimura T, Takahashi MP, et al. Muscleblind-like 2-mediated alternative splicing in the developing brain and dysregulation in myotonic dystrophy. Neuron. 75: 437-50. PMID 22884328 DOI: 10.1016/J.Neuron.2012.05.029  0.84
2012 Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, Kuhn RM, Meyer LR, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Pohl A, Malladi VS, Li CH, ... ... Cline MS, et al. The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Research. 40: D918-23. PMID 22086951 DOI: 10.1093/Nar/Gkr1055  0.84
2012 Rosenbloom KR, Dreszer TR, Long JC, Malladi VS, Sloan CA, Raney BJ, Cline MS, Karolchik D, Barber GP, Clawson H, Diekhans M, Fujita PA, Goldman M, Gravell RC, Harte RA, et al. ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Research. 40: D912-7. PMID 22075998 DOI: 10.1093/Nar/Gkr1012  0.84
2012 Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, ... ... Cline MS, et al. An encyclopedia of mouse DNA elements (Mouse ENCODE) Genome Biology. 418. DOI: 10.1186/gb4035  0.84
2011 Cline MS, Karchin R. Using bioinformatics to predict the functional impact of SNVs. Bioinformatics (Oxford, England). 27: 441-8. PMID 21159622 DOI: 10.1093/Bioinformatics/Btq695  0.84
2011 Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, et al. ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Research. 39: D871-5. PMID 21037257 DOI: 10.1093/Nar/Gkq1017  0.84
2011 Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, et al. The UCSC Genome Browser database: update 2011. Nucleic Acids Research. 39: D876-82. PMID 20959295 DOI: 10.1093/Nar/Gkq963  0.84
2010 Salomonis N, Schlieve CR, Pereira L, Wahlquist C, Colas A, Zambon AC, Vranizan K, Spindler MJ, Pico AR, Cline MS, Clark TA, Williams A, Blume JE, Samal E, Mercola M, et al. Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Proceedings of the National Academy of Sciences of the United States of America. 107: 10514-9. PMID 20498046 DOI: 10.1073/Pnas.0912260107  0.84
2010 Du H, Cline MS, Osborne RJ, Tuttle DL, Clark TA, Donohue JP, Hall MP, Shiue L, Swanson MS, Thornton CA, Ares M. Aberrant alternative splicing and extracellular matrix gene expression in mouse models of myotonic dystrophy. Nature Structural & Molecular Biology. 17: 187-93. PMID 20098426 DOI: 10.1038/Nsmb.1720  0.84
2009 Pohl AA, Sugnet CW, Clark TA, Smith K, Fujita PA, Cline MS. Affy exon tissues: exon levels in normal tissues in human, mouse and rat. Bioinformatics (Oxford, England). 25: 2442-3. PMID 19570805 DOI: 10.1093/Bioinformatics/Btp414  0.84
2009 Cline MS, Kent WJ. Understanding genome browsing. Nature Biotechnology. 27: 153-5. PMID 19204697 DOI: 10.1038/Nbt0209-153  0.84
2008 Emig D, Cline MS, Klein K, Kunert A, Mutzel P, Lengauer T, Albrecht M. Integrative visual analysis of the effects of alternative splicing on protein domain interaction networks. Journal of Integrative Bioinformatics. 5. PMID 20134061 DOI: 10.2390/biecoll-jib-2008-101  0.84
2008 Yeung N, Cline MS, Kuchinsky A, Smoot ME, Bader GD. Exploring biological networks with Cytoscape software. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 8.13. PMID 18819078 DOI: 10.1002/0471250953.Bi0813S23  0.84
2008 Emig D, Cline MS, Lengauer T, Albrecht M. Integrating expression data with domain interaction networks. Bioinformatics (Oxford, England). 24: 2546-8. PMID 18710874 DOI: 10.1093/bioinformatics/btn437  0.84
2007 Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, et al. Integration of biological networks and gene expression data using Cytoscape. Nature Protocols. 2: 2366-82. PMID 17947979 DOI: 10.1038/Nprot.2007.324  0.84
2007 Garcia O, Saveanu C, Cline M, Fromont-Racine M, Jacquier A, Schwikowski B, Aittokallio T. GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Bioinformatics (Oxford, England). 23: 394-6. PMID 17127678 DOI: 10.1093/Bioinformatics/Btl605  0.84
2006 Sugnet CW, Srinivasan K, Clark TA, O'Brien G, Cline MS, Wang H, Williams A, Kulp D, Blume JE, Haussler D, Ares M. Unusual intron conservation near tissue-regulated exons found by splicing microarrays. Plos Computational Biology. 2: e4. PMID 16424921 DOI: 10.1371/Journal.Pcbi.0020004  0.84
2005 Ule J, Ule A, Spencer J, Williams A, Hu JS, Cline M, Wang H, Clark T, Fraser C, Ruggiu M, Zeeberg BR, Kane D, Weinstein JN, Blume J, Darnell RB. Nova regulates brain-specific splicing to shape the synapse. Nature Genetics. 37: 844-52. PMID 16041372 DOI: 10.1038/Ng1610  0.84
2005 Cline MS, Blume J, Cawley S, Clark TA, Hu JS, Lu G, Salomonis N, Wang H, Williams A. ANOSVA: a statistical method for detecting splice variation from expression data. Bioinformatics (Oxford, England). 21: i107-15. PMID 15961447 DOI: 10.1093/Bioinformatics/Bti1010  0.84
2004 Karchin R, Cline M, Karplus K. Evaluation of local structure alphabets based on residue burial. Proteins. 55: 508-18. PMID 15103615 DOI: 10.1002/Prot.20008  0.84
2004 Cline MS, Shigeta R, Wheeler RL, Siani-Rose MA, Kulp D, Loraine AE. The effects of alternative splicing on transmembrane proteins in the mouse genome. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 17-28. PMID 14992489  0.84
2004 Cheng J, Sun S, Tracy A, Hubbell E, Morris J, Valmeekam V, Kimbrough A, Cline MS, Liu G, Shigeta R, Kulp D, Siani-Rose MA. NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis. Bioinformatics (Oxford, England). 20: 1462-3. PMID 14962933 DOI: 10.1093/Bioinformatics/Bth087  0.84
2003 Loraine AE, Helt GA, Cline MS, Siani-Rose MA. Exploring alternative transcript structure in the human genome using blocks and InterPro. Journal of Bioinformatics and Computational Biology. 1: 289-306. PMID 15290774 DOI: 10.1142/S0219720003000113  0.84
2003 Wang H, Hubbell E, Hu JS, Mei G, Cline M, Lu G, Clark T, Siani-Rose MA, Ares M, Kulp DC, Haussler D. Gene structure-based splice variant deconvolution using a microarray platform. Bioinformatics (Oxford, England). 19: i315-22. PMID 12855476 DOI: 10.1093/Bioinformatics/Btg1044  0.84
2003 Karchin R, Cline M, Mandel-Gutfreund Y, Karplus K. Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry. Proteins. 51: 504-14. PMID 12784210 DOI: 10.1002/Prot.10369  0.84
2003 Liu G, Loraine AE, Shigeta R, Cline M, Cheng J, Valmeekam V, Sun S, Kulp D, Siani-Rose MA. NetAffx: Affymetrix probesets and annotations. Nucleic Acids Research. 31: 82-6. PMID 12519953 DOI: 10.1093/Nar/Gkg121  0.84
2002 Loraine AE, Helt GA, Cline MS, Siani-Rose MA. Protein-based analysis of alternative splicing in the human genome. Proceedings / Ieee Computer Society Bioinformatics Conference. Ieee Computer Society Bioinformatics Conference. 1: 118-24. PMID 15838129 DOI: 10.1109/CSB.2002.1039335  0.84
2002 Cline MS, Karplus K, Lathrop RH, Smith TF, Rogers RG, Haussler D. Information-theoretic dissection of pairwise contact potentials. Proteins. 49: 7-14. PMID 12211011 DOI: 10.1002/Prot.10198  0.84
2002 Cline M, Hughey R, Karplus K. Predicting reliable regions in protein sequence alignments. Bioinformatics (Oxford, England). 18: 306-14. PMID 11847078 DOI: 10.1093/Bioinformatics/18.2.306  0.84
2001 Karplus K, Karchin R, Barrett C, Tu S, Cline M, Diekhans M, Grate L, Casper J, Hughey R. What is the value added by human intervention in protein structure prediction? Proteins. 86-91. PMID 11835485 DOI: 10.1002/Prot.10021  0.84
1997 Karplus K, Sjolander K, Barrett C, Cline M, Haussler D, Hughey R, Holm L. Predicting Protein Structure Using Hidden Markov Models Proteins. 29: 134-139. DOI: 10.1002/(Sici)1097-0134(1997)1+<134::Aid-Prot18>3.0.Co;2-P  0.64
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