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Melissa S. Cline, Ph.D. - Publications

Affiliations: 
2000 University of California, Santa Cruz, Santa Cruz, CA, United States 
Area:
Computer Science, Biostatistics Biology, Molecular Biology
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33 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
2019 Cline MS, Babbi G, Bonache S, Cao Y, Casadio R, de la Cruz X, Díez O, Gutiérrez-Enríquez S, Katsonis P, Lai C, Lichtarge O, Martelli PL, Mishne G, Moles-Fernández A, Montalban G, et al. Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants. Human Mutation. PMID 31294896 DOI: 10.1002/Humu.23861  0.361
2018 Cline MS, Liao RG, Parsons MT, Paten B, Alquaddoomi F, Antoniou A, Baxter S, Brody L, Cook-Deegan R, Coffin A, Couch FJ, Craft B, Currie R, Dlott CC, Dolman L, et al. BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2. Plos Genetics. 14: e1007752. PMID 30586411 DOI: 10.1371/Journal.Pgen.1007752  0.322
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  0.579
2016 Morozova O, Newton Y, Cline M, Yip S, Rao A, Stuart J, Goldstein T, Salama S, Deyell R, Rassekh SR, Haussler D. Abstract PR14: Harnessing the power of big data to advance pediatric cancer care Cancer Research. 76. DOI: 10.1158/1538-7445.Pedca15-Pr14  0.328
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  0.606
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  0.349
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  0.356
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  0.309
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  0.424
2014 Cline M, Morozova O, Swatloski T, Craft B, Goldman M, Haussler D, Zhu J. Abstract A33: Exploring pediatric cancer genomics with the UCSC Cancer Genomics Browser Cancer Research. 74. DOI: 10.1158/1538-7445.Pedcan-A33  0.306
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  0.339
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  0.386
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  0.318
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  0.387
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  0.369
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  0.57
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  0.379
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  0.387
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  0.317
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  0.358
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  0.32
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  0.308
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  0.709
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  0.43
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  0.736
2003 Shigeta R, Cline M, Liu G, Siani-Rose MA. GPCR-GRAPA-LIB--a refined library of hidden Markov Models for annotating GPCRs. Bioinformatics (Oxford, England). 19: 667-8. PMID 12651732 DOI: 10.1093/Bioinformatics/Btg061  0.352
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  0.458
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  0.349
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  0.598
2002 Cline M, Liu G, Loraine AE, Shigeta R, Cheng J, Mei G, Kulp D, Siani-Rose MA. Structure-based comparison of four eukaryotic genomes. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 127-38. PMID 11928469  0.305
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  0.693
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  0.72
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  0.721
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