Donna Slonim -- Publications

Development, Transcriptional Regulation, and Networks

• Functional genomic analysis of amniotic fluid cell-free mRNA suggests that oxidative stress is significant in Down syndrome fetuses. Donna K. Slonim*, Keiko Koide*, Kirby L. Johnson, Umadevi Tantravahi, Janet M. Cowan, Zina Jarrah, Diana W. Bianchi. Epublished in Proceedings of the National Academy of Sciences USA, May 27th, 2009.

• Evaluating between-pathway models with expression data. Benjamin Hescott, Mark Leiserson, Lenore Cowen, Donna Slonim. RECOMB, pages 372-385, 2009.

• High throughput interaction data reveals degree conservation of hub proteins. Andrew Fox, Daniel Taylor, and Donna K. Slonim. Pacific Symposium on Biocomputing, 14:391-402, 2009.

• Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression. Yanai I, Baugh LR, Smith JJ, Roehrig C, Shen-Orr SS, Claggett JM, Hill AA, Slonim DK, and Hunter CP. Molecular Systems Biology, 4:163, 2008.

• Gene expression analysis in pregnant women and their infants identifies unique fetal biomarkers that circulate in maternal blood. Jill L. Maron, Kirby L. Johnson, Donna Slonim, Chao-Qiang Lai, Marco Ramoni, Gil Alterovitz, Zina Jarrah, Zinger Yang, and Diana W. Bianchi. Journal of Clinical Investigation, 117(10):3007-19, 2007.

• Motif evaluation using leave-one-out scoring. Audrey Girouard, Noah Smith, and Donna Slonim. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), September, 2006.

• Synthetic lethal analysis of C. elegans identifies conserved genetic interactions. L. Ryan Baugh, Joanne C. Wen, Andrew A. Hill, Donna K. Slonim, Eugene L. Brown, and Craig P. Hunter. Genome Biology, 6(4):R45, March, 2005.

• The homeodomain protein PAL-1 specifies a lineage-specific regulatory network in the C. elegans embryo. L. Ryan Baugh, Andrew A. Hill, Julia M. Claggett, Kate Hill-Harfe, Joanne C. Wen, Donna K. Slonim, Eugene L. Brown, and Craig P. Hunter. Development 132(8):1843-54, March, 2005.

• Composition and dynamics of the Caenorhabditis elegans early embryonic transcriptome . L. Ryan Baugh, Andrew A. Hill, Donna K. Slonim, Eugene L. Brown, and Craig P. Hunter. Development, 130(5):889-900, March, 2003.

Cancer Classification and Clinical Pharmacogenomics

• Risk factors associated with beta-amyloid(1-42) immunotherapy in preimmunization gene expression patterns of blood cells. Margot O'Toole, Derek B. Janszen, Donna K. Slonim, Padmalatha S. Reddy, Debra K. Ellis, Holly M. Legault, Andrew A. Hill, Maryann Z. Whitley, William M. Mounts, Krystina Zuberek, Frederick W. Immermann, Ronald S. Black, and Andrew J. Dorner. Archives of Neurology, 62:1531-6 October, 2005. Editorial about the article, from the same issue.

• Transcriptional profiles in peripheral blood mononuclear cells prognostic of clinical outcomes in patients with advanced renal cell carcinoma. Michael E. Burczynski, Natalie C. Twine, Gary Dukart, Bonnie Marshall, Manuel Hidalgo, Walter Stadler, Theodore Logan, Janice Dutcher, Gary Hudes, William L. Trepicchio, Andrew Strahs, Fred Immermann, Donna K. Slonim, and Andrew J. Dorner. Clinical Cancer Research, 11(3):1181-1189, Feb, 2005.

• Disease-associated expression profiles in PBMCs from patients with advanced renal cell carcinoma. Natalie C. Twine, Jennifer A. Stover, Bonnie Marshall, Gary Dukart, Manuel Hidalgo, Walter Stadler, Theodore Logan, Janice Dutcher, Gary Hudes, Andrew J. Dorner, Donna K. Slonim, William L. Trepicchio, and Michael E. Burczynski. Cancer Research, 63:6069-6075, September 15, 2003.

• Chemosensitivity prediction by transcriptional profiling. Jane E. Staunton, Donna K. Slonim, Hilary A. Coller, Pablo Tamayo, Michael J. Angelo, Johnny Park, Uwe Scherf, Jae K. Lee, William O. Reinhold, John N. Weinstein, Eric S. Lander, Todd R. Golub. Proceedings of the National Academy of Sciences USA, 98(19):10787-10792, September, 2001.

• Transcriptional profiling in cancer: the path to clinical pharmacogenomics. Donna K. Slonim. Pharmacogenomics, 2(2):123-136, May, 2001.

• Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Todd R. Golub*, Donna K. Slonim*, Pablo Tamayo, Christine Huard, Michelle Gassenbeek, Jill Mesirov, Hilary Coller, Mignon Loh, James R. Downing, Mark A. Caligiuri, Clara D. Bloomfield, and Eric S. Lander. Science, 286(5439):531-537, October, 1999.

Microarray Data Analysis Methods

• From patterns to pathways: gene expression data analysis comes of age. Donna K. Slonim. Nature Genetics, 32(S):502-508, December, 2002.

• Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls. Andrew A. Hill, Eugene L. Brown, Maryann Z. Whitley, Greg Tucker-Kellogg, Craig P. Hunter, and Donna K. Slonim. Genome Biology, 2(12):R55, November, 2001.

• Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Atul J. Butte, Pablo Tamayo, Donna Slonim, Todd R. Golub, Isaac S. Kohane. Proceedings of the National Academy of Sciences USA, 97(22):12182-12186, October, 2000.

• Class prediction and discovery using gene expression data. Donna K. Slonim, Pablo Tamayo, Jill P. Mesirov, Todd R. Golub, and Eric S. Lander. Proceedings of the Fourth Annual Conference on Computational Molecular Biology (RECOMB) , 263-272, April, 2000.

• Interpreting gene expression with self-organizing maps: Methods and application to hematopoietic differentiation. Pablo Tamayo, Donna Slonim, Jill Mesirov, Qing Zhu, Sutisak Kitareewan, Ethan Dmitrovsky, Eric S. Lander, and Todd R. Golub. Proceedings of the National Academy of Sciences USA, 96(6):2907-2912, March, 1999.

Genome Maps and Mapping Methods

• A YAC-based physical map of the mouse genome. Chad Nusbaum*, Donna K. Slonim*, Katrina L. Harris, Bruce W. Birren, Robert G. Steen, Lincoln D. Stein, Joyce Miller, William F. Dietrich, Robert Nahf, Victoria Wang, Olga Merport, Andrew B. Castle, Zeeshan Hussain, Gail Farino, Delphine Gray, Mechele O. Anderson, Richard Devine, Lloyd T. Horton Jr., Dorothy F. Courtney, James Tam, Matthew Cadman, Andrew R. Haynes, Christine Heuston, Tracy Marsland, Anne Southwell, Pamel Trickett, Mark A. Strivens, Mark T. Ross, Wojciech Makalowski, Yixun Xu, Mark S. Boguski, Nigel P. Carter, Paul Denny, Steve D. M. Brown, Thomas J. Hudson and Eric S. Lander. Nature Genetics, 22(4):388 - 393, August, 1999.

• A radiation hybrid map of the mouse genome. William J. Van Etten, Robert G. Steen, Huy Nguyen, Andrew B. Castle, Donna K. Slonim, Bing Ge, Chad Nusbaum, Greg D. Schuler, Eric S. Lander, and Thomas J. Hudson. Nature Genetics, 22(4):384 - 387, August, 1999.

• A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat. Robert G. Steen*, Anne E. Kwitek-Black*, Christopher Glenn*, Jo Gullings-Handley, William Van Etten, O. Scott Atkinson, Diane Appel, Simon Twigger, Melanie Muir, Tim Mull, Mary Granados, Mushira Kissebah, Kerri Russo, Robbin Crane, Michael Popp, Marc Peden, Tara Matise, Donna M. Brown, Jian Lu, Stephen Kingsmore, Peter J. Tonellato, Steve Rozen, Donna Slonim, Peter Young, Margit Knoblauch, Abraham Provoost, Detlev Ganten, Steven D. Colman, Jonathan Rothberg, Eric S. Lander, and Howard J. Jacob. Genome Research, 9:1046R, May, 1999.

• A physical map of 30,000 human genes. Panos Deloukas, et al. Science, 282: 744-746, October, 1998.

• Building human genome maps with radiation hybrids. Donna Slonim, Leonid Kruglyak, Lincoln Stein, and Eric Lander. Journal of Computational Biology, 4(4):487-504, December, 1997.

• A gene map of the human genome. Greg Schuler, et al. Science, 274: 540-546, October, 1996.

• An STS-based map of the human genome. Thomas J. Hudson, Lincoln D. Stein, Sebastian S. Gerety, Junli Ma, Andrew B. Castle, James Silva, Donna K. Slonim, Rafael Baptista, Leonid Kruglyak, Shu-Hua Xu, Xintong Hu, Angela M. E. Colbert, Carl Rosenberg, Mary Pat Reeve-Daly, Steve Rozen, Lester Hui, Xiaoyun Wu, Christina Vestergaard, Kimberly M. Wilson, Jane S. Bae, Shanak Maitra, Soula Ganiatsas, Cheryl A. Evans, Margaret M. DeAngelis, Kimberly A. Ingalls, Robert W. Nahf, Lloyd T. Horton Jr., Michele Oskin Anderson, Alville J. Collymore, Wenjuan Ye, Vardouhie Kouyoumjian, Irena S. Zemsteva, James Tam, Richard Devine, Dorothy F. Courtney, Michelle Turner Renaud, Huy Nguyen, Tara J. O'Connor, Cécile Fizames, Sabine Fauré, Gabor Gyapay, Colette Dib, Jean Morissette, James B. Orlin, Bruce W. Birren, Nathan Goodman, Jean Weissenbach, Trevor L. Hawkins, Simon Foote, David C. Page, and Eric S. Lander. Science, 270(5244): 1945-1954, December, 1995.

Computational Models of Machine Learning

• Learning with unreliable boundary queries. Avrim Blum, Prasad Chalasani, Sally Goldman, and Donna Slonim. Journal of Computer and System Sciences, 56:209-222, 1998.

• Learning from Imperfect Data in Theory and Practice. Donna Slonim. Ph.D. Thesis, Massachusetts Institute of Technology. Available as Technical Report MIT/LCS/TR-670, June, 1996.

• The power of team exploration: Two robots can learn unlabeled directed graphs. Michael Bender and Donna Slonim. Proceedings of the Thirty-Fifth Annual Symposium on Foundations of Computer Science (FOCS), 75-85, November, 1994.

• Randomly fallible teachers: Learning monotone DNF with an incomplete membership oracle. Dana Angluin and Donna Slonim. Machine Learning, 14(1):7-26, January, 1994.

Last updated June, 2009.