The BUMP Publications
Read about research from UROP students working in the Biology Department!
- Been an author on a journal publication?
- Written an abstract for the Undergraduate Symposium?
- Written an abstract or paper for 7.18?
- Had your name included on an abstract for a scientific meeting?
We want to include it here. Email us!
- Different labs have different policies, and you should ask about these when you join a lab.
- Being an author indicates that one has made a substantial contribution to a paper. For example, if your data makes one or more figures in a paper, you will likely be an author on the paper.
- For smaller research contributions, you will be acknowledged at the end of the paper, but not included as an author.
- But remember, a successful UROP is not marked by whether a publication bears your name. A good letter of recommendation is worth much more than your name on a publication.
- Abstracts for various meetings count as publications. These could include:
The Biology Dept. Undergraduate Symposium
A national or international symposium
An MIT departmental retreat
In all cases, written permission from your faculty research advisor and graduate student/postdoc mentor is necessary to add your abstract to this site.
Reporting year 2007-2008
Arup Sarma, who worked in Chris Burge’s lab, is an author on a paper published in Science: Sandberg, R., Neilson, J.R., Sarma, A., Sharp, P.A., Burge, C.B. (2008). “Proliferating cells express mRNAs with shortened 3’ untranslated regions and fewer microRNA target siges.” Science 320, 1643-1647.
Woon Teck Yap, who worked in Prof. Darrell Irvine’s lab, published a paper in Biomacromolecules: Jain, Siddharta; Yap, Woon Teck; and Irvine, Darrell J. “Synthesis of Protein-Loaded Hydrogel Particles in an Aqueous Two-Phase System for Coincident Antigen and CpG Oligonucleotide Delivery to Antigen-Presenting Cells.” Biomacromolecules. 2005, 6, 2590-2600.
Pooja Sodha worked in Tyler Jacks’ lab and coauthored “BAX and BAK: Required for the Hematopoietic but not the Gastrointestinal Syndrome after Radiation.” David G. Kirsch, 1,2 Philip M. Santiago, 1 Emmanuelle di Tomasso, 2 Wu-Shiun Hou, 1 Talya Dayton, 1 Pooja Sodha, 1 Kim Mercer, 1 Rhianna Cohen, 1 Osamu Tekeyushi, 3 Stanley Korsmeyer, 3 Roderick Bronson, 4 Carla F. Kim, 1 Kevin M. Haigis, 1 Rakesh K. Jain,2 Tyler Jacks1,5
Grace Lo, who worked in Rudolf Jaenisch’s lab, was an author on three papers:
Lin, H., Yamada, Y., Nguyen, S., Linhart, H., Jacksno-Grusby, L., Meissner, A., Meletis, D., Lo, G. & Jaenisch, R. Suppression of intestinal neoplasia by deletion of Dnmt3b. MCB 26, 2976-83 (2006).
Linhart, H.G., Lin, H., Yamada, Y., Moran, E., Steine, E.J., Gokhale, S., Lo, G., Cantu, E., Ehrich, M., He, T., Meissner, A. & Jaenisch, R. Dnmt3b promotes tumorigenesis in vivo by gene-specific de novo methylation and transcriptional silencing. Genes Dev. 21: 3110-3122. (2007).
Paper accepted for publication by Genes & Development: Linhart, H.G., Lin, H., Yamada, Y., Moran, E., Steine, E., Gokhale, S., Lo, G., Cantu, E., Ehrinch, M., He, Timothy, Meissner, A., and Jaenisch, R. “Dnmt3b promotes tumorigenesis in vivo by gene-specific de novo methylation and transcriptional silencing.”
Alejandro Ochoa worked in Amy Keating’s lab and published Grigoryan, G., Ochao, A., Keating, A.E. “Computing van Der Waals energies in the context of the rotamer approximation.” Proteins 2007 Sep 1;68(4):863-78.
Shirin Pillay worked in Amy Keating’s lab, co-authored Zizlsperger, N., Malashkevich, V.N., Pillay, S., and Keating, A.E. "Analysis of coiled-coil interactions between core proteins of the spindle pole body." Biochemistry 2008 in press.
Rebecca Motola-Barnes worked in Troy Littleton’s lab, was an author on Rodal, A.A., Motola-Barnes, R.N. & Littleton, J.T. (2008) Nervous Wreck and Cdc42 cooperate to regulate endocytic actin assembly during synaptic growth. J. Neuroscience 28, 8316-8325.
Danielle Pigneri worked in Troy Littleton’s lab and published Rodal, A.A., Pigneri, D., Yu, A., Rodal, R. & Littleton, J.T. (2005) Cytoskeletal regulation of neuronal structure and function. Cold Spring Harbor Neurobiology of Drosophila Abstracts, p. 204.
Daon Ha from Harvey Lodish’s lab was an author on Kotani, A., D. Ha, J. Hsieh, P. Rao, D. Schotte, M. den Boer, S. Armstrong, and H. F. Lodish. miR-128b is a potent glucocorticoid sensitizer in MLL-AF4 Acute Lymphocytic Leukemia cells and exerts synergistic effects with miR-221 Blood submitted (2008).
Eva Klinman worked in Harvey Lodish’s lab; she published Herrlich, A., E. Klinman, J. Fu, C. Sadegh, and H. F. Lodish Ectodomain cleavage of the EGF ligands HB-EGF, neuregulin1-beta and TGF-alpha is specifically triggered by different stimuli and involves different PKC isoenzymes. FASEB Journal in press (2008).
Stephanie Wang conducted research in the Lodish lab and co-authored Zhou, B., S. Wang, C, Mayr, D.P. Bartel, and H. F. Lodish miR-150, a microRNA expressed in mature B and T cells, blocks early B cell development when expressed prematurely. Proc. Natl. Acad. Sci. USA 104: 7080 –7085 (2007).
Jennifer Young worked in Bob Weinberg’s lab and co-authored a paper submitted to Nature Cell Biology, pending acceptance: Rai, P., Onder, T.T., Young, J.J., Pang, B. McFaline, J. Dedon, P.C., and Weinberg, R.A. (2007) Elimination of oxidized nucleotides is necessary to prevent rapid onset of cellular senescence.
The following students are expected to submit papers for publication in the near future: Kathy Xie from David Bartel’s lab, Grace Yuen from Jianzhu Chen’s lab, Tristan Kooistra from Dennis Kim’s lab (at least three papers), Elizabeth Gillenwater and Katherine Romer from Monty Krieger’s lab, and Lauren Rodda from Jeroen Saeij’s lab.
Alejandro Ochoa, who worked in Amy Keating’s lab, is an author on a paper published in Proteins: Grigoryan, G., Ochao, A., Keating, A.E. “Computing van Der Waals energies in the context of the rotamer approximation.” Proteins 2007 Sep 1;68(4):863-78.
Grace Lo, from Rudolph Jaenisch’s lab, is an author on a paper accepted for publication by Genes & Development: Linhart, H.G., Lin, H., Yamada, Y., Moran, E., Steine, E., Gokhale, S., Lo, G., Cantu, E., Ehrinch, M., He, Timothy, Meissner, A., and Jaenisch, R. “Dnmt3b promotes tumorigenesis in vivo by gene-specific de novo methylation and transcriptional silencing.
Eric Von Nostrand, who worked in Chris Burge’s lab, had the following publications: Wang, Z., Xiao, X., Van Nostrand, E., Burge, C.B. “General and specific functions of exonic splicing silencers in splicing control.” Mol Cell 2006 Jul 7;23(1):61-70. Epub 2006 Jun 22. and Yeo, GW., Van Nostrand, E., Holste, D., Poggio, T., Burge, C.B. “Identification and analysis of alternative splicing events conserved in human and mouse.” Proc Natl Acad Sci USA 2005 Feb 22;102(8):2850-5. Epub 2005 Feb 11.
Stephanie Wang, who worked in Harvey Lodish’s lab, was included in: Zhou, Wang, S., Mayr, C., Bartel, D.P., and Lodish, H.F. “miR-150, a microRNA expressed in mature B and T cells, b locks early B cell development when expressed prematurely.” Proc. Natl, Acad. Sci. USA 104: 7080-7085, 2006.
Alicia Zhou, who worked in Robert Weinberg’s lab, was an author on: Mani, S.A., Yang, J., Brooks, M. Schwaninger, G., Zhou, A., Miura, N., Kutok, J.L., Hartwell, K., Richardson, A.L., and Weinberg, R. “Mesenchyme Forkhead 1 (FOXC2) plays a key role in metastasis and is associated with aggressive basal-like breast cancers.” Proc. Natl. Acad. Sci. USA 2007 June 12; 104(24):10069-10074.
Heather Pressler, from Robert Langer’s lab, was an author of a paper published in Biomaterials: Gerecht, S., Townsend, S., Pressler, H., Zhu, H., Nijist, C., Bruggeman, J., Nichol, J., and Langer, R. “A porous photocurable elastomer for cell encapsulation and culture.” Biomaterials, 28: 4825-4826, 2007.
Shuai Chen, from Alex Rich’s lab, was an author on Wong, B., Chen, S., Kwon, J., and Rich, A. “Characterization of Z-DNA as a nucleosome-boundary element in yeast Saccharomyces cerevisiae.” Proc. Natl. Acad. Sci. USA 2007 Feb 13; 104(7): 2229-2234.
Radhika Jagannathan, who worked in Frank Gertler’s lab, was an author on a paper published in Developmental Cell: Krause, M., Leslie, J.D., Stewart, M., Lafuente, E.M., Valderrama, F., Jagannathan, R., Strasser, G.A., Rubinson, D.A., Liu, H., Way, M., Yaffe, M.B., Boussiotis, V.A., and Gertler, F.B. “Lamellipodin, an ena/VASP ligand, is implicated in regulation of lamellipodial dynamics.” Developmental Cell 2004 Oct; 7:1-20.
Dan Yuan, who worked in Graham Walker’s lab, was an author on Kobayashi, H., Simmons, L.A., Yuan, D.S., Broughton, W.J. and Walker, G.C. “Multiple Ku orthologs Mediate DNA Non-Homologous End-joining in the Free-living Form and During Chronic Infection of Sinorhizobium meliloti. Molecular Microbiology. In press.
We expect that Erqi Liu from Richard Hynes’ lab, Arup Sarma in Chris Burge’s lab, Dawn Zhang in Jianzhu Chen’s lab, Alicia DeFrancesco and Brianne Holmbeck in Penny Chisholm’s lab, Elizabeth Gillenwater and Katherine Romer in Monty Krieger’s lab, Tristan Kooistra in Dennis Kim’s lab, and Caroline Barker, Yao Luo, and Amy Norovich in Frank Gertler’s lab, will be included in publications.
Alex Bagley is an author on a paper published in Molecular Cell: Sarbassov, D.D., Ali, S,M, Sengupta, S., Sheen, J.-H., Hsu, P.P., Bagley, A.F., Markhard, A.L. and Sabatini, D.M. (2006) Prolonged Rapamycin Treatment Inhibits mTORC2 Assembly and Akt/PKB. Molecular Cell 22: 159-168.
Jerry Treho, who worked in David Bartel’s lab as an EXROP student, will be part of a publication expected to be out soon, titled “A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana”, submitted to Genes & Development.
Jenny Ruan and Heidi Holley of Hazel Sive’s lab will be included in publications expected to be out in 2007. The papers are tentatively titled: Gutzman, J; Holley, H and Sive, H. Laminins are required for morphogenesis of the zebrafish mid-hindbrain constriction, and Lowery, L; Ruan, J and Sive, H. Role of beta NaKATPase subunits in zebrafish brain ventricle lumen inflation.
We expect that Amy Choung who worked in Mary-Lou Pardue’s lab, and Hannah Zhou, who worked in Jianzhu Chen’s lab, will be included in publications.
The most recent publication to stem from students’ research in the microbial Genetics Project Lab is a paper describing mechanisms of horizontal DNA transfer between soil bacteria: Yang JC, Lessard PA, Sengupta N, Windsor SD, O'Brien XM, Bramucci M, Tomb JF, Nagarajan V, Sinskey AJ. (2006) TraA is required for megaplasmid conjugation in Rhodococcus erythropolis AN12. Plasmid. (Epub ahead of print) - .
In this paper, the authors acknowledged the Howard Hughes Medical Institute’s support of undergraduate research in the Project Lab. This publication brings to a total of eight the number of Project Lab students who have published portions of their coursework in widely distributed, peer-reviewed journals in the past three years.
Since the last report in November 2005, the following papers including HHMI-supported UROP students have been submitted or published.
Shuai Chen, summer 2005 UROP student in Alexander Rich’s lab, is a co-author on a paper being submitted to PNAS: Wong, B., Chen, S., Rich, A. “Characterization of Z-DNA as a nucleosome-boundary element in the yeast Saccaromyces cerevisiae”.
Cameron Sadegh, summer 2005 UROP student in Harvey Lodish’s lab, is a co-author on a paper published in Blood: Liu Y., Pop R., Sadegh C., Brugnara C., Haase V.H., Socolovsky M. “Suppression of Fas-FasL coexpression by erythropoietin mediates erythroblast expansion during the erythropoietic stress response in vivo”, Blood (2006) Jul 1;108(1):123-33; Epub Mar 9 2006.
A paper from Hazel Sive’s lab which includes summer 2005 UROP student Jamie Rubin is currently under review. Lowery, L.A., Rubin, J., Sive, H. “Sfpq/whitesnake is required for cell survival and correct neuronal development in the zebrafish.” (2006)