Recent papers published by GG & D graduate students

2014 Publications

Rogacheva MV, Manhart CM, Chen C, Guarne A, Surtees J, Alani E.(2014) Mlh1-Mlh3, A meiotic crossover and DNA mismatch repair factor, is a Msh2-Msh3-stimulated endonuclease. J Biol Chem. Feb 28;289(9):5664-72. PMID: 24403070  PMCID: PMC3937641

Chen C, Jomaa A, Ortega J, Alani EE. (2014) Pch2 is a hexameric ring ATPase that remodels the chromosome axis protein Hop1. Proc Natla Acad Sci USA Jan 7;111(1):E44-53 PMID: 24367111

Choi, J.Y. and Aquadro, C.F. (2014) The coevolutionary period of Wolbachia pipientis infecting Drosophila ananassae and its impact on the evolution of the host germline stem cell regulating genes.  Mol. Biol. Evol. Sep. 31(9): 2457-71.  PMID: 24974378.  PMCID: PMC4137719.

Satyaki, P.R., Cuykendall, T.N., Wei, K.H., Brideau, N.J., Kwak, H., Aruna, S., Ferree, P.M., Ji, S., and Barbash, D.A. (2014) The Hmr and Lhr hybrid incompatibility genes suppress a broad range of heterochromatic repeats.  PLoS Genet. Mar 20; 10(3): e1004240.  PMID: 24651406.  PMCID: PMC3961192.

Szeto, K., Reinholt, S.J., Duarte, F.M., Pagano, J.M., Ozer, A., Yao, L., Lis, J.T., and Craighead, H.G. (2014) High-throughput binding characterization of RNA aptamer selections using a microplate-based multiplex microcolumn device.  Anal. Bioanal. Chem. 406(11): 2727-32.  PMID: 24553662.  PMCID: PMC3975076.

Goodrich, J.K., Di Rienzi, S.C., Poole, .AC., Koren, O., Walters, W.A., Caporaso, J.G., Knight, R., and Ley, R.E. (2014) Conducting a microbiome study.  Cell. Jul 17; 158(2): 250-62.  PMID: 25036628.  PMCID: in progress.

Ji, Y., Sun, S., Goodrich, J.K., Kim, H., Poole, A.C., Duhamel, G.E., Ley, R.E. and Qi, L. (2014) Diet-induced alterations in gut microflora contribute to lethal pulmonary damage in TLR2/TLR4-deficient mice.  Cell Rep. Jul 10;8(2): 137-49.  PMID: 24953658.  PMCID: PMC4103790.

Das J, Fragoza R, Lee HR, Cordero NA, Guo Y, Meyer MJ, Vo TV, Wang X, Yu H.(2014 ) Exploring mechanisms of human disease through structurally resolved protein interactome networks. Mol Biosyst. Jan;10(1):9-17. PMID: 24096645 PMCID: PMC4061614

Hale, J.J., Amin, N.M., George, C., Via, Z., Shi, H., and Liu, J. (2014) A role of the LIN-12/Notch signaling pathway in diversifying the non-striated egg-laying muscles in C. elegans.  Dev. Biol. May 15; 389(2): 137-48. PMID:  24512688.  PMCID: PMC3981933.

Laflamme, B.A., Avila, F.W., Michalski, K., and Wolfner, M.F. (2014) A Drosophila protease cascade member, seminal metalloprotease-1, is activated stepwise by male factors and requires female factors for full activity.  Genetics 196(4): 1117-29.  PMID: 24514904.  PMCID: PMC3982676.

Han Y, Gao X, Liu B, Wan J, Zhang X, Qian SB. (2014) Ribosome profiling reveals sequence-independent post-initiation pausing as a signature of translation. Cell Res. Jul;24(7):842-51 PMID: 24903108

Liu B, Qian SB. (2014)  Translational reprogramming in cellular stress response. Wiley Interdiscip Rev RNA. May-Jun;5(3):301-15. PMID: 24375939 PMCID: 3991730

Luo, Y., Hartford, S.A., Zeng, R., Southard, T.L., Shima, N., and Schimenti, J.C. (2014) Hypersensitivity of primordial germ cells to compromised replication-associated DNA repair involves ATM-p53-p21 signaling.  PLoS Genet. Jul 10 10(7): e1004471.  PMID: 25010009.  PMCID: PMC4091704.

Meyer, H.M. and Roeder, A.H. (2014) Stochasticity in plant cellular growth and patterning.  Front Plant Sci.Sep 8; 5: 420. Review.  PMID: 25250034

Murphy PJ, Cipriany BR, Wallin CB, Ju CY, Szeto K, Hagarman JA, Benitez JJ, Craighead HG, Soloway PD. (2014) Single-molecule analysis of combinatiorial epigenomic states in normal and tumor cells. Proc Natl Acad Sci USA  May 7;110(19):7772-7 PMID: 23610441

Shook, M.S. and Richards, E.J. (2014) VIM proteins regulate transcription exclusively through the MET1 cytosine methylation pathway.  Epigenetics. July;9(7): 980-6.  PMID: 24762702.  PMCID: PMC4143413.

Sirot, L.K., Findlay, G.D., Sitnik, J.L., Frasheri, D., Avila, F.W., and Wolfner, M.F. (2014) Molecular characterization and evolution of a gene family encoding both female- and male-specific reproductive proteins in Drosophila.  Mol. Biol. Evol. June3;31(6): 1554-67.  PMID: 24682282.  PMCID: PMC4032134.

Findlay, G.D., Sitnik, J.L., Wang, W., Aquadro, C.F., Clark, N.L., and Wolfner, M.F. (2014) Evolutionary rate covariation identifies new members of a protein network required for Drosophila melanogaster female post-mating responses.  PLoS Genet. Jan;10(1): e1004108.  PMID: 24453993.  PMCID: PMC3894160.

Sitnik, J.L., Francis, C., Hens, K., Huybrechts, R., Wolfner, M.F., Callaerts, P. (2014) Neprilysins: an evolutionarily conserved family of metalloproteases that play important roles in reproduction in Drosophila.  Genetics. Mar; 196(3): 781-97.  PMID: 24395329.  PMCID: PMC3948806.

Qiao, H., Prasada Rao, H.B., Yang, Y., Fong, J.H., Cloutier, J.M., Deacon, D.C., Nagel, K.E., Swartz, R.K., Strong, E., Holloway, J.K., Cohen, P.E., Schimenti, J., Ward, J., and Hunter, N. (2014) Antagonistic roles of ubiquitin ligase HEI10 and SUMO ligase RNF212 regulate meiotic recombination.  Nat. Genet. 46(2): 194-9. PMID:  24390283. 

Tian, C., Shi, H., Xiong, S., Hu, F., Xiong, W.C., and Liu, J. (2014) The neogenin/DCC homolog UNC-40 promotes BMP signaling via the RGM protein DRAG-1 in C. elegans.  Development 140(19): 4070-80. PMID: 24004951.  PMCID: PMC3775419.

Szeto K, Reinholt SJ, Duarte FM, Pagano JM, Ozer A, Yao L, Lis JT, Craighead HG. (2014)  High-throughput binding characterization of RNA aptamer selections using a microplate-based multiplex microcolumn device. Anal Bioanal Chem. Apr; 406(11); 2727-32. PMID: 24553662  PMCID: PMC3975076

Satyaki PR, Cuykendall TN, Wei KH, Brideau NJ, Kwak H. Aruna S, Ferree PM, Ji S, Barbash DA. (2014) The Hmr and Lhr hybrid incompatibility genes suppress a broad range of heterochromatic repeats. PLoS Genet. Mar 20;10(3):e1004240. PMID: 24651406 PMCID: PMC3961192

Wei, K.H., Clark, A.G., and Barbash, D.A. (2014) Limited gene misregulation is exacerbated by allele-specific upregulation in lethal hybrids between Drosophila melanogaster and Drosophila simulans.  Mol. Biol. Evol. Jul;31(7): 1767-78.  PMID: 24723419.  PMCID: PMC4069615.

Zhou, A. and Pawlowski, W.P. (2014) Regulation of meiotic gene expression in plants.  Front. Plant Sci. Aug; 5: 413. doi: Review.  PMID: 25202317.  PMCID: PMC4142721.


2013 Publications

Apger-McGluaghon, J. Wolfner, MF (2013) Post-mating change in excretion by mated Drosophila melanogaster females is a long-term response that depends on sex peptide and sperm. J. Ins. Physiol.,59,1024-1030. PMID: 23891750 PMCID: PMC3923306

Awan AR,  Manfredo A, Pleiss JA. Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans. Proc Natl Acad Sci USA. 2013 Jul 30:110(31): 12762-7 PMID: 23861491 PMCID: PMC3732940

Chen, C., Jomma, A, Ortega, J., Alani, E. (2013) Pch2 is a hexameric ring ATOase that remodels the chromosome axis protein. Hop1. Proc.Natl.Acad.Sci. USA 111, E44-E53. PMC3890899 PMCID: PMC3890899

Sonntag Brown M, Lim E, Chen C, Nishant KT, Alani E. Genetic analysis of mlh3 mutations reveals interations between crossover promoting factors during meiosis in baker’s yeast. G3 (Bethesda) 2013 Jan;3(1):9-22 PMID: 23316435  PMCID: PMC3538346

Conn CS, Qian SB. Nutrient signaling in protein homeostasis: an increase in quantity at the expense of quality. Sci Signal. 2013 Apr 16;6(271) PMID: 23592839  PMCID: PMC3992710

Latulippe DR, Szeto K, Ozer A, Duarte FM, Kelly CV, Pagano JM, White BS, Shalloway D, Lis JT, Craighead HG. Multiplexed microcolumn-based process for efficient selection of RNA aptamers. Anal chem. 2013 Mar 19;85(6):3417-24. PMID: 23398198  PMCID: PMC3753675

DiRienzi SC, Sharon I, Wrighton KC, Koren O, Hug LA, Thomas BC, Goodrich JK, Spector TD, Banfield JF, Ley RE. (2013) The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. Elife: Oct 1;2:e01102. PMID: 24137540 PMCID: PMC3787301

Gligorov, D, Sitnik JL, Maeda R, Wolfner, MF, Karch F. (2013) Novel regulation of Abdominal B in the Drosophila male accessory glad reveals an essential role for secondary cell products in maintaining the female post mating response.  PLoS Genetics 3, e1003395.

Guertin MJ, Lis JT. (2013) Mechanisms by which transcription factors gain access to target sequence elements in chromatin.  Curr Opin Genet Dev. 23(2):116-23 PMID: 23266217  PMCID: PMC3651763

Scheitz CJ, Guo Y, Early AM, Harshamn LG, Clark AG. (2013) Heritability and inter-population differences in lipid profiles of Drosophila melanogaster. PLoS One. Aug 27;8(8):e72726. PMID: 24013349  PMCID: PMC3754969

Guo Y, Wei X, Das J, Grimson A, Lipkin SM, Clark AG, Yu H. (2013)  Dissecting disease inheritance modes in a three-dimensional protein network challenges the “guilt-by-assocation” principle. Am J Hum Genet. Jul 11;93(1):78-89. PMID: 23791107   PMCID: PMC3710751

Larracuente, A and AG Clark. (2013) Surprising differences in the variability of Y chromosomes in African and Cosmopolitan populations of Drosophila melanogaster. Genetics 193-201-214 PMID: 23086221  PMCID: PMC3527246

Liu B, Han Y, Qian SB. (2013) Cotranslational response to proteotoxic stress by elongation pausing of ribosomes. Mol Cell. Feb 7; 49(3):453-63  PMID: 23290916  PMCID: PMC3570626

Lyndake AM, Lim PX, Mleczko JM, Diggins CE, Holloway JK, Holmes RJ, Kan R, Schlafer DH, Freire R, Cohen PE, Weiss RS. (2013) Conditional inactivation of the DNA damage response gene Hus1 in mouse testis reveals separable roles for components of the RAD9-RAD1-HUS1 complex in meiotic chromosome maintenance. PLoS Genet 9(2):e1003320.. PMIC: 23468651

Zhang J, Bonasio R, Strino F, Kluger Y, Holloway JK, Modzelewski AJ, Cohen PE, Reinberg D. (2013) SFMBT1 functions with LSD1 to regulate expression of canonical Histone genes and chromatin-related factors. Genes Dev. 27(7):749-66  PMID: 23592795  PMCID: PMC3639416

Murphy PJ, Cipriany BR, Wallin CB, JU CY, Szeto K, Hagarman JA, Benitez JJ, Craighead HG, Soloway PD (2013) Single-molecule analysis of combinatorial epigenomic states in normal and tumor cells. Proc Natl Acad Sci USA 110(19):7772-7  PMID: 23610441  PMCID: PMC3651511

Saunders A, Core LJ, Sutcliffe C, Lis JT, Ashe HL. (2013) Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription.  Genes Dev. 27(10):1146-58  PMID: 23699410 PMCID: PMC367648

Cui J, Sartain CV, Pleiss JA, Wolfner MF> Cytoplasmic polyadenylation is a major mRNA regulator during oogenesis and egg activation in Drosophila. (2013)  Dev Biol. Nov 1;383(1):121-31 PMID: 23978535  PMCID: PMC3821703

Sartain CV, Wolfner MF. ( 2013) Calcium and egg activation in Drosophila. Cell Calcium. Jan;53(1):10-5 PMID: 23218670  PMCID: PMC3566373

Scheitz CJ, Guo Y, Early AM, Harsham LG, Clark AG.(2013)  Heritability and inter-population differences in lipid profiles of Drosophila melanogaster. PLoS One. Aug 27;8(8):e72726. PMID: 24013349  PMCID: PMC3754969

Scheitz CJ, Tumbar T. (2013) New insights into the role of Runx1 in epithelial stem cell biology and pathology. J Cell Biochem. May;1145(5):985-93 PMID: 23150456

Scott JG, Leichter CA, Rinkevich FD, Harris SA, Su C, Aberegg LC, Moon R, Geden CJ, Gerry AC, Taylor DB, Byford RL, Watson W, Johnson G, Boxler D, Zurek L. (2013) Insecticide resistance in house flies from the United States: resistance levels and frequency  of pyrethroid resistance alleles.  Pestic Biochem Physiol. 2013 Nov;107(3):377-84 PMID: 24267700

Del Campo ML, Halitschke R, Short SM, Lazzaro BP, Kessler A. (2013) Dietary plant phenolic improves survival of bacterial infection in Manduca sexta caterpillars. Entomol Exp Appl. 146(3):321-331 PMID: 23420018  PMCID: PMC3570171

Brenet F, Kermani P, Spektor, Rafii S, Scandura JM. TGFβ restore hematopoietic homeostasis after myelosuppressive chemotherapy.  (2013) J Exp Med. 11;210(3):623-39 PMID: 23440043  PMCID: PMC3600905

Tian C, Shi H, Xiong S, Hu F, Xiong W, Liu J. (2013) The neogenin/DCC homolog UNC-40 promotes BMP signaling via the RGM protein DRAG-1 in C. elegans. Development 140:4070-4080  PMID: 24004951  PMCID: PMC3775419

Wallace MD, Southard TL, Schimenti KJ, Schimenti JC. (2013) Role of DNA damage response pathways in preventing carcinogenesis caused by intrinsic replication stress. Oncongene. Jul 10;33(28):2688-95 PMID: 23975433  PMCID: PMC3936004

Wang X, Clark AG. (2013) Using next-generation RNA sequencing to identify imprinted genes. Heredity, Mar 12. PMID: 24619182 Pub Med In progress.

Wang X, Douglas KC, Wandeberg JL, Clark AG, Samollow PB (2013). Chromosome-wide profiling of X-chromosome inactivation and epigenetic states in fetal brain and placenta of the opossum, Monodelphis domestica. Genome Res. 24(1):70-83 PMID: 24065774  PMCID: PMC3875863

Wang X, D Wheeler, A Avery A Rajo, J-H Choi, JK Colbourn, AG Clark, JH Werren. (2013) Function and evolutionary divergence of methylation of the genome of Nasonia vitripennis. PLoS Genetics (10):e1003872  PMID: 24130511  PMCID: PMC3794928

Wang X, Miller DC, Harman R, Antczak DF, Clark AG (2013) Paternally expressed genes predominate in the placenta.  Proc. Natl. Acad. Sci USA 110:10705-10710 PMID: 23754418  PMCID: PMC3696791

Welsh IC, Thomsen M, Gludish DW, Alfonso-Parra C, Bai Y, Martin JF, Kurpios NA. (2013) Integration of the left-right Ritz2 transcription and Wnt signaling drives asymmetric gut morphogenesis via Daam 2. Dev Cell.  Sept 20; 26(6):629-44 PMID: 24091014 PMCID: 3965270

Zhen C,  Wang YL (2013)  Molecular monitoring of chronic myeloid leukemia: international standardization of BCR-ABL 1 quantitation.  J Mol Diagn. Sep;15(5):556-64 PMID: 23876601


2012 Publications

Chuang, C. H., Yang, D., Bai, G., Freeland, A., Pruitt, S. C., and Schimenti, J. C. (2012) Post-transcriptional homeostasis and regulation of MCM2-7 in mammalian cells. Nucleic Acids Res. 40, 4914-4924.

Koren, O., Goodrich, J. K., Cullender, T. C., Spor, A., Laitinen, K., Kling Bäckhed, H., Gonzalez, A., Werner, J. J., Angenent, L. T., Knight, R., Bäckhed, F., Isolauri, E., Salminen, S., and Ley, R. E. (2012) Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell150, 470-480.

Carvalho, F. A., Koren, O., Goodrich, J. K., Johansson, M. E. V., Nalbantoglu, I., Aitken, J. D., Su, Y., Chassaing, B., Walters, W. A., González, A., Clemente,  J. C., Cullender, T. C., Barnich, N., Darfeuille-Michaud, A., Vijay-Kumar, M., Knight, R., Ley, R. E., and Gewirtz, A.T. (2012) Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. Cell Host & Microbe 12, 139-152.

Jarvis, J. P., Scheinfeldt, L. B., Soi, S., Lambert, C., Omberg, L., Ferwerda, B., Froment, A., Bodo, J. M., Beggs, W., Hoffman, G. E., Mezey, J. G., and Tishkoff, S. A. (2012)  Patterns of ancestry, signatures of natural selection and genetic association with stature in western African pygmies.  PLoS Genetics 8, e1002641.

Makvandi-Nejad, S., Hoffman, G. E., Allen, J. J., Chu, E., Gu, E., Chandler, A. M., Loredo, A. I., Bellone, R. R., Mezey, J. G., Brooks, S. A., Sutter, N. B. (2012) Four loci explain 83% of size variation in the horse.  PLoS One 7, e39929.

Logsdon, B. A., Hoffman, G. E., and Mezey, J. G. (2012) Mouse obesity network reconstruction with a variational Bayes algorithm to employ aggressive false positive control.  BMC Bioinformatics 13, 53.

Madlung, A., Henkhaus, N., Jurevic, L., Kahsai, E. A., Bernhard, J. (2012) Natural variation and persistent developmental instabilities in geographically diverse accessions of the allopolyploid Arabidopsis suecica.  Physiologia Plantarum 144, 123-133.

Lee, S.*, Liu, B.*, Lee, S.*, Shen, B., and Qian, S.-B. (2012) Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution.  Proc. Natl. Acad. Sci. USA 109, E2424-2432. *These authors contributed equally to the work.

Han, Y., David, A., Liu, B., Bennink, J. R., Yewdell, J. W., and Qian, S.-B. (2012) Monitoring co-translational protein folding in mammalian cells at codon resolution.  Proc. Natl. Acad. Sci. USA 109, 12467-12472.

Lyndaker, A. M., Modzelewski, A. J., and Welsh, I. C. (2012) Reproductive and developmental genomics retreat at Cornell University.  Mol. Reprod. Dev. 79, 588-591.

Modzelewski,  A. J., Holmes, R. J., Hilz,  S., Grimson, A., and Cohen, P. E. (2012) AGO4 regulates entry into meiosis and influences silencing of sex chromosomes in the male mouse germline. Develop. Cell 23, 251-264.

Elliott, L. E., Saracco, S. A., and Fox, T. D. (2012) Multiple roles of the Cox20 chaperone in assembly of Saccharomyces cerevisiae cytochrome c oxidase. Genetics 190, 559-67.
Brideau, C. and Soloway, P. (2012) Data mining as a discovery tool for imprinted genes.  Methods Mol. Biol. 925, 89-134.

Benítez, J.,  Topolancik, J.,  Tian, H. C.,  Wallin, C. B.,  Latulippe, D. R.,  Szeto, K.,  Murphy, P. J., Cipriany, B. R.,  Levy, S. L., Soloway, P. D., and Craighead, H. (2012) Microfluidic extraction, stretching and analysis of human chromosomal DNA from single cells.  Lab on a Chip, accepted, DOI: 10.1039/C2LC40955K (   

Cipriany, B. R., Murphy, P. J., Hagarman, J. A., Cerf, A., Latulippe, D., Levy, S. L., Benitez, J. J., Tan, C. P., Topolancik, J., Soloway, P. D., and Craighead, H. G. (2012) Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidics channel.  Proc. Natl. Acad. Sci. USA 109, 8477-8482.

Park, Y. J., Herman, H., Gao, Y., Lindroth, A. M., Hu, B. Y., Murphy, P. J., Putnam, J. R., and Soloway, P. D. (2012) Sequences sufficient for programming imprinted germline DNA methylation defined. PLoS One 7, e33024.

Ma, X., Rogacheva, M. V., Nishant, K. T., Zanders, S., Bustamante, C. D., and Alani, E. (2012) Mutation hot spots in yeast caused by long-range clustering of homopolymeric sequences.  Cell Rep. 1, 36-42.