Papers, Pre/Post-Prints, and Presentations by Faculty in the School of Biology.

Recent Submissions

  • An Unprecedented Aggregation of Whale Sharks, Rhincodon typus, in Mexican Coastal Waters of the Caribbean Sea 

    de la Parra Venegas, Rafael; Hueter, Robert; González Cano, Jaime; Tyminski, John; Remolina, Gregorio; Maslanka, Mike; Ormos, Andrea; Weigt, Lee; Carlson, Bruce; Dove, Alistair (Georgia Institute of TechnologyOxford University Press, 2011-04)
    Whale sharks, Rhincodon typus, are often perceived as solitary behemoths that live and feed in the open ocean. To the contrary, evidence is accumulating that they are gregarious and form seasonal aggregations in some coastal ...
  • Dual coding of siRNAs and miRNAs by Plant Transposable Elements 

    Piriyapongsa, Jittima; Jordan, I. King (Georgia Institute of TechnologyCold Spring Harbor Laboratory Press, 2008-03)
    We recently proposed a specific model whereby miRNAs encoded from short nonautonomous DNA-type TEs known as MITEs evolved from corresponding ancestral full-length (autonomous) elements that originally encoded short interfering ...
  • Conversion of Stable RNA Hairpin to a Metastable Dimer in Frozen Solution 

    Sun, Xueguang; Li, J. Michael; Wartell, Roger M. (Georgia Institute of TechnologyCold Spring Harbor Laboratory Press, 2007-12)
    Previous studies employing a 79-nucleotide (nt) RNA indicated that this RNA could form two bands in a native polyacrylamide gel while one band was observed in a denaturing gel. This report describes an investigation on the ...
  • The RNA Ontology Consortium: An Open Invitation to the RNA Community 

    Leontis, Neocles B.; Altman, Russ B.; Berman, Helen M.; Brenner, Steven E.; Brown, James W.; Engelke, David R.; Harvey, Stephen C.; Holbrook, Stephen R.; Jossinet, Fabrice; Lewis, Suzanna E.; Major, François; Mathews, David H.; Richardson, Jane S.; Williamson, James R.; Westhof, Eric (Georgia Institute of TechnologyCold Spring Harbor Laboratory Press, 2006-04)
    The aim of the RNA Ontology Consortium (ROC) is to create an integrated conceptual framework—an RNA Ontology (RO)—with a common, dynamic, controlled, and structured vocabulary to describe and characterize RNA sequences, ...
  • Translational Suppressors and Antisuppressors Alter the Efficiency of the Ty1 Translational Frameshift 

    Burck, Carol L.; Chernoff, Yury O.; Liu, Rong; Farabaugh, Philip J.; Liebman, Susan W. (Georgia Institute of TechnologyCold Spring Harbor Laboratory Press, 1999-05)
    Certain viruses, transposons, and cellular genes have evolved specific sequences that induce high levels of specific translational errors. Such “programmed misreading” can result in levels of frameshifting or nonsense codon ...
  • Anomalies in the Expression Profile of Interspecific Hybrids of Drosophila melanogaster and Drosophila simulans 

    Ranz, José M.; Namgyal, Kalsang; Gibson, Greg; Hartl, Daniel L. (Georgia Institute of TechnologyCold Spring Harbor Laboratory Press, 2004-03)
    When females of Drosophila melanogaster and males of Drosophila simulans are mated, the male progeny are inviable, whereas the female progeny display manifold malformations and are sterile. These abnormalities result from ...
  • Ribonuclease P RNA: Models of the 15/16 Bulge From Escherichia Coli and the P15 Stem Loop of Bacillus Subtilis 

    Easterwood, Thomas R.; Harvey, Stephen C. (Georgia Institute of TechnologyCold Spring Harbor Laboratory Press, 1997-06)
    The Escherichia coli ribonuclease P RNA 15/16 internal bulge loop and the Bacillus subtilis P15 stem loop are important substrate binding sites for the CCA-3' terminus of pre-tRNA. Models of E. coli 15/16 bulge loop and ...
  • Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training 

    Ter-Hovhannisyan,Vardges; Lomsadze, Alexandre; Chernoff, Yury O.; Borodovsky, Mark (Georgia Institute of TechnologyCold Spring Harbor Laboratory Press, 2008-12)
    We describe a new ab initio algorithm, GeneMark-ES version 2, that identifies protein-coding genes in fungal genomes. The algorithm does not require a predetermined training set to estimate parameters of the underlying ...
  • High-resolution mapping of h1 linker histone variants in embryonic stem cells. 

    Cao, Kaixiang; Lailler, Nathalie; Zhang, Yunzhe; Kumar, Ashwath; Uppal, Karan; Liu, Zheng; Lee, Eva K.; Wu, Hongwei; Medrzycki, Magdalena; Pan, Chenyi; Ho, Po-Yi; Cooper, Guy P. , Jr.; Dong, Xiao; Bock, Christoph; Bouhassira, Eric E.; Fan, Yuhong (Georgia Institute of TechnologyPublic Library of Science, 2013-04)
    H1 linker histones facilitate higher-order chromatin folding and are essential for mammalian development. To achieve highresolution mapping of H1 variants H1d and H1c in embryonic stem cells (ESCs), we have established a ...
  • Identification of target genes of the homeotic gene Antennapedia by enhancer detection 

    Wagner-Bernholz, Juliane T.; Wilson, Clive; Gibson, Greg; Schuh, Reinhard; Gehring, Walter J. (Georgia Institute of TechnologyCold Spring Harbor Laboratory Press, 2003-08)
    Localized expression of the homeotic gene Antennapedia (Antp) in Drosophila melanogaster is required for normal development of the thoracic segments. When the Antp gene is expressed ectopically in the larval primordium of ...
  • Deep phylogeny-how a tree can help characterize early life on Earth 

    Gaucher, Eric A.; Kratzer, James T.; Randall, Ryan N. (Georgia Institute of TechnologyCold Spring Harbor Laboratory Press, 2010-01)
    The Darwinian concept of biological evolution assumes that life on Earth shares a common ancestor. The diversification of this common ancestor through speciation events and vertical transmission of genetic material implies ...
  • Lineage-specific gene expansions in bacterial and archaeal genomes 

    Jordan, I. King; Makarova, Kira S.; Spouge, John L.; Wolf, Yuri I.; Koonin, Eugene V. (Georgia Institute of TechnologyCold Spring Harbor Laboratory Press, 2001-04)
    Gene duplication is an important mechanistic antecedent to the evolution of new genes and novel biochemical functions. In an attempt to assess the contribution of gene duplication to genome evolution in archaea and bacteria, ...
  • Essential genes are more evolutionarily conserved than non-essential genes in bacteria 

    Jordan, I. King; Rogozin, Igor B.; Wolf, Yuri I.; Koonin, Eugene V. (Georgia Institute of TechnologyCold Spring Harbor Laboratory Press, 2002-06)
    The “knockout-rate” prediction holds that essential genes should be more evolutionarily conserved than are nonessential genes. This is because negative (purifying) selection acting on essential genes is expected to be more ...
  • Recombination has little effect on the rate of sequence divergence in pseudoautosomal boundary 1 among humans and great 

    Yi, Soojin; Summers, Tyrone J.; Pearson, Nathaniel M.; Li, Wen-Hsiung (Georgia Institute of TechnologyCold Spring Harbor Laboratory Press, 2004-01)
    Recent studies indicated that recombination is strongly mutagenic. In particular, data from the mouse pseudoautosomal boundary (PAB) suggested that locally intensive recombination increased the nucleotide substitution rate ...
  • Retrotransposons and their recognition of pol II promoters: A comprehensive survey of the transposable elements derived from the complete genome sequence of Schizosaccharomyces pombe 

    Bowen, Nathan J.; Jordan, I. King; Epstein, Jonathan A.; Wood, Valerie; Levin, Henry L. (Georgia Institute of TechnologyCold Spring Harbor Laboratory Press, 2003-09)
    The complete DNA sequence of the genome of Schizosaccharomyces pombe provides the opportunity to investigate the entire complement of transposable elements (TEs), their association with specific sequences, their chromosomal ...
  • Reduction of Hox gene expression by H1 depletion 

    Zhang, Yunzhe; Liu, Zheng; Medrzycki, Magdalena; Cao, Kaixiang; Fan, Yuhong (Georgia Institute of TechnologyPublic Library of Science, 2012-06-11)
    The evolutionarily conserved homeotic (Hox) genes are organized in clusters and expressed collinearly to specify body patterning during embryonic development. Chromatin reorganization and decompaction are intimately connected ...
  • Parent-Offspring Transmission of Adipocytokine Levels and Their Associations with Metabolic Traits 

    Al-Daghri, Nasser M.; Al-Attas, Omar S.; Alokail, Majed S.; Alkharfy, Khalid M.; Yakout, Sobhy M.; Sabico, Shaun B.; Gibson, Greg; Chrousos, George P.; Kumar, Sudhesh (Georgia Institute of TechnologyPublic Library of Science, 2011-04-04)
    Adipose tissue secreted cytokines (adipocytokines) have significant effects on the physiology and pathology of human metabolism relevant to diabetes and cardiovascular disease. We determined the relationship of the pattern ...
  • Histone H1 depletion impairs embryonic stem cell differentiation 

    Zhang, Yunzhe; Cooke, Marissa; Panjwani, Shiraj; Cao, Kaixiang; Krauth, Beth; Ho, Po-Yi; Medrzycki, Magdalena; Berhe, Dawit T.; Pan, Chenyi; McDevitt, Todd C.; Fan, Yuhong (Georgia Institute of TechnologyPublic Library of Science, 2012-05-12)
    Pluripotent embryonic stem cells (ESCs) are known to possess a relatively open chromatin structure; yet, despite efforts to characterize the chromatin signatures of ESCs, the role of chromatin compaction in stem cell fate ...
  • Destabilization and recovery of a yeast prion after mild heat shock 

    Newnam, Gary P.; Birchmore, Jennifer L.; Chernoff, Yury O. (Georgia Institute of TechnologyAcademic Press, 2011-05-06)
    Yeast prion [PSI+] is a self-perpetuating amyloid of the translational termination factor Sup35. Although [PSI+] propagation is modulated by heat shock proteins (Hsps), high temperature was previously reported to have ...
  • Huntingtin toxicity in yeast model depends on polyglutamine aggregation mediated by a prion-like protein Rnq1 

    Meriin, Anatoli B.; Zhang, Xiaoqian; He, Xiangwei; Newnam, Gary P.; Chernoff, Yury O.; Sherman, Michael Y. (Georgia Institute of TechnologyRockefeller University Press, 2002-06-10)
    The cause of Huntington’s disease is expansion of polyglutamine (polyQ) domain in huntingtin, which makes this protein both neurotoxic and aggregation prone. Here we developed the first yeast model, which establishes a ...

View more