Selected Publications

The Department of Biological Sciences has a strong history of research going back to our founding. Faculty, postdocs, graduate students, and undergraduate students all contribute to our research mission. We work with scientific colleagues across the University and around the world. Our productivity speaks volumes about our commitment to research. Please refer to the profile pages for an updated listing of publications by each faculty member.

Faculty Publications (selected) listed by year, since 2015

2024 Publications (selected)

  • Baiz MD, Wood AW, Toews DPL (2024) Association between the gut microbiome and carotenoid plumage phenotype in an avian hybrid zone. Proc Biol Sci 291:20240238. https://www.ncbi.nlm.nih.gov/pubmed/38628125
  • Birkemeier M, Swindle A, Bowman J, Lynch VJ (2024) Pervasive loss of regulated necrotic cell death genes in elephants, hyraxes, and sea cows (Paenungualta). bioRxiv. https://www.ncbi.nlm.nih.gov/pubmed/38617256
  • Bowman J, Lynch VJ (2024) Rapid evolution of genes with anti-cancer functions during the origins of large bodies and cancer resistance in elephants. bioRxiv. https://www.ncbi.nlm.nih.gov/pubmed/38463968
  • Fleck SJ, Tomlin C, da Silva Coelho FA, Richter M, Danielson ES, Backenstose N, Krabbenhoft T, Lindqvist C, Albert VA (2024) High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species. Commun Biol 7:54. https://www.ncbi.nlm.nih.gov/pubmed/38184717
  • Gong C, Chakraborty D, Koudelka GB (2024) A prophage encoded ribosomal RNA methyltransferase regulates the virulence of Shiga-toxin-producing Escherichia coli (STEC). Nucleic Acids Res 52:856-871. https://www.ncbi.nlm.nih.gov/pubmed/38084890
  • LaFountain JR, Jr., Seaman CE, Cohan CS, Oldenbourg R (2024) Sliding of antiparallel microtubules drives bipolarization of monoastral spindles. Cytoskeleton (Hoboken) 81:167-183. https://www.ncbi.nlm.nih.gov/pubmed/37812128
  • Miles LS, Waterman H, Ayoub NA, Garb JE, Haney RA, Rosenberg MS, Krabbenhoft TJ, Verrelli BC (2024) Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider. J Hered. https://www.ncbi.nlm.nih.gov/pubmed/38567866
  • Pajic P, Landau L, Gokcumen O, Ruhl S (2024) Emergence of saliva protein genes in the secretory calcium-binding phosphoprotein (SCPP) locus and accelerated evolution in primates. bioRxiv. https://www.ncbi.nlm.nih.gov/pubmed/38405690
  • Pujari AN, Cullen PJ (2024) Modulators of MAPK pathway activity during filamentous growth in Saccharomyces cerevisiae. G3 (Bethesda). https://www.ncbi.nlm.nih.gov/pubmed/38560781
  • Raghavan I, Juman R, Wang ZQ (2024) The non-mevalonate pathway requires a delicate balance of intermediates to maximize terpene production. Appl Microbiol Biotechnol 108:245. https://www.ncbi.nlm.nih.gov/pubmed/38421431
  • Salojarvi J et al. (2024) The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nat Genet 56:721-731. https://www.ncbi.nlm.nih.gov/pubmed/38622339
  • Tomlin CM, Rajaraman S, Sebesta JT, Scheen AC, Bendiksby M, Low YW, Salojarvi J, Michael TP, Albert VA, Lindqvist C (2024) Allopolyploid origin and diversification of the Hawaiian endemic mints. Nat Commun 15:3109. https://www.ncbi.nlm.nih.gov/pubmed/38600100

2023 Publications (selected)

  • Albert VA, Krabbenhoft TJ (2023) Navigating the CoGe Online Software Suite for Polyploidy Research. Methods Mol Biol 2545:19-45. https://www.ncbi.nlm.nih.gov/pubmed/36720806
  • Aqil A, Gill S, Gokcumen O, Malhi RS, Reese EA, Smith JL, Heaton TT, Lindqvist C (2023) A paleogenome from a Holocene individual supports genetic continuity in Southeast Alaska. iScience 26:106581. https://www.ncbi.nlm.nih.gov/pubmed/37138779
  • Aqil A, Speidel L, Pavlidis P, Gokcumen O (2023) Balancing selection on genomic deletion polymorphisms in humans. Elife 12. https://www.ncbi.nlm.nih.gov/pubmed/36625544
  • Banerjee R, Gunawardena S (2023) Glycogen synthase kinase 3beta (GSK3beta) and presenilin (PS) are key regulators of kinesin-1-mediated cargo motility within axons. Front Cell Dev Biol 11:1202307. https://www.ncbi.nlm.nih.gov/pubmed/37363727
  • Bowman J, Enard D, Lynch VJ (2023) Phylogenomics reveals an almost perfect polytomy among the almost ungulates (Paenungulata). bioRxiv. https://www.ncbi.nlm.nih.gov/pubmed/38106080
  • Brakey DJ, Schatz KC, Paul MJ, Daniels D (2023) The role of glucagon-like peptide-1 (GLP-1) in fluid and food intakes in vasopressin-deficient Brattleboro rats. Physiol Behav 262:114093. https://www.ncbi.nlm.nih.gov/pubmed/36706972
  • Caeiro-Dias G, Osborne MJ, Waterman HM, Krabbenhoft TJ, Turner TF (2023) Limited evidence for extensive genetic differentiation between X and Y chromosomes in Hybognathus amarus (Cypriniformes: Leuciscidae). J Hered 114:470-487. https://www.ncbi.nlm.nih.gov/pubmed/37347974
  • Carroll E, Ravi Gopal B, Raghavan I, Mukherjee M, Wang ZQ (2023) A cytochrome P450 CYP87A4 imparts sterol side-chain cleavage in digoxin biosynthesis. Nat Commun 14:4042. https://www.ncbi.nlm.nih.gov/pubmed/37422531
  • Chaubey AH, Sojka SE, Onukwufor JO, Ezak MJ, Vandermeulen MD, Bowitch A, Vodickova A, Wojtovich AP, Ferkey DM (2023) The Caenorhabditis elegans innexin INX-20 regulates nociceptive behavioral sensitivity. Genetics 223. https://www.ncbi.nlm.nih.gov/pubmed/36753530
  • da Silva Coelho FA, Gill S, Tomlin CM, Papavassiliou M, Farley SD, Cook JA, Sonsthagen SA, Sage GK, Heaton TH, Talbot SL, Lindqvist C (2023) Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska. Mol Ecol 32:3641-3656. https://www.ncbi.nlm.nih.gov/pubmed/37096383
  • Elliff J, Biswas A, Roshan P, Kuppa S, Patterson A, Mattice J, Chinnaraj M, Burd R, Walker SE, Pozzi N, Antony E, Bothner B, Origanti S (2023) Dynamic states of eIF6 and SDS variants modulate interactions with uL14 of the 60S ribosomal subunit. Nucleic Acids Res 51:1803-1822. https://www.ncbi.nlm.nih.gov/pubmed/36651285
  • Gonzalez B, Aldea M, Cullen PJ (2023) Chaperone-Dependent Degradation of Cdc42 Promotes Cell Polarity and Shields the Protein from Aggregation. Mol Cell Biol 43:200-222. https://www.ncbi.nlm.nih.gov/pubmed/37114947
  • Gonzalez B, Mirzaei M, Basu S, Pujari AN, Vandermeulen MD, Prabhakar A, Cullen PJ (2023) Turnover and bypass of p21-activated kinase during Cdc42-dependent MAPK signaling in yeast. J Biol Chem 299:105297. https://www.ncbi.nlm.nih.gov/pubmed/37774975
  • Kelly SL, Strobel EJ (2023) Systematic analysis of cotranscriptional RNA folding using transcription elongation complex display. bioRxiv. https://www.ncbi.nlm.nih.gov/pubmed/38187752
  • Krzystek TJ, White JA, Rathnayake R, Thurston L, Hoffmar-Glennon H, Li Y, Gunawardena S (2023) HTT (huntingtin) and RAB7 co-migrate retrogradely on a signaling LAMP1-containing late endosome during axonal injury. Autophagy 19:1199-1220. https://www.ncbi.nlm.nih.gov/pubmed/36048753
  • Liu Y, Koudelka G (2023) O-Polysaccharides of LPS Modulate E. coli Uptake by Acanthamoeba castellanii. Microorganisms 11. https://www.ncbi.nlm.nih.gov/pubmed/37374879
  • Liu Y, Koudelka GB (2023) The Oligosaccharide Region of LPS Governs Predation of E. coli by the Bacterivorous Protist, Acanthamoeba castellanii. Microbiol Spectr 11:e0293022. https://www.ncbi.nlm.nih.gov/pubmed/36648221
  • Lu D, Parisi LR, Gokcumen O, Atilla-Gokcumen GE (2023) SREBP activation contributes to fatty acid accumulations in necroptosis. RSC Chem Biol 4:310-322. https://www.ncbi.nlm.nih.gov/pubmed/37034406
  • Lynch VJ (2023) Is there a loophole in Dollo's law? A DevoEvo perspective on irreversibility (of felid dentition). J Exp Zool B Mol Dev Evol 340:509-517. https://www.ncbi.nlm.nih.gov/pubmed/35644942
  • Lynch VJ, Wagner GP (2023) Cooption of polyalanine tract into a repressor domain in the mammalian transcription factor HoxA11. J Exp Zool B Mol Dev Evol 340:486-495. https://www.ncbi.nlm.nih.gov/pubmed/34125492
  • MacGuigan DJ, Krabbenhoft TJ, Harrington RC, Wainwright DK, Backenstose NJC, Near TJ (2023) Lacustrine speciation associated with chromosomal inversion in a lineage of riverine fishes. Evolution 77:1505-1521. https://www.ncbi.nlm.nih.gov/pubmed/37094800
  • Mukherjee M, Wang ZQ (2023) A well-characterized polycistronic-like gene expression system in yeast. Biotechnol Bioeng 120:260-271. https://www.ncbi.nlm.nih.gov/pubmed/36168285
  • Muter J, Lynch VJ, McCoy RC, Brosens JJ (2023) Human embryo implantation. Development 150. https://www.ncbi.nlm.nih.gov/pubmed/37254877
  • Nisler CR, Narui Y, Scheib E, Choudhary D, Bowman JD, Mandayam Bharathi H, Lynch VJ, Sotomayor M (2023) Interpreting the Evolutionary Echoes of a Protein Complex Essential for Inner-Ear Mechanosensation. Mol Biol Evol 40. https://www.ncbi.nlm.nih.gov/pubmed/36911992
  • Raghavan I, Ravi Gopal B, Carroll E, Wang ZQ (2023) Cardenolide Increase in Foxglove after 2,1,3-Benzothiadiazole Treatment Reveals a Potential Link between Cardenolide and Phytosterol Biosynthesis. Plant Cell Physiol 64:107-116. https://www.ncbi.nlm.nih.gov/pubmed/36222367
  • Raviv L, Jacobson SL, Plotnik JM, Bowman J, Lynch V, Benitez-Burraco A (2023) Elephants as an animal model for self-domestication. Proc Natl Acad Sci U S A 120:e2208607120. https://www.ncbi.nlm.nih.gov/pubmed/37011191
  • Russell M, Aqil A, Saitou M, Gokcumen O, Masuda N (2023) Gene communities in co-expression networks across different tissues. PLoS Comput Biol 19:e1011616. https://www.ncbi.nlm.nih.gov/pubmed/37976327
  • Santollo J, Daniels D, Leshem M, Schulkin J (2023) Sex Differences in Salt Appetite: Perspectives from Animal Models and Human Studies. Nutrients 15. https://www.ncbi.nlm.nih.gov/pubmed/36615865
  • Saul F et al. (2023) Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis. Nat Plants 9:2000-2015. https://www.ncbi.nlm.nih.gov/pubmed/37996654
  • Schaff H, Dey P, Heiss C, Keiser G, Moro TR, Azadi P, Patel P, Free SJ (2023) Characterization of the need for galactofuranose during the Neurospora crassa life cycle. Fungal Genet Biol 168:103826. https://www.ncbi.nlm.nih.gov/pubmed/37541569
  • Shoma JF, Ernan B, Keiser G, Heiss C, Azadi P, Free SJ (2023) Genetic Characterization of the Acidic and Neutral Glycosphingolipid Biosynthetic Pathways in Neurospora crassa. Microorganisms 11. https://www.ncbi.nlm.nih.gov/pubmed/37630653
  • Strobel EJ (2023) Isolation of E. coli RNA polymerase transcription elongation complexes by selective solid-phase photoreversible immobilization. Methods Enzymol 691:223-250. https://www.ncbi.nlm.nih.gov/pubmed/37914448
  • Sun YH et al. (2023) Amniotes co-opt intrinsic genetic instability to protect germ-line genome integrity. Nat Commun 14:812. https://www.ncbi.nlm.nih.gov/pubmed/36781861
  • Swinter K, Salah D, Rathnayake R, Gunawardena S (2023) PolyQ-Expansion Causes Mitochondria Fragmentation Independent of Huntingtin and Is Distinct from Traumatic Brain Injury (TBI)/Mechanical Stress-Mediated Fragmentation Which Results from Cell Death. Cells 12. https://www.ncbi.nlm.nih.gov/pubmed/37830620
  • Szyjka CE, Strobel EJ (2023) Observation of coordinated cotranscriptional RNA folding events. bioRxiv. https://www.ncbi.nlm.nih.gov/pubmed/36865203
  • Szyjka CE, Strobel EJ (2023) Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing. Nat Commun 14:7839. https://www.ncbi.nlm.nih.gov/pubmed/38030633
  • Vandermeulen MD, Cullen PJ (2023) Ecological inducers of the yeast filamentous growth pathway reveal environment-dependent roles for pathway components. mSphere 8:e0028423. https://www.ncbi.nlm.nih.gov/pubmed/37732804
  • Veilleux CC, Garrett EC, Pajic P, Saitou M, Ochieng J, Dagsaan LD, Dominy NJ, Perry GH, Gokcumen O, Melin AD (2023) Human subsistence and signatures of selection on chemosensory genes. Commun Biol 6:683. https://www.ncbi.nlm.nih.gov/pubmed/37400713
  • Vijjamarri AK, Niu X, Vandermeulen MD, Onu C, Zhang F, Qiu H, Gupta N, Gaikwad S, Greenberg ML, Cullen PJ, Lin Z, Hinnebusch AG (2023) Decapping factor Dcp2 controls mRNA abundance and translation to adjust metabolism and filamentation to nutrient availability. bioRxiv. https://www.ncbi.nlm.nih.gov/pubmed/36711592
  • Yilmaz F, Karageorgiou C, Kim K, Pajic P, Beck CR, Human Genome Structural Variation C, Torregrossa AM, Lee C, Gokcumen O (2023) Ancient AMY1 gene duplications primed the amylase locus for adaptive evolution upon the onset of agriculture. bioRxiv. https://www.ncbi.nlm.nih.gov/pubmed/38077078

2022 Publications (selected)

  • Ballinger MJ, Christian RC, Moore LD, Taylor DJ, Sabet A (2022) Evolution and diversity of inherited viruses in the Nearctic phantom midge, Chaoborus americanus. Virus Evol 8:veac018. https://www.ncbi.nlm.nih.gov/pubmed/35356639
  • Bernal MA, Yule DL, Stott W, Evrard L, Dowling TE, Krabbenhoft TJ (2022) Concordant patterns of morphological, stable isotope and genetic variation in a recent ecological radiation (Salmonidae: Coregonus spp.). Mol Ecol 31:4495-4509. https://www.ncbi.nlm.nih.gov/pubmed/35785504
  • Bowitch A, Chinsky TM, Yu MC, Ferkey DM (2022) The C. elegans OCTR-1 and Human Alpha-2A Adrenergic Receptors are Methylated within the Third Intracellular Loop by Human PRMT5 in vitro. MicroPubl Biol 2022. https://www.ncbi.nlm.nih.gov/pubmed/35622502
  • Burlingham SR, Wong NF, Peterkin L, Lubow L, Dos Santos Passos C, Benner O, Ghebrial M, Cast TP, Xu-Friedman MA, Sudhof TC, Chanda S (2022) Induction of synapse formation by de novo neurotransmitter synthesis. Nat Commun 13:3060. https://www.ncbi.nlm.nih.gov/pubmed/35650274
  • Campelo Dos Santos AL, Owings A, Sullasi HSL, Gokcumen O, DeGiorgio M, Lindo J (2022) Genomic evidence for ancient human migration routes along South America's Atlantic coast. Proc Biol Sci 289:20221078. https://www.ncbi.nlm.nih.gov/pubmed/36322514
  • Chanderbali AS, Jin L, Xu Q, Zhang Y, Zhang J, Jian S, Carroll E, Sankoff D, Albert VA, Howarth DG, Soltis DE, Soltis PS (2022) Buxus and Tetracentron genomes help resolve eudicot genome history. Nat Commun 13:643. https://www.ncbi.nlm.nih.gov/pubmed/35110570
  • Crespi E, Burnap R, Chen J, Das M, Gassman N, Rosa E, Simmons R, Wada H, Wang ZQ, Xiao J, Yang B, Yin J, Goldstone JV (2022) Resolving the Rules of Robustness and Resilience in Biology Across Scales. Integr Comp Biol 61:2163-2179. https://www.ncbi.nlm.nih.gov/pubmed/34427654
  • Freund M, Graus D, Fleischmann A, Gilbert KJ, Lin Q, Renner T, Stigloher C, Albert VA, Hedrich R, Fukushima K (2022) The digestive systems of carnivorous plants. Plant Physiol 190:44-59. https://www.ncbi.nlm.nih.gov/pubmed/35604105
  • Gonzalez B, Cullen PJ (2022) Regulation of Cdc42 protein turnover modulates the filamentous growth MAPK pathway. J Cell Biol 221. https://www.ncbi.nlm.nih.gov/pubmed/36350310
  • Hu G et al. (2022) Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars. Nat Genet 54:73-83. https://www.ncbi.nlm.nih.gov/pubmed/34980919
  • Kelly SL, Szyjka CE, Strobel EJ (2022) Purification of synchronized Escherichia coli transcription elongation complexes by reversible immobilization on magnetic beads. J Biol Chem 298:101789. https://www.ncbi.nlm.nih.gov/pubmed/35247385
  • Kotov AA, Taylor DJ (2022) Daphnia japonica sp. nov. (Crustacea: Cladocera) an eastern Palearctic montane species with mitochondrial discordance. PeerJ 10:e14113. https://www.ncbi.nlm.nih.gov/pubmed/36213509
  • Krabbenhoft CA et al. (2022) Assessing placement bias of the global river gauge network. Nat Sustain 5:586-592. https://www.ncbi.nlm.nih.gov/pubmed/36213515
  • Lama R, Xu C, Galster SL, Querol-Garcia J, Portwood S, Mavis CK, Ruiz FM, Martin D, Wu J, Giorgi MC, Bargonetti J, Wang ES, Hernandez-Ilizaliturri FJ, Koudelka GB, Chemler SR, Munoz IG, Wang X (2022) Small molecule MMRi62 targets MDM4 for degradation and induces leukemic cell apoptosis regardless of p53 status. Front Oncol 12:933446. https://www.ncbi.nlm.nih.gov/pubmed/35992795
  • Lan T, Leppala K, Tomlin C, Talbot SL, Sage GK, Farley SD, Shideler RT, Bachmann L, Wiig O, Albert VA, Salojarvi J, Mailund T, Drautz-Moses DI, Schuster SC, Herrera-Estrella L, Lindqvist C (2022) Insights into bear evolution from a Pleistocene polar bear genome. Proc Natl Acad Sci U S A 119:e2200016119. https://www.ncbi.nlm.nih.gov/pubmed/35666863
  • Low YW et al. (2022) Genomic insights into rapid speciation within the world's largest tree genus Syzygium. Nat Commun 13:5031. https://www.ncbi.nlm.nih.gov/pubmed/36097018
  • Lynch VJ (2022) Evolution: Stress fans the flames of innovation. Curr Biol 32:R158-R160. https://www.ncbi.nlm.nih.gov/pubmed/35231407
  • Maria H, Rusche LN (2022) The DNA replication protein Orc1 from the yeast Torulaspora delbrueckii is required for heterochromatin formation but not as a silencer-binding protein. Genetics 222. https://www.ncbi.nlm.nih.gov/pubmed/35894940
  • Mathuram TL, Townsend DM, Lynch VJ, Bederman I, Ye ZW, Zhang J, Sigurdson WJ, Prendergast E, Jobava R, Ferruzza JP, D'Angelo MR, Hatzoglou M, Perry Y, Blumental-Perry A (2022) A Synthetic Small RNA Homologous to the D-Loop Transcript of mtDNA Enhances Mitochondrial Bioenergetics. Front Physiol 13:772313. https://www.ncbi.nlm.nih.gov/pubmed/35464086
  • Mika K, Lynch VJ (2022) Transposable Elements Continuously Remodel the Regulatory Landscape, Transcriptome, and Function of Decidual Stromal Cells. Genome Biol Evol 14. https://www.ncbi.nlm.nih.gov/pubmed/36423206
  • Mika K, Whittington CM, McAllan BM, Lynch VJ (2022) Gene expression phylogenies and ancestral transcriptome reconstruction resolves major transitions in the origins of pregnancy. Elife 11. https://www.ncbi.nlm.nih.gov/pubmed/35770963
  • Mukherjee M, Blair RH, Wang ZQ (2022) Machine-learning guided elucidation of contribution of individual steps in the mevalonate pathway and construction of a yeast platform strain for terpenoid production. Metab Eng 74:139-149. https://www.ncbi.nlm.nih.gov/pubmed/36341776
  • Nikkanen J, Leong YA, Krause WC, Dermadi D, Maschek JA, Van Ry T, Cox JE, Weiss EJ, Gokcumen O, Chawla A, Ingraham HA (2022) An evolutionary trade-off between host immunity and metabolism drives fatty liver in male mice. Science 378:290-295. https://www.ncbi.nlm.nih.gov/pubmed/36264814
  • Pajic P, Shen S, Qu J, May AJ, Knox S, Ruhl S, Gokcumen O (2022) A mechanism of gene evolution generating mucin function. Sci Adv 8:eabm8757. https://www.ncbi.nlm.nih.gov/pubmed/36026444
  • Patel P, Free SJ (2022) Characterization of Neurospora crassa GH16, GH17, and GH72 gene families of cell wall crosslinking enzymes. Cell Surf 8:100073. https://www.ncbi.nlm.nih.gov/pubmed/35079668
  • Patel PK, Tung SK, Porfirio S, Sonon R, Azadi P, Free SJ (2022) Extracellular targeting of Neurospora crassa cell wall and secreted glycoproteins by DFG-5. Fungal Genet Biol 160:103686. https://www.ncbi.nlm.nih.gov/pubmed/35306147
  • Pechuk V, Goldman G, Salzberg Y, Chaubey AH, Bola RA, Hoffman JR, Endreson ML, Miller RM, Reger NJ, Portman DS, Ferkey DM, Schneidman E, Oren-Suissa M (2022) Reprogramming the topology of the nociceptive circuit in C. elegans reshapes sexual behavior. Curr Biol 32:4372-4385 e4377. https://www.ncbi.nlm.nih.gov/pubmed/36075218
  • Peng L, Dumevi RM, Chitto M, Haarmann N, Berger P, Koudelka G, Schmidt H, Mellmann A, Dobrindt U, Berger M (2022) A Robust One-Step Recombineering System for Enterohemorrhagic Escherichia coli. Microorganisms 10. https://www.ncbi.nlm.nih.gov/pubmed/36144292
  • Rupert CB, Rusche LN (2022) The Pathogenic Yeast Candida parapsilosis Forms Pseudohyphae through Different Signaling Pathways Depending on the Available Carbon Source. mSphere 7:e0002922. https://www.ncbi.nlm.nih.gov/pubmed/35766504
  • Saitou M, Masuda N, Gokcumen O (2022) Similarity-Based Analysis of Allele Frequency Distribution among Multiple Populations Identifies Adaptive Genomic Structural Variants. Mol Biol Evol 39. https://www.ncbi.nlm.nih.gov/pubmed/34718708
  • Shi L, Palmer K, Wang H, Xu-Friedman MA, Sun W (2022) Low Intensity Noise Exposure Enhanced Auditory Loudness and Temporal Processing by Increasing Excitability of DCN. Neural Plast 2022:6463355. https://www.ncbi.nlm.nih.gov/pubmed/36452876
  • Strobel EJ, Kelly SL, Szyjka CE (2022) Isolation of synchronized E. coli elongation complexes for solid-phase and solution-based in vitro transcription assays. Methods Enzymol 675:159-192. https://www.ncbi.nlm.nih.gov/pubmed/36220269
  • Szyjka CE, Strobel EJ (2022) Cotranscriptional RNA Chemical Probing. Methods Mol Biol 2518:291-330. https://www.ncbi.nlm.nih.gov/pubmed/35666452
  • Vandermeulen MD, Cullen PJ (2022) Gene by Environment Interactions reveal new regulatory aspects of signaling network plasticity. PLoS Genet 18:e1009988. https://www.ncbi.nlm.nih.gov/pubmed/34982769
  • Vazquez JM, Pena MT, Muhammad B, Kraft M, Adams LB, Lynch VJ (2022) Parallel evolution of reduced cancer risk and tumor suppressor duplications in Xenarthra. Elife 11. https://www.ncbi.nlm.nih.gov/pubmed/36480266
  • Wang W, Cho H, Lee JW, Lee SK (2022) The histone demethylase Kdm6b regulates subtype diversification of mouse spinal motor neurons during development. Nat Commun 13:958. https://www.ncbi.nlm.nih.gov/pubmed/35177643
  • Wong NF, Xu-Friedman MA (2022) Time Course of Activity-Dependent Changes in Auditory Nerve Synapses Reveals Multiple Underlying Cellular Mechanisms. J Neurosci 42:2492-2502. https://www.ncbi.nlm.nih.gov/pubmed/35181597
  • Wong NF, Xu-Friedman MA (2022) Induction of Activity-Dependent Plasticity at Auditory Nerve Synapses. J Neurosci 42:6211-6220. https://www.ncbi.nlm.nih.gov/pubmed/35790402
  • Younger S, Boutros S, Cargnin F, Jeon S, Lee JW, Lee SK, Raber J (2022) Behavioral Phenotypes of Foxg1 Heterozygous Mice. Front Pharmacol 13:927296. https://www.ncbi.nlm.nih.gov/pubmed/35754477
  • Zhao G, Rusche LN (2022) Sirtuins in Epigenetic Silencing and Control of Gene Expression in Model and Pathogenic Fungi. Annu Rev Microbiol 76:157-178. https://www.ncbi.nlm.nih.gov/pubmed/35609947

2021 Publications (selected)

  • Banerjee R, Chakraborty P, Yu MC, Gunawardena S (2021) A stop or go switch: glycogen synthase kinase 3beta phosphorylation of the kinesin 1 motor domain at Ser314 halts motility without detaching from microtubules. Development 148. https://www.ncbi.nlm.nih.gov/pubmed/34940839
  • Berghoff EG, Glenwinkel L, Bhattacharya A, Sun H, Varol E, Mohammadi N, Antone A, Feng Y, Nguyen K, Cook SJ, Wood JF, Masoudi N, Cros CC, Ramadan YH, Ferkey DM, Hall DH, Hobert O (2021) The Prop1-like homeobox gene unc-42 specifies the identity of synaptically connected neurons. Elife 10. https://www.ncbi.nlm.nih.gov/pubmed/34165428
  • Bowitch A, Sahoo A, Clark AM, Ntangka C, Raut KK, Gollnick P, Yu MC, Pascal SM, Walker SE, Ferkey DM (2021) Methylation of the D2 dopamine receptor affects binding with the human regulatory proteins Par-4 and Calmodulin. MicroPubl Biol 2021. https://www.ncbi.nlm.nih.gov/pubmed/33598640
  • Cervantes-Perez SA, Yong-Villalobos L, Florez-Zapata NMV, Oropeza-Aburto A, Rico-Resendiz F, Amasende-Morales I, Lan T, Martinez O, Vielle-Calzada JP, Albert VA, Herrera-Estrella L (2021) Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba. Sci Rep 11:15725. https://www.ncbi.nlm.nih.gov/pubmed/34344949
  • Cheung VC, Peng CY, Marinic M, Sakabe NJ, Aneas I, Lynch VJ, Ober C, Nobrega MA, Kessler JA (2021) Pluripotent stem cell-derived endometrial stromal fibroblasts in a cyclic, hormone-responsive, coculture model of human decidua. Cell Rep 35:109138. https://www.ncbi.nlm.nih.gov/pubmed/34010658
  • da Silva Coelho FA, Gill S, Tomlin CM, Heaton TH, Lindqvist C (2021) An early dog from southeast Alaska supports a coastal route for the first dog migration into the Americas. Proc Biol Sci 288:20203103. https://www.ncbi.nlm.nih.gov/pubmed/33622130
  • Eaton KM, Bernal MA, Backenstose NJC, Yule DL, Krabbenhoft TJ (2021) Nanopore Amplicon Sequencing Reveals Molecular Convergence and Local Adaptation of Rhodopsin in Great Lakes Salmonids. Genome Biol Evol 13. https://www.ncbi.nlm.nih.gov/pubmed/33247716
  • Ferkey DM, Sengupta P, L'Etoile ND (2021) Chemosensory signal transduction in Caenorhabditis elegans. Genetics 217. https://www.ncbi.nlm.nih.gov/pubmed/33693646
  • Garibian PG, Karabanov DP, Neretina AN, Taylor DJ, Kotov AA (2021) Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision. PeerJ 9:e11310. https://www.ncbi.nlm.nih.gov/pubmed/33981506
  • Glaberman S, Bulls SE, Vazquez JM, Chiari Y, Lynch VJ (2021) Concurrent Evolution of Antiaging Gene Duplications and Cellular Phenotypes in Long-Lived Turtles. Genome Biol Evol 13. https://www.ncbi.nlm.nih.gov/pubmed/34792580
  • Huisman C, Kim YA, Jeon S, Shin B, Choi J, Lim SJ, Youn SM, Park Y, K CM, Kim S, Lee SK, Lee S, Lee JW (2021) The histone H3-lysine 4-methyltransferase Mll4 regulates the development of growth hormone-releasing hormone-producing neurons in the mouse hypothalamus. Nat Commun 12:256. https://www.ncbi.nlm.nih.gov/pubmed/33431871
  • Krabbenhoft TJ, MacGuigan DJ, Backenstose NJC, Waterman H, Lan T, Pelosi JA, Tan M, Sandve SR (2021) Chromosome-Level Genome Assembly of Chinese Sucker (Myxocyprinus asiaticus) Reveals Strongly Conserved Synteny Following a Catostomid-Specific Whole-Genome Duplication. Genome Biol Evol 13. https://www.ncbi.nlm.nih.gov/pubmed/34383883
  • Krzystek TJ, Banerjee R, Thurston L, Huang J, Swinter K, Rahman SN, Falzone TL, Gunawardena S (2021) Differential mitochondrial roles for alpha-synuclein in DRP1-dependent fission and PINK1/Parkin-mediated oxidation. Cell Death Dis 12:796. https://www.ncbi.nlm.nih.gov/pubmed/34404758
  • Liu X, Moshiri H, He Q, Sahoo A, Walker SE (2021) Deletion of the N-Terminal Domain of Yeast Eukaryotic Initiation Factor 4B Reprograms Translation and Reduces Growth in Urea. Front Mol Biosci 8:787781. https://www.ncbi.nlm.nih.gov/pubmed/35047555
  • Maria H, Kapoor S, Liu T, Rusche LN (2021) Conservation of a DNA Replication Motif among Phylogenetically Distant Budding Yeast Species. Genome Biol Evol 13. https://www.ncbi.nlm.nih.gov/pubmed/34132803
  • Marinic M, Mika K, Chigurupati S, Lynch VJ (2021) Evolutionary transcriptomics implicates HAND2 in the origins of implantation and regulation of gestation length. Elife 10. https://www.ncbi.nlm.nih.gov/pubmed/33522483
  • Mika K, Marinic M, Singh M, Muter J, Brosens JJ, Lynch VJ (2021) Evolutionary transcriptomics implicates new genes and pathways in human pregnancy and adverse pregnancy outcomes. Elife 10. https://www.ncbi.nlm.nih.gov/pubmed/34623259
  • Mukherjee M, Caroll E, Wang ZQ (2021) Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning. J Vis Exp. https://www.ncbi.nlm.nih.gov/pubmed/33616121
  • Pliss A, Kuzmin AN, Lita A, Kumar R, Celiku O, Atilla-Gokcumen GE, Gokcumen O, Chandra D, Larion M, Prasad PN (2021) A Single-Organelle Optical Omics Platform for Cell Science and Biomarker Discovery. Anal Chem 93:8281-8290. https://www.ncbi.nlm.nih.gov/pubmed/34048235
  • Prabhakar A, Gonzalez B, Dionne H, Basu S, Cullen PJ (2021) Spatiotemporal control of pathway sensors and cross-pathway feedback regulate a differentiation MAPK pathway in yeast. J Cell Sci 134. https://www.ncbi.nlm.nih.gov/pubmed/34347092
  • Pradhan AJ, Lu D, Parisi LR, Shen S, Berhane IA, Galster SL, Bynum K, Monje-Galvan V, Gokcumen O, Chemler SR, Qu J, Kay JG, Atilla-Gokcumen GE (2021) Protein acylation by saturated very long chain fatty acids and endocytosis are involved in necroptosis. Cell Chem Biol 28:1298-1309 e1297. https://www.ncbi.nlm.nih.gov/pubmed/33848465
  • Rusche LN (2021) Stable Positions of Epigenetically Inherited Centromeres in the Emerging Fungal Pathogen Candida auris and Its Relatives. mBio 12:e0103621. https://www.ncbi.nlm.nih.gov/pubmed/34225489
  • Sahoo A, He Q, Walker SE (2021) Flipping the Switch: An Unexpected Role for aEF1B in Modulating aEF1A Interactions with the Ribosome and tRNA. J Mol Biol 433:167052. https://www.ncbi.nlm.nih.gov/pubmed/34015279
  • Saitou M, Resendez S, Pradhan AJ, Wu F, Lie NC, Hall NJ, Zhu Q, Reinholdt L, Satta Y, Speidel L, Nakagome S, Hanchard NA, Churchill G, Lee C, Atilla-Gokcumen GE, Mu X, Gokcumen O (2021) Sex-specific phenotypic effects and evolutionary history of an ancient polymorphic deletion of the human growth hormone receptor. Sci Adv 7:eabi4476. https://www.ncbi.nlm.nih.gov/pubmed/34559564
  • Starr I, Seiffert-Sinha K, Sinha AA, Gokcumen O (2021) Evolutionary context of psoriatic immune skin response. Evol Med Public Health 9:474-486. https://www.ncbi.nlm.nih.gov/pubmed/35154781
  • Strobel EJ (2021) Preparation of E. coli RNA polymerase transcription elongation complexes by selective photoelution from magnetic beads. J Biol Chem 297:100812. https://www.ncbi.nlm.nih.gov/pubmed/34023383
  • Strobel EJ (2021) Efficient Linear dsDNA Tagging Using Deoxyuridine Excision*. Chembiochem 22:3214-3224. https://www.ncbi.nlm.nih.gov/pubmed/34547157
  • Strobel EJ (2021) Preparation and Characterization of Internally Modified DNA Templates for Chemical Transcription Roadblocking. Bio Protoc 11:e4141. https://www.ncbi.nlm.nih.gov/pubmed/34604447
  • Vazquez JM, Lynch VJ (2021) Pervasive duplication of tumor suppressors in Afrotherians during the evolution of large bodies and reduced cancer risk. Elife 10. https://www.ncbi.nlm.nih.gov/pubmed/33513090
  • Wang ZQ, Song H, Koleski EJ, Hara N, Park DS, Kumar G, Min Y, Dauenhauer PJ, Chang MCY (2021) A dual cellular-heterogeneous catalyst strategy for the production of olefins from glucose. Nat Chem 13:1178-1185. https://www.ncbi.nlm.nih.gov/pubmed/34811478
  • Weber M, Basu S, Gonzalez B, Greslehner GP, Singer S, Haskova D, Hasek J, Breitenbach M, C WG, Cullen PJ, Rinnerthaler M (2021) Actin Cytoskeleton Regulation by the Yeast NADPH Oxidase Yno1p Impacts Processes Controlled by MAPK Pathways. Antioxidants (Basel) 10. https://www.ncbi.nlm.nih.gov/pubmed/33671669
  • Zhao G, Rusche LN (2021) Genetic Analysis of Sirtuin Deacetylases in Hyphal Growth of Candida albicans. mSphere 6. https://www.ncbi.nlm.nih.gov/pubmed/33952658

2020 Publications (selected)

  • Ahart ZC, Martin LE, Kemp BR, Dutta Banik D, Roberts SGE, Torregrossa AM, Medler KF (2020) Differential Effects of Diet and Weight on Taste Responses in Diet-Induced Obese Mice. Obesity (Silver Spring) 28:284-292. https://www.ncbi.nlm.nih.gov/pubmed/31891242
  • Albert VA, Renner T (2020) Aquatic angiosperm ambiguities answered. Nat Plants 6:181-183. https://www.ncbi.nlm.nih.gov/pubmed/32055049
  • Banerjee R, White JA, 2nd, Gunawardena S (2020) In Vivo Visualization of Moving Synaptic Cargo Complexes within Drosophila Larval Segmental Axons. Methods Mol Biol 2143:293-300. https://www.ncbi.nlm.nih.gov/pubmed/32524488
  • Basu S, Gonzalez B, Li B, Kimble G, Kozminski KG, Cullen PJ (2020) Functions for Cdc42p BEM adaptors in regulating a differentiation-type MAP kinase pathway. Mol Biol Cell 31:491-510. https://www.ncbi.nlm.nih.gov/pubmed/31940256
  • Busch MH et al. (2020) What's in a Name? Patterns, Trends, and Suggestions for Defining Non-Perennial Rivers and Streams. Water (Basel) 12:1980. https://www.ncbi.nlm.nih.gov/pubmed/33274073
  • Dutta Banik D, Benfey ED, Martin LE, Kay KE, Loney GC, Nelson AR, Ahart ZC, Kemp BT, Kemp BR, Torregrossa AM, Medler KF (2020) A subset of broadly responsive Type III taste cells contribute to the detection of bitter, sweet and umami stimuli. PLoS Genet 16:e1008925. https://www.ncbi.nlm.nih.gov/pubmed/32790785
  • Eaaswarkhanth M, Dos Santos ALC, Gokcumen O, Al-Mulla F, Thanaraj TA (2020) Genome-Wide Selection Scan in an Arabian Peninsula Population Identifies a TNKS Haplotype Linked to Metabolic Traits and Hypertension. Genome Biol Evol 12:77-87. https://www.ncbi.nlm.nih.gov/pubmed/32068798
  • Fry E, Kim SK, Chigurapti S, Mika KM, Ratan A, Dammermann A, Mitchell BJ, Miller W, Lynch VJ (2020) Functional Architecture of Deleterious Genetic Variants in the Genome of a Wrangel Island Mammoth. Genome Biol Evol 12:48-58. https://www.ncbi.nlm.nih.gov/pubmed/32031213
  • Garibian PG, Neretina AN, Taylor DJ, Kotov AA (2020) Partial revision of the neustonic genus Scapholeberis Schoedler, 1858 (Crustacea: Cladocera): decoding of the barcoding results. PeerJ 8:e10410. https://www.ncbi.nlm.nih.gov/pubmed/33304655
  • Gokcumen O (2020) Archaic hominin introgression into modern human genomes. Am J Phys Anthropol 171 Suppl 70:60-73. https://www.ncbi.nlm.nih.gov/pubmed/31702050
  • Holmquist ML, Ihms EC, Gollnick P, Wysocki VH, Foster MP (2020) Population Distributions from Native Mass Spectrometry Titrations Reveal Nearest-Neighbor Cooperativity in the Ring-Shaped Oligomeric Protein TRAP. Biochemistry 59:2518-2527. https://www.ncbi.nlm.nih.gov/pubmed/32558551
  • Humphrey KM, Zhu L, Hickman MA, Hasan S, Maria H, Liu T, Rusche LN (2020) Evolution of Distinct Responses to Low NAD(+) Stress by Rewiring the Sir2 Deacetylase Network in Yeasts. Genetics 214:855-868. https://www.ncbi.nlm.nih.gov/pubmed/32071196
  • Jamalzadeh S, Pujari AN, Cullen PJ (2020) A Rab escort protein regulates the MAPK pathway that controls filamentous growth in yeast. Sci Rep 10:22184. https://www.ncbi.nlm.nih.gov/pubmed/33335117
  • Krabbenhoft TJ, Myers BJE, Wong JP, Chu C, Tingley RW, 3rd, Falke JA, Kwak TJ, Paukert CP, Lynch AJ (2020) FiCli, the Fish and Climate Change Database, informs climate adaptation and management for freshwater fishes. Sci Data 7:124. https://www.ncbi.nlm.nih.gov/pubmed/32317639
  • Kumar R, Maulik M, Pathirana RU, Cullen PJ, Edgerton M (2020) Sho1p Connects Glycolysis to Ras1-cAMP Signaling and Is Required for Microcolony Formation in Candida albicans. mSphere 5. https://www.ncbi.nlm.nih.gov/pubmed/32641426
  • Li J et al. (2020) Slow Growth and Increased Spontaneous Mutation Frequency in Respiratory Deficient afo1(-) Yeast Suppressed by a Dominant Mutation in ATP3. G3 (Bethesda) 10:4637-4648. https://www.ncbi.nlm.nih.gov/pubmed/33093184
  • Marinic M, Lynch VJ (2020) Relaxed constraint and functional divergence of the progesterone receptor (PGR) in the human stem-lineage. PLoS Genet 16:e1008666. https://www.ncbi.nlm.nih.gov/pubmed/32302297
  • Marinic M, Rana S, Lynch VJ (2020) Derivation of endometrial gland organoids from term placenta. Placenta 101:75-79. https://www.ncbi.nlm.nih.gov/pubmed/32937244
  • Mehle EA, Sojka SE, K CM, Zel RM, Reese SJ, Ferkey DM (2020) The C. elegans TRPV channel proteins OSM-9 and OCR-2 contribute to aversive chemical sensitivity. MicroPubl Biol 2020. https://www.ncbi.nlm.nih.gov/pubmed/32666046
  • Oropeza-Aburto A, Cervantes-Perez SA, Albert VA, Herrera-Estrella L (2020) Agrobacterium tumefaciens mediated transformation of the aquatic carnivorous plant Utricularia gibba. Plant Methods 16:50. https://www.ncbi.nlm.nih.gov/pubmed/32308728
  • Patel A, Abozeid SM, Cullen PJ, Morrow JR (2020) Co(II) Macrocyclic Complexes Appended with Fluorophores as paraCEST and cellCEST Agents. Inorg Chem 59:16531-16544. https://www.ncbi.nlm.nih.gov/pubmed/33138368
  • Patel A, Asik D, Snyder EM, Dilillo AE, Cullen PJ, Morrow JR (2020) Binding and Release of FeIII Complexes from Glucan Particles for the Delivery of T(1) MRI Contrast Agents. ChemMedChem 15:1050-1057. https://www.ncbi.nlm.nih.gov/pubmed/32168421
  • Prabhakar A, Chow J, Siegel AJ, Cullen PJ (2020) Regulation of intrinsic polarity establishment by a differentiation-type MAPK pathway in S. cerevisiae. J Cell Sci 133. https://www.ncbi.nlm.nih.gov/pubmed/32079658
  • Ravi BG, Guardian MGE, Dickman R, Wang ZQ (2020) High-resolution tandem mass spectrometry dataset reveals fragmentation patterns of cardiac glycosides in leaves of the foxglove plants. Data Brief 30:105464. https://www.ncbi.nlm.nih.gov/pubmed/32300626
  • Ravi BG, Guardian MGE, Dickman R, Wang ZQ (2020) Profiling and structural analysis of cardenolides in two species of Digitalis using liquid chromatography coupled with high-resolution mass spectrometry. J Chromatogr A 1618:460903. https://www.ncbi.nlm.nih.gov/pubmed/32035664
  • Rusche LN (2020) Mobile DNAs and switching mating types in yeast. Elife 9. https://www.ncbi.nlm.nih.gov/pubmed/32515351
  • Saitou M, Gaylord EA, Xu E, May AJ, Neznanova L, Nathan S, Grawe A, Chang J, Ryan W, Ruhl S, Knox SM, Gokcumen O (2020) Functional Specialization of Human Salivary Glands and Origins of Proteins Intrinsic to Human Saliva. Cell Rep 33:108402. https://www.ncbi.nlm.nih.gov/pubmed/33207190
  • Saitou M, Gokcumen O (2020) An Evolutionary Perspective on the Impact of Genomic Copy Number Variation on Human Health. J Mol Evol 88:104-119. https://www.ncbi.nlm.nih.gov/pubmed/31522275
  • Sinha S, Jones BM, Traniello IM, Bukhari SA, Halfon MS, Hofmann HA, Huang S, Katz PS, Keagy J, Lynch VJ, Sokolowski MB, Stubbs LJ, Tabe-Bordbar S, Wolfner MF, Robinson GE (2020) Behavior-related gene regulatory networks: A new level of organization in the brain. Proc Natl Acad Sci U S A. https://www.ncbi.nlm.nih.gov/pubmed/32661177
  • Taskent O, Lin YL, Patramanis I, Pavlidis P, Gokcumen O (2020) Analysis of Haplotypic Variation and Deletion Polymorphisms Point to Multiple Archaic Introgression Events, Including from Altai Neanderthal Lineage. Genetics 215:497-509. https://www.ncbi.nlm.nih.gov/pubmed/32234956
  • Taylor DJ, Connelly SJ, Kotov AA (2020) The Intercontinental phylogeography of neustonic daphniids. Sci Rep 10:1818. https://www.ncbi.nlm.nih.gov/pubmed/32020006
  • Thamadilok S, Choi KS, Ruhl L, Schulte F, Kazim AL, Hardt M, Gokcumen O, Ruhl S (2020) Human and Nonhuman Primate Lineage-Specific Footprints in the Salivary Proteome. Mol Biol Evol 37:395-405. https://www.ncbi.nlm.nih.gov/pubmed/31614365
  • Vandermeulen MD, Cullen PJ (2020) New Aspects of Invasive Growth Regulation Identified by Functional Profiling of MAPK Pathway Targets in Saccharomyces cerevisiae. Genetics 216:95-116. https://www.ncbi.nlm.nih.gov/pubmed/32665277
  • Wang W, Cho H, Kim D, Park Y, Moon JH, Lim SJ, Yoon SM, McCane M, Aicher SA, Kim S, Emery B, Lee JW, Lee S, Park Y, Lee SK (2020) PRC2 Acts as a Critical Timer That Drives Oligodendrocyte Fate over Astrocyte Identity by Repressing the Notch Pathway. Cell Rep 32:108147. https://www.ncbi.nlm.nih.gov/pubmed/32937136
  • White JA, 2nd, Krzystek TJ, Hoffmar-Glennon H, Thant C, Zimmerman K, Iacobucci G, Vail J, Thurston L, Rahman S, Gunawardena S (2020) Excess Rab4 rescues synaptic and behavioral dysfunction caused by defective HTT-Rab4 axonal transport in Huntington's disease. Acta Neuropathol Commun 8:97. https://www.ncbi.nlm.nih.gov/pubmed/32611447
  • Xu D, Gokcumen O, Khurana E (2020) Loss-of-function tolerance of enhancers in the human genome. PLoS Genet 16:e1008663. https://www.ncbi.nlm.nih.gov/pubmed/32243438
  • Xu Z et al. (2020) Tandem gene duplications drive divergent evolution of caffeine and crocin biosynthetic pathways in plants. BMC Biol 18:63. https://www.ncbi.nlm.nih.gov/pubmed/32552824
  • Zhuang X, Wong NF, Sun W, Xu-Friedman MA (2020) Mechanisms and Functional Consequences of Presynaptic Homeostatic Plasticity at Auditory Nerve Synapses. J Neurosci 40:6896-6909. https://www.ncbi.nlm.nih.gov/pubmed/32747441
  • Zimmer MA et al. (2020) Zero or not? Causes and consequences of zero-flow stream gage readings. WIREs Water 7. https://www.ncbi.nlm.nih.gov/pubmed/32802326

2019 Publications (selected)

  • Anderson EN, Hirpa D, Zheng KH, Banerjee R, Gunawardena S (2019) The Non-amyloidal Component Region of alpha-Synuclein Is Important for alpha-Synuclein Transport Within Axons. Front Cell Neurosci 13:540.
  • Lindgren, J., Nilsson,D.E., Sjövall, P., Jarenmark, M., Ito, S., Wakamatsu, K., Kear, B.P., Schultz, B.P., Sylvestersen,R.L., Madsen, H., LaFountain, J.R. Jr., Alwmark,C., Eriksson, M.E., Hall, S.A., Lindgren, P., Rodríguez-Meizoso, I. and Ahlberg, P. 2019. Fossil insect eyes shed light on trilobite optics and the arthropod pigment screen. Nature. 573 (7772), 122-125. doi: 10.1038/s41586-019-1473-
  • Acevedo A, Berthel A, DuBois D, Almon RR, Jusko WJ, Androulakis IP (2019) Pathway-Based Analysis of the Liver Response to Intravenous Methylprednisolone Administration in Rats: Acute Versus Chronic Dosing. Gene Regul Syst Bio 13:1177625019840282.
  • Aijaz I, Koudelka GB (2019) Cheating, facilitation and cooperation regulate the effectiveness of phage-encoded exotoxins as antipredator molecules. Microbiologyopen 8:e00636.
  • Ao J, Bandyopadhyay S, Free SJ (2019) Characterization of the Neurospora crassa DHN melanin biosynthetic pathway in developing ascospores and peridium cells. Fungal Biol 123:1-9.
  • Ayyar VS, DuBois DC, Almon RR, Jusko WJ (2019) Modeling Corticosteroid Pharmacokinetics & Pharmacodynamics - III: Estrous Cycle- and Estrogen Receptor-Dependent Antagonism of GILZ Enhancement by Corticosteroids. J Pharmacol Exp Ther.
  • Ayyar VS, DuBois DC, Nakamura T, Almon RR, Jusko WJ (2019) Modeling Corticosteroid Pharmacokinetics and Pharmacodynamics - II: Sex Differences in Methylprednisolone Pharmacokinetics and Corticosterone Suppression. J Pharmacol Exp Ther.
  • Ayyar VS, Song D, DuBois DC, Almon RR, Jusko WJ (2019) Modeling Corticosteroid Pharmacokinetics and Pharmacodynamics - I: Determination and Prediction of Dexamethasone and Methylprednisolone Tissue Binding in the Rat. J Pharmacol Exp Ther.
  • Ballinger, M. J. and Taylor, D. J. 2019. Evolutionary persistence of insect bunyavirus infection despite host acquisition and expression of the viral nucleoprotein gene. Virus Evolution 5(2): vez017.
  • Berger P, Kouzel IU, Berger M, Haarmann N, Dobrindt U, Koudelka GB, Mellmann A (2019) Carriage of Shiga toxin phage profoundly affects Escherichia coli gene expression and carbon source utilization. BMC Genomics 20:504.
  • Chow J, Dionne HM, Prabhakar A, Mehrotra A, Somboonthum J, Gonzalez B, Edgerton M, Cullen PJ (2019) Aggregate Filamentous Growth Responses in Yeast. mSphere 4.
  • Chow J, Starr I, Jamalzadeh S, Muniz O, Kumar A, Gokcumen O, Ferkey DM, Cullen PJ (2019) Filamentation Regulatory Pathways Control Adhesion-Dependent Surface Responses in Yeast. Genetics.
  • Davis RB, Likhite N, Jackson CA, Liu T, Yu MC (2019) Robust repression of tRNA gene transcription during stress requires protein arginine methylation. Life Sci Alliance 2.
  • Fischer AU, Muller NIC, Deller T, Del Turco D, Fisch JO, Griesemer D, Kattler K, Maraslioglu A, Roemer V, Xu-Friedman MA, Walter J, Friauf E (2019) GABA is a modulator, rather than a classical transmitter, in the medial nucleus of the trapezoid body-lateral superior olive sound localization circuit. J Physiol 597:2269-2295.
  • Fritz AJ, Sehgal N, Pliss A, Xu J, Berezney R (2019) Chromosome territories and the global regulation of the genome. Genes Chromosomes Cancer 58:407-426.
  • Gao Y, Dutta Banik D, Muna MM, Roberts SG, Medler KF (2019) The WT1-BASP1 complex is required to maintain the differentiated state of taste receptor cells. Life Sci Alliance 2.
  • Hansen T, Thant C, White JA, 2nd, Banerjee R, Thuamsang B, Gunawardena S (2019) Excess active P13K rescues huntingtin-mediated neuronal cell death but has no effect on axonal transport defects. Apoptosis 24:341-358.
  • Kar B, Patel P, Ao J, Free SJ (2019) Neurospora crassa family GH72 glucanosyltransferases function to crosslink cell wall glycoprotein N-linked galactomannan to cell wall lichenin. Fungal Genet Biol 123:60-69.
  • Kar B, Patel P, Free SJ (2019) Trichophyton rubrum LysM proteins bind to fungal cell wall chitin and to the N-linked oligosaccharides present on human skin glycoproteins. PLoS One 14:e0215034.
  • Kotov AA, Taylor DJ (2019) Contrasting endemism in pond-dwelling cyclic parthenogens: the Daphnia curvirostris species group (Crustacea: Cladocera). Sci Rep 9:6812.
  • Lauer AM, Dent ML, Sun W, Xu-Friedman MA (2019) Effects of Non-traumatic Noise and Conductive Hearing Loss on Auditory System Function. Neuroscience 407:182-191.
  • Lin YL, Gokcumen O (2019) Fine-Scale Characterization of Genomic Structural Variation in the Human Genome Reveals Adaptive and Biomedically Relevant Hotspots. Genome Biol Evol 11:1136-1151.
  • Liu X, Schuessler PJ, Sahoo A, Walker SE (2019) Reconstitution and analyses of RNA interactions with eukaryotic translation initiation factors and ribosomal preinitiation complexes. Methods 162-163:42-53.
  • Nair SK, Basu S, Sen B, Lin MH, Kumar AN, Yuan Y, Cullen PJ, Sarkar D (2019) Colloidal Gels with Tunable Mechanomorphology Regulate Endothelial Morphogenesis. Sci Rep 9:1072.
  • Pajic P, Pavlidis P, Dean K, Neznanova L, Romano RA, Garneau D, Daugherity E, Globig A, Ruhl S, Gokcumen O (2019) Independent amylase gene copy number bursts correlate with dietary preferences in mammals. Elife 8.
  • Quillen EE, Norton HL, Parra EJ, Lona-Durazo F, Ang KC, Illiescu FM, Pearson LN, Shriver MD, Lasisi T, Gokcumen O, Starr I, Lin YL, Martin AR, Jablonski NG (2019) Shades of complexity: New perspectives on the evolution and genetic architecture of human skin. Am J Phys Anthropol 168 Suppl 67:4-26.
  • Saitou M, Gokcumen O (2019) Resolving the Insertion Sites of Polymorphic Duplications Reveals a HERC2 Haplotype under Selection. Genome Biol Evol 11:1679-1690.
  • Salojarvi J et al. (2019) Author Correction: Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch. Nat Genet 51:1187-1189.
  • Srivastava A, Kumar Sarsani V, Fiddes I, Sheehan SM, Seger RL, Barter ME, Neptune-Bear S, Lindqvist C, Korstanje R (2019) Genome assembly and gene expression in the American black bear provides new insights into the renal response to hibernation. DNA Res 26:37-44.
  • Zuykova, E. I. , Bochkarev, N. A., Taylor, D. J. and Kotov, A. A. 2019. Unexpected endemism in the Daphnia longispina complex (Crustacea: Cladocera) in Southern Siberia. PLoS ONE 14(9): e0221527. 

 

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2018 Publications (selected)

  • Ayyar VS, Sukumaran S, DuBois DC, Almon RR, Jusko WJ (2018) Modeling Corticosteroid Pharmacogenomics and Proteomics in Rat Liver. J Pharmacol Exp Ther 367:168-183.
  • Ayyar VS, Sukumaran S, DuBois DC, Almon RR, Qu J, Jusko WJ (2018) Receptor/gene/protein-mediated signaling connects methylprednisolone exposure to metabolic and immune-related pharmacodynamic actions in liver. J Pharmacokinet Pharmacodyn 45:557-575.
  • Banerjee R, Rudloff Z, Naylor C, Yu MC, Gunawardena S (2018) The presenilin loop region is essential for glycogen synthase kinase 3 beta (GSK3beta) mediated functions on motor proteins during axonal transport. Hum Mol Genet 27:2986-3001.
  • Barbolina MV, Kulikova VV, Tsvetikova MA, Anufrieva NV, Revtovich SV, Phillips RS, Gollnick PD, Demidkina TV, Faleev NG (2018) Serine 51 residue of Citrobacter freundii tyrosine phenol-lyase assists in C-alpha-proton abstraction and transfer in the reaction with substrate. Biochimie 147:63-69.
  • Bowitch A, Michaels KL, Yu MC, Ferkey DM (2018) The Protein Arginine Methyltransferase PRMT-5 Regulates SER-2 Tyramine Receptor-Mediated Behaviors in Caenorhabditis elegans. G3 (Bethesda) 8:2389-2398.
  • Chakraborty D, Clark E, Mauro SA, Koudelka GB (2018) Molecular Mechanisms Governing "Hair-Trigger" Induction of Shiga Toxin-Encoding Prophages. Viruses 10.
  • Chow J, Notaro M, Prabhakar A, Free SJ, Cullen PJ (2018) Impact of Fungal MAPK Pathway Targets on the Cell Wall. J Fungi (Basel) 4.
  • Colella JP, Lan T, Schuster SC, Talbot SL, Cook JA, Lindqvist C (2018) Whole-genome analysis of Mustela erminea finds that pulsed hybridization impacts evolution at high latitudes. Commun Biol 1:51.
  • Dutta Banik D, Martin LE, Freichel M, Torregrossa AM, Medler KF (2018) TRPM4 and TRPM5 are both required for normal signaling in taste receptor cells. Proc Natl Acad Sci U S A 115:E772-E781.
  • Edwards MR, Liu H, Shabman RS, Ginell GM, Luthra P, Ramanan P, Keefe LJ, Kollner B, Amarasinghe GK, Taylor DJ, Leung DW, Basler CF (2018) Conservation of Structure and Immune Antagonist Functions of Filoviral VP35 Homologs Present in Microbat Genomes. Cell Rep 24:861-872 e866.
  • Gonzalez B, Vazquez J, Cullen PJ, Mas A, Beltran G, Torija MJ (2018) Aromatic Amino Acid-Derived Compounds Induce Morphological Changes and Modulate the Cell Growth of Wine Yeast Species. Front Microbiol 9:670.
  • Iacobucci GJ, Gunawardena S (2018) Ethanol stimulates the in vivo axonal movement of neuropeptide dense-core vesicles in Drosophila motor neurons. J Neurochem 144:466-482.
  • Jain S, Donkin J, Frey MJ, Peltier S, Gunawardena S, Cooper DL (2018) Phenotypical variability in congenital FVII deficiency follows the ISTH-SSC severity classification guidelines: a review with illustrative examples from the clinic. J Blood Med 9:211-218.
  • Koudelka GB, Arnold JW, Chakraborty D (2018) Evolution of STEC virulence: Insights from the antipredator activities of Shiga toxin producing E. coli. Int J Med Microbiol 308:956-961.
  • LaFountain JR, Jr., Cohan CS (2018) Methods to study meiosis in insect spermatocytes. Methods Cell Biol 145:249-267.
  • Lesnek AJ, Briner JP, Lindqvist C, Baichtal JF, Heaton TH (2018) Deglaciation of the Pacific coastal corridor directly preceded the human colonization of the Americas. Sci Adv 4:eaar5040.
  • Mavroudis PD, DuBois DC, Almon RR, Jusko WJ (2018) Modeling circadian variability of core-clock and clock-controlled genes in four tissues of the rat. PLoS One 13:e0197534.
  • Mavroudis PD, DuBois DC, Almon RR, Jusko WJ (2018) Daily variation of gene expression in diverse rat tissues. PLoS One 13:e0197258.
  • Norman KL, Shively CA, De La Rocha AJ, Mutlu N, Basu S, Cullen PJ, Kumar A (2018) Inositol polyphosphates regulate and predict yeast pseudohyphal growth phenotypes. PLoS Genet 14:e1007493.
  • Saitou M, Lizardo DY, Taskent RO, Millner A, Gokcumen O, Atilla-Gokcumen GE (2018) An evolutionary transcriptomics approach links CD36 to membrane remodeling in replicative senescence. Mol Omics 14:237-246.
  • Saitou M, Satta Y, Gokcumen O (2018) Complex Haplotypes of GSTM1 Gene Deletions Harbor Signatures of a Selective Sweep in East Asian Populations. G3 (Bethesda) 8:2953-2966.
  • Saitou M, Satta Y, Gokcumen O, Ishida T (2018) Complex evolution of the GSTM gene family involves sharing of GSTM1 deletion polymorphism in humans and chimpanzees. BMC Genomics 19:293.
  • Sehgal N, Sylves ME, Sahoo A, Chow J, Walker SE, Cullen PJ, Berry JO (2018) CRISPR Gene Editing in Yeast: An Experimental Protocol for an Upper-Division Undergraduate Laboratory Course. Biochem Mol Biol Educ 46:592-601.
  • Song D, DuBois DC, Almon RR, Jusko WJ (2018) Modeling Sex Differences in Anti-inflammatory Effects of Dexamethasone in Arthritic Rats. Pharm Res 35:203.
  • Warner BE, Ballinger MJ, Yerramsetty P, Reed J, Taylor DJ, Smith TJ, Bruenn JA (2018) Cellular production of a counterfeit viral protein confers immunity to infection by a related virus. PeerJ 6:e5679.
  • Zuykova, E. I. , Simonov, E. P., Bochkarev, N. A., Taylor, D. J. and Kotov, A. A. 2018. Resolution of the Daphnia umbra problem (Crustacea: Cladocera) using an integrated taxonomic approach. Zoological Journal of the Linnean Society. ZLY15
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2017 Publications (selected)

  • Ao J, Free SJ (2017) Genetic and biochemical characterization of the GH72 family of cell wall transglycosylases in Neurospora crassa. Fungal Genet Biol 101:46-54.
  • Ayyar VS, Almon RR, DuBois DC, Sukumaran S, Qu J, Jusko WJ (2017) Functional proteomic analysis of corticosteroid pharmacodynamics in rat liver: Relationship to hepatic stress, signaling, energy regulation, and drug metabolism. J Proteomics 160:84-105.
  • Ayyar VS, DuBois DC, Almon RR, Jusko WJ (2017) Mechanistic Multi-Tissue Modeling of Glucocorticoid-Induced Leucine Zipper Regulation: Integrating Circadian Gene Expression with Receptor-Mediated Corticosteroid Pharmacodynamics. J Pharmacol Exp Ther 363:45-57.
  • Ballinger MJ, Medeiros AS, Qin J, Taylor DJ (2017) Unexpected differences in the population genetics of phasmavirids (Bunyavirales) from subarctic ponds. Virus Evol 3:vex015.
  • Bekpen C, Kunzel S, Xie C, Eaaswarkhanth M, Lin YL, Gokcumen O, Akdis CA, Tautz D (2017) Segmental duplications and evolutionary acquisition of UV damage response in the SPATA31 gene family of primates and humans. BMC Genomics 18:222.
  • Chen X, DuBois DC, Almon RR, Jusko WJ (2017) Interrelationships between Infliximab and Recombinant Tumor Necrosis Factor-alpha in Plasma Using Minimal Physiologically Based Pharmacokinetic Models. Drug Metab Dispos 45:790-797.
  • Chen X, DuBois DC, Almon RR, Jusko WJ (2017) Characterization and Interspecies Scaling of rhTNF-alpha Pharmacokinetics with Minimal Physiologically Based Pharmacokinetic Models. Drug Metab Dispos 45:798-806.
  • Fukushima K et al. (2017) Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory. Nat Ecol Evol 1:59.
  • Gokcumen O (2017) Evolution, Function, and Deconstructing Histories: A New Generation of Anthropological Genetics. Hum Biol 89:5-6.
  • Haase EM, Kou Y, Sabharwal A, Liao YC, Lan T, Lindqvist C, Scannapieco FA (2017) Comparative genomics and evolution of the amylase-binding proteins of oral streptococci. BMC Microbiol 17:94.
  • Hamon P, Grover CE, Davis AP, Rakotomalala JJ, Raharimalala NE, Albert VA, Sreenath HL, Stoffelen P, Mitchell SE, Couturon E, Hamon S, de Kochko A, Crouzillat D, Rigoreau M, Sumirat U, Akaffou S, Guyot R (2017) Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content. Mol Phylogenet Evol 109:351-361.
  • Hanner AS, Rusche LN (2017) The Yeast Heterochromatin Protein Sir3 Experienced Functional Changes in the AAA+ Domain After Gene Duplication and Subfunctionalization. Genetics 207:517-528.
  • Ihms EC, Kleckner IR, Gollnick P, Foster MP (2017) Mechanistic Models Fit to Variable Temperature Calorimetric Data Provide Insights into Cooperativity. Biophys J 112:1328-1338.
  • Kamisoglu K, Acevedo A, Almon RR, Coyle S, Corbett S, Dubois DC, Nguyen TT, Jusko WJ, Androulakis IP (2017) Understanding Physiology in the Continuum: Integration of Information from Multiple -Omics Levels. Front Pharmacol 8:91.
  • Kontturi J, Osama R, Deng X, Bashandy H, Albert VA, Teeri TH (2017) Functional characterization and expression of GASCL1 and GASCL2, two anther-specific chalcone synthase like enzymes from Gerbera hybrida. Phytochemistry 134:38-45.
  • Kumar R, Breindel C, Saraswat D, Cullen PJ, Edgerton M (2017) Candida albicans Sap6 amyloid regions function in cellular aggregation and zinc binding, and contribute to zinc acquisition. Sci Rep 7:2908.
  • Lan T, Gill S, Bellemain E, Bischof R, Nawaz MA, Lindqvist C (2017) Evolutionary history of enigmatic bears in the Tibetan Plateau-Himalaya region and the identity of the yeti. Proc Biol Sci 284.
  • Lan T, Renner T, Ibarra-Laclette E, Farr KM, Chang TH, Cervantes-Perez SA, Zheng C, Sankoff D, Tang H, Purbojati RW, Putra A, Drautz-Moses DI, Schuster SC, Herrera-Estrella L, Albert VA (2017) Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome. Proc Natl Acad Sci U S A 114:E4435-E4441.
  • Li X, DuBois DC, Almon RR, Jusko WJ (2017) Modeling Sex Differences in Pharmacokinetics, Pharmacodynamics, and Disease Progression Effects of Naproxen in Rats with Collagen-Induced Arthritis. Drug Metab Dispos 45:484-491.
  • Li X, DuBois DC, Almon RR, Jusko WJ (2017) Effect of Disease-Related Changes in Plasma Albumin on the Pharmacokinetics of Naproxen in Male and Female Arthritic Rats. Drug Metab Dispos 45:476-483.
  • Li X, DuBois DC, Song D, Almon RR, Jusko WJ, Chen X (2017) Modeling Combined Immunosuppressive and Anti-inflammatory Effects of Dexamethasone and Naproxen in Rats Predicts the Steroid-Sparing Potential of Naproxen. Drug Metab Dispos 45:834-845.
  • Lizardo DY, Lin YL, Gokcumen O, Atilla-Gokcumen GE (2017) Regulation of lipids is central to replicative senescence. Mol Biosyst 13:498-509.
  • Marsh LA, Carrera S, Shandilya J, Heesom KJ, Davidson AD, Medler KF, Roberts SG (2017) BASP1 interacts with oestrogen receptor alpha and modifies the tamoxifen response. Cell Death Dis 8:e2771.
  • McAdams NM, Patterson A, Gollnick P (2017) Identification of a Residue (Glu60) in TRAP Required for Inducing Efficient Transcription Termination at the trp Attenuator Independent of Binding Tryptophan and RNA. J Bacteriol 199.
  • Montes A, Bisson MA, Gardella JA, Jr., Aga DS (2017) Uptake and transformations of engineered nanomaterials: Critical responses observed in terrestrial plants and the model plant Arabidopsis thaliana. Sci Total Environ 607-608:1497-1516.
  • Muddukrishna B, Jackson CA, Yu MC (2017) Protein arginine methylation of Npl3 promotes splicing of the SUS1 intron harboring non-consensus 5' splice site and branch site. Biochim Biophys Acta Gene Regul Mech 1860:730-739.
  • Munoz AM, Yourik P, Rajagopal V, Nanda JS, Lorsch JR, Walker SE (2017) Active yeast ribosome preparation using monolithic anion exchange chromatography. RNA Biol 14:188-196.
  • Nie J, DuBois DC, Xue B, Jusko WJ, Almon RR (2017) Effects of High-Fat Feeding on Skeletal Muscle Gene Expression in Diabetic Goto-Kakizaki Rats. Gene Regul Syst Bio 11:1177625017710009.
  • Salojarvi J et al. (2017) Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch. Nat Genet 49:904-912.
  • Taskent RO, Alioglu ND, Fer E, Melike Donertas H, Somel M, Gokcumen O (2017) Variation and Functional Impact of Neanderthal Ancestry in Western Asia. Genome Biol Evol 9:3516-3524.
  • Taskent RO, Gokcumen O (2017) The Multiple Histories of Western Asia: Perspectives from Ancient and Modern Genomes. Hum Biol 89:107-117.
  • Xu D, Jaber Y, Pavlidis P, Gokcumen O (2017) VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences. BMC Bioinformatics 18:426.
  • Xu D, Pavlidis P, Taskent RO, Alachiotis N, Flanagan C, DeGiorgio M, Blekhman R, Ruhl S, Gokcumen O (2017) Archaic Hominin Introgression in Africa Contributes to Functional Salivary MUC7 Genetic Variation. Mol Biol Evol 34:2704-2715.
  • Xu-Friedman MA (2017) Measuring the Basic Physiological Properties of Synapses. Cold Spring Harb Protoc 2017.
  • Xu-Friedman MA (2017) Preparing Brain Slices to Study Basic Synaptic Properties. Cold Spring Harb Protoc 2017.
  • Yerramsetty P, Agar EM, Yim WC, Cushman JC, Berry JO (2017) An rbcL mRNA-binding protein is associated with C3 to C4 evolution and light-induced production of Rubisco in Flaveria. J Exp Bot 68:4635-4649.
  • Yoshinari S, Liu Y, Gollnick P, Ho CK (2017) Cleavage of 3'-terminal adenosine by archaeal ATP-dependent RNA ligase. Sci Rep 7:11662.
  • Zhang T, Zhao Y, Juntheikki I, Mouhu K, Broholm SK, Rijpkema AS, Kins L, Lan T, Albert VA, Teeri TH, Elomaa P (2017) Dissecting functions of SEPALLATA-like MADS box genes in patterning of the pseudanthial inflorescence of Gerbera hybrida. New Phytol 216:939-954.
  • Zhuang X, Sun W, Xu-Friedman MA (2017) Changes in Properties of Auditory Nerve Synapses following Conductive Hearing Loss. J Neurosci 37:323-332.
  • Zou D, Hennessey TM (2017) Behavioral Effects of a Chemorepellent Receptor Knockout Mutation in Tetrahymena thermophila. mSphere 2.
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2016 Publications

  • Ao J, Aldabbous M, Notaro MJ, Lojacono M, Free SJ (2016) A proteomic and genetic analysis of the Neurospora crassa conidia cell wall proteins identifies two glycosyl hydrolases involved in cell wall remodeling. Fungal Genet Biol 94:47-53.
  • Arnold JW, Spacht D, Koudelka GB (2016) Determinants that govern the recognition and uptake of Escherichia coli O157 : H7 by Acanthamoeba castellanii. Cell Microbiol 18:1459-1470.
  • Basu S, Vadaie N, Prabhakar A, Li B, Adhikari H, Pitoniak A, Chow J, Chavel CA, Cullen PJ (2016) Spatial landmarks regulate a Cdc42-dependent MAPK pathway to control differentiation and the response to positional compromise. Proc Natl Acad Sci U S A 113:E2019-2028.
  • Berry JO, Mure CM, Yerramsetty P (2016) Regulation of Rubisco gene expression in C4 plants. Curr Opin Plant Biol 31:23-28.
  • Carretero-Paulet L, Albert VA (2016) Studying Evolutionary Dynamics of Gene Families Encoding SUMO-Activating Enzymes with SeaView and ProtTest. Methods Mol Biol 1450:273-284.
  • Carretero-Paulet L, Albert VA (2016) Sequence Search and Comparative Genomic Analysis of SUMO-Activating Enzymes Using CoGe. Methods Mol Biol 1450:261-272.
  • Colon MP, Chakraborty D, Pevzner Y, Koudelka GB (2016) Mechanisms that Determine the Differential Stability of Stx(+) and Stx(-) Lysogens. Toxins (Basel) 8:96.
  • Cullen PJ, Edgerton M (2016) Unmasking fungal pathogens by studying MAPK-dependent cell wall regulation in Candida albicans. Virulence 7:502-505.
  • Eaaswarkhanth M, Xu D, Flanagan C, Rzhetskaya M, Hayes MG, Blekhman R, Jablonski NG, Gokcumen O (2016) Atopic Dermatitis Susceptibility Variants in Filaggrin Hitchhike Hornerin Selective Sweep. Genome Biol Evol 8:3240-3255.
  • Gu H, Yoshinari S, Ghosh R, Ignatochkina AV, Gollnick PD, Murakami KS, Ho CK (2016) Structural and mutational analysis of archaeal ATP-dependent RNA ligase identifies amino acids required for RNA binding and catalysis. Nucleic Acids Res 44:2337-2347.
  • Hindman R, Gollnick P (2016) Nucleoside Triphosphate Phosphohydrolase I (NPH I) Functions as a 5' to 3' Translocase in Transcription Termination of Vaccinia Early Genes. J Biol Chem 291:14826-14838.
  • Koteyeva NK, Voznesenskaya EV, Berry JO, Cousins AB, Edwards GE (2016) The unique structural and biochemical development of single cell C4 photosynthesis along longitudinal leaf gradients in Bienertia sinuspersici and Suaeda aralocaspica (Chenopodiaceae). J Exp Bot 67:2587-2601.
  • Kotov AA, Karabanov DP, Bekker EI, Neretina TV, Taylor DJ (2016) Phylogeography of the Chydorus sphaericus Group (Cladocera: Chydoridae) in the Northern Palearctic. PLoS One 11:e0168711.
  • Krzyzanowski MC, Woldemariam S, Wood JF, Chaubey AH, Brueggemann C, Bowitch A, Bethke M, L'Etoile ND, Ferkey DM (2016) Aversive Behavior in the Nematode C. elegans Is Modulated by cGMP and a Neuronal Gap Junction Network. PLoS Genet 12:e1006153.
  • Lindqvist C, Roy T, Lydersen C, Kovacs KM, Aars J, Wiig O, Bachmann L (2016) Genetic diversity of historical Atlantic walruses (Odobenus rosmarus rosmarus) from Bjornoya and Haoya (Tusenoyane), Svalbard, Norway. BMC Res Notes 9:112.
  • Liu L, Free SJ (2016) Characterization of the Sclerotinia sclerotiorum cell wall proteome. Mol Plant Pathol 17:985-995.
  • Pajic P, Lin YL, Xu D, Gokcumen O (2016) The psoriasis-associated deletion of late cornified envelope genes LCE3B and LCE3C has been maintained under balancing selection since Human Denisovan divergence. BMC Evol Biol 16:265.
  • Popova EV, Petrusek A, Korinek V, Mergeay J, Bekker EI, Karabanov DP, Galimov YR, Neretina TV, Taylor DJ, Kotov AA (2016) Revision of the Old World Daphnia (Ctenodaphnia) similis group Cladocera: Daphniidae). Zootaxa 4161:1-40.
  • Roy T, Catlin NS, Garner DM, Cantino PD, Scheen AC, Lindqvist C (2016) Evolutionary relationships within the lamioid tribe Synandreae (Lamiaceae) based on multiple low-copy nuclear loci. PeerJ 4:e2220.
  • Rupert CB, Heltzel JM, Taylor DJ, Rusche LN (2016) Sporadic Gene Loss After Duplication Is Associated with Functional Divergence of Sirtuin Deacetylases Among Candida Yeast Species. G3 (Bethesda) 6:3297-3305.
  • Saraswat D, Kumar R, Pande T, Edgerton M, Cullen PJ (2016) Signaling mucin Msb2 Regulates adaptation to thermal stress in Candida albicans. Mol Microbiol 100:425-441.
  • Sehgal N, Fritz AJ, Vecerova J, Ding H, Chen Z, Stojkovic B, Bhattacharya S, Xu J, Berezney R (2016) Large-scale probabilistic 3D organization of human chromosome territories. Hum Mol Genet 25:419-436.
  • Sehgal N, Seifert B, Ding H, Chen Z, Stojkovic B, Bhattacharya S, Xu J, Berezney R (2016) Reorganization of the interchromosomal network during keratinocyte differentiation. Chromosoma 125:389-403.
  • Shandilya J, Gao Y, Nayak TK, Roberts SG, Medler KF (2016) AP1 transcription factors are required to maintain the peripheral taste system. Cell Death Dis 7:e2433.
  • Shandilya J, Medler KF, Roberts SG (2016) Regulation of AURORA B function by mitotic checkpoint protein MAD2. Cell Cycle 15:2196-2201.
  • Tate J, Boldt RL, McFadden BD, D'Costa SM, Lewandowski NM, Shatzer AN, Gollnick P, Condit RC (2016) Biochemical analysis of the multifunctional vaccinia mRNA capping enzyme encoded by a temperature sensitive virus mutant. Virology 487:27-40.
  • Taylor, D. J., Ballinger, M. J., Medeiros, A. S., and Kotov, A. A. 2016. Climate-associated tundra thaw pond formation and range expansion of boreal zooplankton predators. Ecography 39: 43-53. 
  • Tica J, Lee E, Untergasser A, Meiers S, Garfield DA, Gokcumen O, Furlong EE, Park PJ, Stutz AM, Korbel JO (2016) Next-generation sequencing-based detection of germline L1-mediated transductions. BMC Genomics 17:342.
  • Toal KL, Radziwon KE, Holfoth DP, Xu-Friedman MA, Dent ML (2016) Audiograms, gap detection thresholds, and frequency difference limens in cannabinoid receptor 1 knockout mice. Hear Res 332:217-222.
  • Welch AJ, Collins K, Ratan A, Drautz-Moses DI, Schuster SC, Lindqvist C (2016) Data characterizing the chloroplast genomes of extinct and endangered Hawaiian endemic mints (Lamiaceae) and their close relatives. Data Brief 7:900-922.
  • Welch AJ, Collins K, Ratan A, Drautz-Moses DI, Schuster SC, Lindqvist C (2016) The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae). Mol Phylogenet Evol 99:16-33.
  • White JA, Banerjee R, Gunawardena S (2016) Axonal Transport and Neurodegeneration: How Marine Drugs Can Be Used for the Development of Therapeutics. Mar Drugs 14.
  • Woolford CA, Lagree K, Xu W, Aleynikov T, Adhikari H, Sanchez H, Cullen PJ, Lanni F, Andes DR, Mitchell AP (2016) Bypass of Candida albicans Filamentation/Biofilm Regulators through Diminished Expression of Protein Kinase Cak1. PLoS Genet 12:e1006487.
  • Xu D, Pavlidis P, Thamadilok S, Redwood E, Fox S, Blekhman R, Ruhl S, Gokcumen O (2016) Recent evolution of the salivary mucin MUC7. Sci Rep 6:31791.
  • Yang Y, Ramamurthy B, Neef A, Xu-Friedman MA (2016) Low Somatic Sodium Conductance Enhances Action Potential Precision in Time-Coding Auditory Neurons. J Neurosci 36:11999-12009.
  • Yerramsetty P, Stata M, Siford R, Sage TL, Sage RF, Wong GK, Albert VA, Berry JO (2016) Evolution of RLSB, a nuclear-encoded S1 domain RNA binding protein associated with post-transcriptional regulation of plastid-encoded rbcL mRNA in vascular plants. BMC Evol Biol 16:141.
  • Zhao Y, Zhang T, Broholm SK, Tahtiharju S, Mouhu K, Albert VA, Teeri TH, Elomaa P (2016) Evolutionary Co-Option of Floral Meristem Identity Genes for Patterning of the Flower-Like Asteraceae Inflorescence. Plant Physiol 172:284-296.
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2015 Publications (selected)

  • Adhikari H, Caccamise LM, Pande T, Cullen PJ (2015) Comparative Analysis of Transmembrane Regulators of the Filamentous Growth Mitogen-Activated Protein Kinase Pathway Uncovers Functional and Regulatory Differences. Eukaryot Cell 14:868-883.
  • Adhikari H, Cullen PJ (2015) Role of phosphatidylinositol phosphate signaling in the regulation of the filamentous-growth mitogen-activated protein kinase pathway. Eukaryot Cell 14:427-440.
  • Adhikari H, Vadaie N, Chow J, Caccamise LM, Chavel CA, Li B, Bowitch A, Stefan CJ, Cullen PJ (2015) Role of the unfolded protein response in regulating the mucin-dependent filamentous-growth mitogen-activated protein kinase pathway. Mol Cell Biol 35:1414-1432.
  • Albert VA, Carretero-Paulet L (2015) A genome to unveil the mysteries of orchids. Nat Genet 47:3-4.
  • Ao J, Chinnici JL, Maddi A, Free SJ (2015) The N-Linked Outer Chain Mannans and the Dfg5p and Dcw1p Endo-alpha-1,6-Mannanases Are Needed for Incorporation of Candida albicans Glycoproteins into the Cell Wall. Eukaryot Cell 14:792-803.
  • Ayyar VS, Almon RR, Jusko WJ, DuBois DC (2015) Quantitative tissue-specific dynamics of in vivo GILZ mRNA expression and regulation by endogenous and exogenous glucocorticoids. Physiol Rep 3.
  • Carretero-Paulet L, Chang TH, Librado P, Ibarra-Laclette E, Herrera-Estrella L, Rozas J, Albert VA (2015) Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba. Genome Biol Evol 7:444-456.
  • Carretero-Paulet L, Librado P, Chang TH, Ibarra-Laclette E, Herrera-Estrella L, Rozas J, Albert VA (2015) High Gene Family Turnover Rates and Gene Space Adaptation in the Compact Genome of the Carnivorous Plant Utricularia gibba. Mol Biol Evol 32:1284-1295.
  • Chen X, DuBois DC, Almon RR, Jusko WJ (2015) Biodistribution of etanercept to tissues and sites of inflammation in arthritic rats. Drug Metab Dispos 43:898-907.
  • Cullen PJ (2015) Investigating filamentous growth and biofilm/mat formation in budding yeast. Cold Spring Harb Protoc 2015:235-238.
  • Cullen PJ (2015) Evaluating the activity of the filamentous growth mitogen-activated protein kinase pathway in yeast. Cold Spring Harb Protoc 2015:276-283.
  • Cullen PJ (2015) Evaluating yeast filamentous growth at the single-cell level. Cold Spring Harb Protoc 2015:272-275.
  • Cullen PJ (2015) Biofilm/Mat assays for budding yeast. Cold Spring Harb Protoc 2015:172-175.
  • Cullen PJ (2015) The plate-washing assay: a simple test for filamentous growth in budding yeast. Cold Spring Harb Protoc 2015:168-171.
  • Ibarra-Laclette E, Mendez-Bravo A, Perez-Torres CA, Albert VA, Mockaitis K, Kilaru A, Lopez-Gomez R, Cervantes-Luevano JI, Herrera-Estrella L (2015) Deep sequencing of the Mexican avocado transcriptome, an ancient angiosperm with a high content of fatty acids. BMC Genomics 16:599.
  • Ibarra-Laclette E, Zamudio-Hernandez F, Perez-Torres CA, Albert VA, Ramirez-Chavez E, Molina-Torres J, Fernandez-Cortes A, Calderon-Vazquez C, Olivares-Romero JL, Herrera-Estrella A, Herrera-Estrella L (2015) De novo sequencing and analysis of Lophophora williamsii transcriptome, and searching for putative genes involved in mescaline biosynthesis. BMC Genomics 16:657.
  • Kapoor S, Zhu L, Froyd C, Liu T, Rusche LN (2015) Regional centromeres in the yeast Candida lusitaniae lack pericentromeric heterochromatin. Proc Natl Acad Sci U S A 112:12139-12144.
  • Li R, Puri S, Tati S, Cullen PJ, Edgerton M (2015) Candida albicans Cek1 mitogen-activated protein kinase signaling enhances fungicidal activity of salivary histatin 5. Antimicrob Agents Chemother 59:3460-3468.
  • Li S, Pan XX, Berry JO, Wang Y, Naren, Ma S, Tan S, Xiao W, Zhao WZ, Sheng XY, Yin LP (2015) OsSEC24, a functional SEC24-like protein in rice, improves tolerance to iron deficiency and high pH by enhancing H(+) secretion mediated by PM-H(+)-ATPase. Plant Sci 233:61-71.
  • Li S, Zhang X, Zhang XY, Xiao W, Berry JO, Li P, Jin S, Tan S, Zhang P, Zhao WZ, Yin LP (2015) Expression of Malus xiaojinensis IRT1 (MxIRT1) protein in transgenic yeast cells leads to degradation through autophagy in the presence of excessive iron. Yeast 32:499-517.
  • Likhite N, Jackson CA, Liang MS, Krzyzanowski MC, Lei P, Wood JF, Birkaya B, Michaels KL, Andreadis ST, Clark SD, Yu MC, Ferkey DM (2015) The protein arginine methyltransferase PRMT5 promotes D2-like dopamine receptor signaling. Sci Signal 8:ra115.
  • Lin CS, Chen JJ, Huang YT, Chan MT, Daniell H, Chang WJ, Hsu CT, Liao DC, Wu FH, Lin SY, Liao CF, Deyholos MK, Wong GK, Albert VA, Chou ML, Chen CY, Shih MC (2015) The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family. Sci Rep 5:9040.
  • Lon HK, DuBois DC, Earp JC, Almon RR, Jusko WJ (2015) Modeling effects of dexamethasone on disease progression of bone mineral density in collagen-induced arthritic rats. Pharmacol Res Perspect 3:e00169.
  • Medler KF (2015) Honing in on the ATP Release Channel in Taste Cells. Chem Senses 40:449-451.
  • Medler KF (2015) Calcium signaling in taste cells. Biochim Biophys Acta 1853:2025-2032.
  • Ngodup T, Goetz JA, McGuire BC, Sun W, Lauer AM, Xu-Friedman MA (2015) Activity-dependent, homeostatic regulation of neurotransmitter release from auditory nerve fibers. Proc Natl Acad Sci U S A 112:6479-6484.
  • Pitoniak A, Chavel CA, Chow J, Smith J, Camara D, Karunanithi S, Li B, Wolfe KH, Cullen PJ (2015) Cdc42p-interacting protein Bem4p regulates the filamentous-growth mitogen-activated protein kinase pathway. Mol Cell Biol 35:417-436.
  • Pliss A, Fritz AJ, Stojkovic B, Ding H, Mukherjee L, Bhattacharya S, Xu J, Berezney R (2015) Non-Random Patterns in the Distribution of NOR-Bearing Chromosome Territories in Human Fibroblasts: A Network Model of Interactions. J Cell Physiol 230:427-439.
  • Pliss A, Kuzmin AN, Kachynski AV, Baev A, Berezney R, Prasad PN (2015) Fluctuations and synchrony of RNA synthesis in nucleoli. Integr Biol (Camb) 7:681-692.
  • Quintero-Rivera F et al. (2015) MATR3 disruption in human and mouse associated with bicuspid aortic valve, aortic coarctation and patent ductus arteriosus. Hum Mol Genet 24:2375-2389.
  • Roy T, Cole LW, Chang TH, Lindqvist C (2015) Untangling reticulate evolutionary relationships among New World and Hawaiian mints (Stachydeae, Lamiaceae). Mol Phylogenet Evol 89:46-62.
  • Roy T, Lindqvist C (2015) New insights into evolutionary relationships within the subfamily Lamioideae (Lamiaceae) based on pentatricopeptide repeat (PPR) nuclear DNA sequences. Am J Bot 102:1721-1735.
  • Xue B, Nie J, Wang X, DuBois DC, Jusko WJ, Almon RR (2015) Effects of High Fat Feeding on Adipose Tissue Gene Expression in Diabetic Goto-Kakizaki Rats. Gene Regul Syst Bio 9:15-26.
  • Yang H, Xu-Friedman MA (2015) Skipped-stimulus approach reveals that short-term plasticity dominates synaptic strength during ongoing activity. J Neurosci 35:8297-8307.
  • Yang Y, Adowski T, Ramamurthy B, Neef A, Xu-Friedman MA (2015) High-speed dynamic-clamp interface. J Neurophysiol 113:2713-2720.
  • Yang Y, Xu-Friedman MA (2015) Different pools of glutamate receptors mediate sensitivity to ambient glutamate in the cochlear nucleus. J Neurophysiol 113:3634-3645.

 

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