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Submissions from 2025

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What ‘unexplored’ means: mapping regions with digitized natural history records to look for ‘biodiversity blindspots’, Laymon Ball, Sheila Rodríguez-Machado, Diego Paredes-Burneo, Samantha Rutledge, David A. Boyd, David Vander Pluym, Spenser Babb-Biernacki, Austin S. Chipps, Rafet Öztürk, Yahya Terzi, et al.

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The Contemporary Distribution of Scincine Lizards Does Not Reflect Their Biogeographic Origin, Aniruddha Datta-Roy, Matthew C. Brandley, Christopher C. Austin, Aaron M. Bauer, David James Harris, Salvador Carranza, Kanishka D.B. Ukuwela, Anslem De Silva, Krystal A. Tolley, K. Praveen Karanth, et al.

Evaluating the antibacterial activity of engineered phage ФEcSw endolysin against multi-drug-resistant Escherichia coli strain Sw1, Maheswaran Easwaran, Rajiv Gandhi Govindaraj, Misagh Naderi, Michal Brylinski, Mahanama De Zoysa, and Hyun Jin Shin

Speciation with gene flow in an island endemic hummingbird, Caroline Duffie Judy, Gary R. Graves, John E. McCormack, Katherine Faust Stryjewski, and Robb T. Brumfield

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EC2Vec: A Machine Learning Method to Embed Enzyme Commission (EC) Numbers into Vector Representations, Mengmeng Liu, Xialong Ni, J. Ramanujam, and Michal Brylinski

Assessing the Adequacy of Morphological Models Using Posterior Predictive Simulations, Laura P.A. Mulvey, Michael R. May, Jeremy M. Brown, Sebastian Höhna, April M. Wright, and Rachel C.M. Warnock

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A Data-Driven Approach to Enhance the Prediction of Bacteria–Metabolite Interactions in the Human Gut Microbiome Using Enzyme Encodings and Metabolite Structural Embeddings, Gopal Srivastava and Michal Brylinski

Machine Learning Techniques to Infer Protein Structure and Function from Sequences: A Comprehensive Review, Gopal Srivastava, Mengmeng Liu, Xialong Ni, Limeng Pu, and Michal Brylinski

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Complex Models of Sequence Evolution Improve Fit, But Not Gene Tree Discordance, for Tetrapod Mitogenomes, Benjamin S. Toups, Robert C. Thomson, and Jeremy M. Brown

Submissions from 2024

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New records of seahorses (Teleostei: Syngnathidae: Hippocampus) from Kuwait in the Arabian (Persian) Gulf, James M. Bishop, Manickam Nithyanandan, A. J. Turner, Link Morgan, and Prosanta Chakrabarty

The mechanistic, genetic and evolutionary causes of bird eye colour variation, Eamon C. Corbett, Robb T. Brumfield, and Brant C. Faircloth

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Iron–sulfur cluster assembly scaffold protein IscU is required for activation of ferric uptake regulator (Fur) in Escherichia coli, Huangen Ding

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The Expected Behaviors of Posterior Predictive Tests and Their Unexpected Interpretation, Luiza Guimarães Fabreti, Lyndon M. Coghill, Robert C. Thomson, Sebastian Höhna, and Jeremy M. Brown

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Song and genetic divergence within a subspecies of white-crowned sparrow (Zonotrichia leucophrys nuttalli), Amy Rongyan Luo, Sara Lipshutz, Jennifer Phillips, Robb T. Brumfield, and Elizabeth Perrault Derryberry

Implications of headwater contact zones for the riverine barrier hypothesis: a case study of the Blue-capped Manakin (Lepidothrix coronata), Andre E. Moncrieff, Brant C. Faircloth, Rosalind C. Remsen, Anna E. Hiller, Cristhian Felix, Angelo P. Capparella, Alexandre Aleixo, Thomas Valqui, and Robb T. Brumfield

Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops), Lukas J. Musher, Glaucia Del-Rio, Rafael S. Marcondes, Robb T. Brumfield, Gustavo A. Bravo, and Gregory Thom

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Lineage diversity in a Melanesian lizard radiation (Gekkonidae: Nactus) further highlights exceptional diversity and endemism in eastern Papua New Guinea, Paul M. Oliver, Fred Kraus, Christopher C. Austin, Leonardo G. Tedeschi, Aurora R. O’Brien, and Simon T. Maddock

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Metabarcoding the Arctic Ocean Helps Reveal Its Hidden Microbial Community Composition, Rafet Çağrı Öztürk, Yahya Terzi, Sheila Rodríguez-Machado, Ersan Başar, Ali Muzaffer Feyzioğlu, Dilek Ustaoğlu, Ertuğrul Ağırbaş, and Prosanta Chakrabarty

Subspecies-level distribution maps for birds of the Amazon basin and adjacent areas, Marco Antonio Rego, Glaucia Del-Rio, and Robb T. Brumfield

Whole snake genomes from eighteen families of snakes (Serpentes: Caenophidia) and their applications to systematics, Jackson R. Roberts, Justin M. Bernstein, Christopher C. Austin, Taylor Hains, Joshua Mata, Michael Kieras, Stacy Pirro, and Sara Ruane

Systematics and biogeography of a Sunda-Papuan snake lineage (Natricidae: Tropidonophis Jan 1863), Jackson R. Roberts, Fred Kraus, Allen Allison, Stephen J. Richards, Bulisa Iova, Burhan Tjaturadi, Sara Ruane, and Christopher C. Austin

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Disentangling historical relationships within Poeciliidae (Teleostei: Cyprinodontiformes) using ultraconserved elements, Sheila Rodríguez-Machado, Diego J. Elías, Caleb D. McMahan, Anna Gruszkiewicz-Tolli, Kyle R. Piller, and Prosanta Chakrabarty

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Erratum to "Disentangling historical relationships within Poeciliidae (Teleostei: Cyprinodontiformes) using ultraconserved elements" [Mol. Phylogenet. Evol. 190 (2024) 107965, Sheila Rodríguez-Machado, Diego J. Elías, Caleb D. McMahan, Anna Gruszkiewicz-Tolli, Kyle R. Piller, and Prosanta Chakrabarty

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Editorial: Structure and function of trans-membrane proteins, Irena Roterman, Michal Brylinski, Fabio Polticelli, and Alexandre G. de Brevern

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An island ‘endemic’ born out of hybridization between introduced lineages, Jessie F. Salter, Robb T. Brumfield, and Brant C. Faircloth

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Reassignment of a junior synonym of Lepisosteus oculatus Winchell 1864 to L. platostomus Rafinesque 1820, Daniel Sinopoli, Thomas J. Near, Solomon R. David, and Prosanta Chakrabarty

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VenomCap: An exon-capture probe set for the targeted sequencing of snake venom genes, Scott L. Travers, Carl R. Hutter, Christopher C. Austin, Stephen C. Donnellan, Matthew D. Buehler, Christopher E. Ellison, and Sara Ruane

Submissions from 2023

Effect of high-risk factors on postoperative major adverse cardiovascular and cerebrovascular events trends following bariatric surgery in the United States from 2012 to 2019, Linda Adepoju, Denise Danos, Christian Green, Michael W. Cook, Philip R. Schauer, and Vance L. Albaugh

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Identification of oral therapeutics using an AI platform against the virus responsible for COVID-19, SARS-CoV-2, Adam Bess, Frej Berglind, Supratik Mukhopadhyay, Michal Brylinski, Chris Alvin, Fanan Fattah, and Kishor M. Wasan

Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution, Kevin R. Bredemeyer, La Deana Hillier, Andrew J. Harris, Graham M. Hughes, Nicole M. Foley, Colleen Lawless, Rachel A. Carroll, Jessica M. Storer, Mark A. Batzer, Edward S. Rice, et al.

Tree Set Visualization, Exploration, and Applications, Jeremy M. Brown, Genevieve G. Mount, Kyle A. Gallivan, and James C. Wilgenbusch

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VCP promotes tTAF-target gene expression and spermatocyte differentiation by downregulating mono-ubiquitylated H2A, Tyler J. Butsch, Olga Dubuisson, Alyssa E. Johnson, and K. Adam Bohnert

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Rbp4-Gal4, a germline driver that activates in meiosis, reveals functions for VCP in spermatid development, Tyler J. Butsch, Alyssa E. Johnson, and K. Adam Bohnert

Explaining Life Through Evolution, Prosanta Chakrabarty

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Phylogenomics of trans-Andean tetras of the genus Hyphessobrycon Durbin 1908 (Stethaprioninae: Characidae) and colonization patterns of Middle America, Diego J. Elías, Caleb D. McMahan, Fernando Alda, Carlos García-Alzate, Pamela B. Hart, and Prosanta Chakrabarty

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A high-quality de novo genome assembly for clapper rail (Rallus crepitans), Elisa C. Elizondo, Brant C. Faircloth, Robb T. Brumfield, Subir B. Shakya, Vincenzo A. Ellis, Carl J. Schmidt, Adrienne I. Kovach, and W. Gregory Shriver

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SPIN-4/Spinster supports sperm activation in C. elegans via sphingosine-1-phosphate transport, Yash Flora and K. Adam Bohnert

Conservation implications for the world’s most widely distributed cavefish species complex based on population genomics (Typhlichthys, Percopsiformes), Pamela B. Hart, Matthew L. Niemiller, Jonathan W. Armbruster, and Prosanta Chakrabarty

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Amazonian birds in more dynamic habitats have less population genetic structure and higher gene flow, Oscar Johnson, Camila C. Ribas, Alexandre Aleixo, Luciano N. Naka, Michael G. Harvey, and Robb T. Brumfield

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A reference genome for Bluegill (Centrarchidae: Lepomis macrochirus), William B. Ludt, Eamon C. Corbett, Jerry Kattawar, Prosanta Chakrabarty, and Brant C. Faircloth

Unmasking hidden genetic, vocal, and size variation in the Masked Flowerpiercer along the Andes supports two species separated by Northern Peruvian Low, Silvia C. Martínez-Gómez, Carlos Esteban Lara, J. V. Remsen, Robb T. Brumfield, and Andrés M. Cuervo

Atlas of Australasian hormurid scorpions. I. The genus Hormurus Thorell, 1876 in Papua New Guinea. Exceptional morphological diversity in male and female copulatory structures suggests genital coevolution, Lionel Monod, Christina Lehmann-Graber, Christopher C. Austin, Bulisa Iova, and Lorenzo Prendini

Specimen collection is essential for modern science, Michael W. Nachman, Elizabeth J. Beckman, Rauri C.K. Bowie, Carla Cicero, Chris J. Conroy, Robert Dudley, Tyrone B. Hayes, Michelle S. Koo, Eileen A. Lacey, Christopher H. Martin, et al.

Speciation-by-Extinction, Glenn F. Seeholzer and Robb T. Brumfield

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Skinks of Oceania, New Guinea, and Eastern Wallacea: an underexplored biodiversity hotspot, Alex Slavenko, Allen Allison, Christopher C. Austin, Aaron M. Bauer, Rafe M. Brown, Robert N. Fisher, Ivan Ineich, Bulisa Iova, Benjamin R. Karin, Fred Kraus, et al.

Phylogenomic Analysis of the Parrots of the World Distinguishes Artifactual from Biological Sources of Gene Tree Discordance, Brian Tilston Smith, Jon Merwin, Kaiya L. Provost, Gregory Thom, Robb T. Brumfield, Mateus Ferreira, William M. Mauck, Robert G. Moyle, Timothy F. Wright, and Leo Joseph

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Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons, Erik F. Sørensen, R. Alan Harris, Liye Zhang, Muthuswamy Raveendran, Lukas F.K. Kuderna, Jerilyn A. Walker, Jessica M. Storer, Martin Kuhlwilm, Claudia Fontsere, Lakshmi Seshadri, et al.

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Framework of the Alu Subfamily Evolution in the Platyrrhine Three-Family Clade of Cebidae, Callithrichidae, and Aotidae, Jessica M. Storer, Jerilyn A. Walker, Jasmine N. Baker, Shifat Hossain, Christian Roos, Travis J. Wheeler, and Mark A. Batzer

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Extensive Independent Amplification of Platy-1 Retroposons in Tamarins, Genus Saguinus, Jessica M. Storer, Jerilyn A. Walker, Thomas O. Beckstrom, and Mark A. Batzer

Systematics of the Neopelminae (Aves: Passeriformes: Pipridae) with description of a new genus, Paul van Els, Michael G. Harvey, João M.G. Capurucho, Robb T. Brumfield, Bret M. Whitney, and José F. Pacheco

Environmentally persistent free radicals enhance SARS-CoV-2 replication in respiratory epithelium, Ayaho Yamamoto, Peter D. Sly, Keng Yih Chew, Lavrent Khachatryan, Nelufa Begum, Abrey J. Yeo, Luan D. Vu, and Kirsty R. Short

Submissions from 2022

Scintillation light detection in the 6-m drift-length ProtoDUNE Dual Phase liquid argon TPC, A Abed Abud, B Abi, R Acciarri, M A. Acero, M R. Adames, G Adamov, M Adamowski, and D Adams

Regulation of body weight: Lessons learned from bariatric surgery, Vance L. Albaugh, Yanlin He, Heike Münzberg, Christopher D. Morrison, Sangho Yu, and Hans-Rudolf Berthoud

An Overview of Obesity, Cholesterol, and Systemic Inflammation in Preeclampsia, Morgan C. Alston, Leanne M. Redman, and Jennifer L. Sones

Evaluation of Hemp (Cannabis sativa) (Rosales: Cannabaceae) as an Alternative Host Plant for Polyphagous Noctuid Pests, Nathan C. Arey, Nathan P. Lord, and Jeffrey A. Davis

Predicting Species Boundaries and Assessing Undescribed Diversity in , an Obligate Lung Symbiont, Spenser J. Babb-Biernacki, Jacob A. Esselstyn, and Vinson P. Doyle

Functional traits mediate individualistic species-environment distributions at broad spatial scales while fine-scale species associations remain unpredictable, Jared J. Beck, Daijiang Li, Sarah E. Johnson, David Rogers, Kenneth M. Cameron, Kenneth J. Sytsma, Thomas J. Givnish, and Donald M. Waller

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Artificial Intelligence For The Discovery Of Novel Antimicrobial Agents For Emerging Infectious Diseases, A Bess, F Berglind, S Mukhopadhyay, M Brylinski, A Bess, T F. Cho, C Galliano, and K M. Wasan

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Transcriptomic and ultrastructural evidence indicate that anti-HMGB1 antibodies rescue organic dust-induced mitochondrial dysfunction, Sanjana Mahadev Bhat, Nyzil Massey, Denusha Shrestha, Locke A. Karriker, Tomislav Jelesijevic, Chong Wang, and Chandrashekhar Charavaryamath

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Branching Off: New Insight Into Lysosomes As Tubular Organelles, K A. Bohnert and A E. Johnson

Allosteric Activation of 15-Lipoxygenase-1 by Boswellic Acid Induces the Lipid Mediator Class Switch to Promote Resolution of Inflammation, Friedemann Börner, Simona Pace, Paul M. Jordan, Jana Gerstmeier, Mario Gomez, Antonietta Rossi, Nathaniel C. Gilbert, and Marcia E. Newcomer

Evolution of the albumin protein family in reptiles, Emilie M. Broussard, Zachary B. Rodriguez, and Christopher C. Austin

Biogeography of a neotropical songbird radiation reveals similar diversification dynamics between montane and lowland clades, Nelson Buainain, Mateus Ferreira, Jorge E. Avendaño, Carlos D. Cadena, Brant C. Faircloth, Robb T. Brumfield, Joel Cracraft, and Camila C. Ribas

The effect of obesity on adipose-derived stromal cells and adipose tissue and their impact on cancer, Bruce A. Bunnell, Elizabeth C. Martin, Margarite D. Matossian, Courtney K. Brock, Khoa Nguyen, Bridgette Collins-Burow, and Matthew E. Burow

A meiotic switch in lysosome activity supports spermatocyte development in young flies but collapses with age, Tyler J. Butsch, Olga Dubuisson, Alyssa E. Johnson, and K Adam Bohnert

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Social media: Good or evil?, Prosanta Chakrabarty

GOBIIDAE: GLOSSOGOBIUS, CAVEFISH, TOHO, Prosanta Chakrabarty, Michelle E. Byrnes, John S. Sparks, and Melanie L.J. Stiassny

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Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis), Kin Onn Chan, Carl R. Hutter, Perry L. Wood, Yong-Chao Su, and Rafe M. Brown

Deep ecomorphological and genetic divergence in Steller's Jays (, Aves: Corvidae), Carla Cicero, Nicholas A. Mason, Zheng Oong, Pascal O. Title, Melissa E. Morales, Kevin A. Feldheim, Michelle S. Koo, and Rauri C. Bowie

Predicted Structure and Functions of the Prototypic Alphaherpesvirus Herpes Simplex Virus Type-1 UL37 Tegument Protein, Therese Marie Collantes, Carolyn M. Clark, Farhana Musarrat, Nithya Jambunathan, Seetharama Jois, and Konstantin G. Kousoulas

Environmental Impacts on COVID-19: Mechanisms of Increased Susceptibility, Stephania A. Cormier, Ayaho Yamamoto, Kirsty R. Short, Luan Vu, and William A. Suk

Mechanism of biotin carboxylase inhibition by ethyl 4-[[2-chloro-5-(phenylcarbamoyl)phenyl]sulphonylamino]benzoate, Matthew K. Craft and Grover L. Waldrop

They like to move it (move it): walking kinematics of balitorid loaches of Thailand, Callie H. Crawford, Amani Webber-Schultz, Pamela B. Hart, Zachary S. Randall, Cristian Cerrato-Morales, Audrey B. Kellogg, Haley E. Amplo, Apinun Suvarnaraksha, Lawrence M. Page, Prosanta Chakrabarty, et al.

Peptides and peptidomimetics as therapeutic agents for Covid-19, Achyut Dahal, Jafrin Jobayer Sonju, Konstantin G. Kousoulas, and Seetharama D. Jois

Epidemic time series similarity is related to geographic distance and age structure, Tad A. Dallas, Grant Foster, Robert L. Richards, and Bret D. Elderd

Substrate and low intensity fires influence bacterial communities in longleaf pine savanna, Viet Q. Dao, Stephen E. Potts, Crystal N. Johnson, Benjamin A. Sikes, and William J. Platt

Comparative transcriptomics reveals altered species interaction between the bioeroding sponge Cliona varians and the coral Porites furcata under ocean acidification, Melissa B. DeBiasse, Amber D. Stubler, and Morgan W. Kelly

Displaced clines in an avian hybrid zone (Thamnophilidae: Rhegmatorhina ) within an Amazonian interfluve *, Glaucia Del‐Rio, Marco A. Rego, Bret M. Whitney, Fabio Schunck, Luís F. Silveira, Brant C. Faircloth, and Robb T. Brumfield

Putative Nickel-Dependent Anaerobic Carbon Monoxide Uptake Occurs Commonly in Soils and Sediments at Ambient Temperature and Might Contribute to Atmospheric and Sub-Atmospheric Carbon Monoxide Uptake During Anoxic Conditions, Amber N. DePoy and Gary M. King

Understanding responses to chemical mixtures: looking forward from the past, Charles D. Derby, Timothy S. McClintock, and John Caprio

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The alarming state of freshwater biodiversity in Canada, Jessica E. Desforges, Julia Clarke, Evaline J. Harmsen, Alex M. Jardine, and Jessica A. Robichaud

Phylogeography of Agathistoma (Turbinidae, Tegulinae) snails in tropical and southwestern Atlantic, Ana P. Dornellas, Roberta Graboski, Michael E. Hellberg, and Tito M. C. Lotufo

Field-Based Assessments of Behavioral Patterns During Shiftwork in Police Academy Trainees Using Wearable Technology, Melissa L. Erickson, Will Wang, Julie Counts, Leanne M. Redman, Daniel Parker, Janet L. Huebner, Jessilyn Dunn, and William E. Kraus

Nitric oxide reversibly binds the reduced [2Fe-2S] cluster in mitochondrial outer membrane protein mitoNEET and inhibits its electron transfer activity, Chelsey R. Fontenot, Zishuo Cheng, and Huangen Ding

Ferric uptake regulators (Fur) from Vibrio cholerae and Helicobacter pylori bind a [2Fe–2S] cluster in response to elevation of intracellular free iron content, Chelsey R. Fontenot and Huangen Ding

On the predictability of phenotypic divergence in geographic isolation, Benjamin G. Freeman, Graham A. Montgomery, Julian Heavyside, Andre E. Moncrieff, Oscar Johnson, and Benjamin M. Winger

Neotropical niche evolution of Otoba trees in the context of global biogeography of the nutmeg family, Laura Frost, Daniel A. Santamaría‐Aguilar, Daisy Singletary, and Laura P. Lagomarsino

Helical remodeling augments 5-lipoxygenase activity in the synthesis of proinflammatory mediators, Eden M. Gallegos, Tanner D. Reed, Forge A. Mathes, Nelson V. Guevara, David B. Neau, Wei Huang, Marcia E. Newcomer, and Nathaniel C. Gilbert

Whole-Genome Sequencing and RNA-Seq Reveal Differences in Genetic Mechanism for Flowering Response between Weedy Rice and Cultivated Rice, Richard S. Garcia, Sapphire Coronejo, Jonathan Concepcion, and Prasanta K. Subudhi

Examining the Effects of Induced Plant Defenses on Spodoptera frugiperda Performance, Michael Garvey, Kale Costanza, Scott Grimmell, and Bret Elderd

A Fat-Promoting Botanical Extract From Artemisia Scoparia Exerts Geroprotective Effects On Caenorhabditis Elegans Life Span And Stress Resistance, B Ghosh, H J. Guidry, M Johnston, K A. Bohnert, and B Ghosh

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Phylogenetics of Archerfishes (Toxotidae) and Evolution of the Toxotid Shooting Apparatus, M. G. Girard, M. P. Davis, Tan H.h., D. J. Wedd, P. Chakrabarty, W. B. Ludt, A. P. Summers, and W. L. Smith

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Structure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light reveals the functions of chlorophylls d and f, Christopher J. Gisriel, Gaozhong Shen, Ming-Yang Ho, Vasily Kurashov, and David A. Flesher

Pharmacokinetic profiles of three dose rates of morphine sulfate following single intravenous, intramuscular, and subcutaneous administration in the goat, Emma Gordon, Levent Dirikolu, Chin-Chi Liu, Alexander V. Ulanov, Zhong Li, Matt Welborn, Chance Armstrong, and Danielle Vallotton

Extracytoplasmic Function Sigma Factors Governing Production of the Primary Siderophores in Pathogenic Species, Anne Grove

Structures of Leukotriene Biosynthetic Enzymes and Development of New Therapeutics, Jesper Z. Haeggström and Marcia E. Newcomer

Bison outperform cattle at restoring their home on the range, Kyle E. Harms

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Evolutionary relationships of anglerfishes (Lophiiformes) reconstructed using ultraconserved elements, Pamela B. Hart, Rachel J. Arnold, Fernando Alda, Christopher P. Kenaley, Theodore W. Pietsch, Destinee Hutchinson, and Prosanta Chakrabarty

Transgenerational effects of parental crude oil exposure on the morphology of adult Fundulus grandis, Chelsea Hess, Lauren Little, Charles Brown, Michael Kaller, and Fernando Galvez

Organization of sympathetic innervation of interscapular brown adipose tissue in the mouse, Clara Huesing, Rui Zhang, Sanjeev Gummadi, Nathan Lee, Emily Qualls-Creekmore, Sangho Yu, Christopher D. Morrison, David Burk, Hans Rudolf Berthoud, Winfried Neuhuber, et al.