Biology
Our faculty are interested in a wide range of organisms and research areas. They have received funding from the John Templeton Foundation, the National Institutes of Health, the National Science Foundation, and other prestigious funding agencies and foundations.
Areas of Research include:
- Animal behavior
- Bioinformatics
- Cell biology
- Development
- Ecology
- Evolution
- Genetics
- Marine biology
- Molecular biology
- Molecular evolution/systematics
- Neuroscience
- Physiology
- Population biology
- Signal Transduction
Submissions from 2024
Many-to-many mapping: A simulation study of how the number of traits and tasks affect the evolution of form and function, Philip Bergmann and Isabel Tonelli-Sippel
A genotyping array for the globally invasive vector mosquito, Aedes albopictus, Luciano Veiga Cosme, Margaret Corley, Thomas Johnson, Dave W. Severson, Guiyun Yan, Xiaoming Wang, Nigel Beebe, Andrew Maynard, Mariangela Bonizzoni, Ayda Khorramnejad, Ademir Jesus Martins, José Bento Pereira Lima, and Todd P. Livdahl
The effects of land use change on ant communities in New England, Amelia K.L. Curry, Joseph A. Nelsen, Dale R. Stevens, and Kaitlyn A. Mathis
Transcription factor expression landscape in Drosophila embryonic cell lines, Robert A. Drewell, Daniel Klonaros, and Jacqueline Dresch
The effect of urbanization and temperature on thermal tolerance, foraging performance, and competition in cavity-dwelling ants, Brooke A. Harris, Dale Stevens, and Kaitlyn A. Mathis
Sulfur assimilation using gaseous carbonyl sulfideby the soil fungus Trichoderma harzianum, Ryuka Iizuka, Shohei Hattori, Yusuke Kosaka, Yoshihito Masaki, Yusuke Kawano, Iwao Ohtsu, David Hibbett, Yoko Katayama, and Makoto Yoshida
Are weapon allometries steeper in major or minor males? A meta-analysis, Sydney A. Kochensparger
An exploration of how plant and soil characteristics shape the Hypericum perforatum microbiome in three habitats, Renee H. Petipas, Steven A. Higgins, Chantal Koechli, Spencer J. Davenport, Chandra Jack, Monica A. Geber, and Daniel A. Buckley
Prairie soil improves wheat establishment and accelerates the developmental transition to flowering compared to agricultural soils, Renee H. Petipas, Cassidy Peru, Janice M. Parks, Maren L. Friesen, and Chandra Jack
The role of ant-mediated biological interactions in agroecosystems, Madison Sankovitz, Monique J. Rivera, Tobias Manjarress, and Kaitlyn A. Mathis
Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus, Jacob L. Steenwyck, Charu Balamurugan, Huzefa A. Raja, Carla Gonçalves, Ningxiao Li, Frank Martin, Judith Berman, Nicholas H. Oberlies, John G. Gibbons, Gustavo H. Goldman, David M. Geiser, Jos Houbraken, David Hibbett, and Antonis Rokas
Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria, Lluvia Vargas-Gastélum, Alexander S. Romer, Marjan Ghotbi, Jason W. Dallas, Reed. N. Alexander, Kylie C. Moe, Kerry L. McPhail, George F. Neuhaus, Leila Shadmani, Joseph W. Spatafora, Jason E. Stajich, Javier F. Tabima, and Donald M. Walker
Capitella teleta gets left out: possible evolutionary shift causes loss of left tissues rather than increased neural tissue from dominant-negative BMPR1, Nicole B. Webster and Néva P. Meyer
Population-level immunologic variation in wild threespine stickleback (Gasterosteus aculeatus), Anika M. Wohlleben, Javier F. Tabima, Néva P. Meyer, and Natalie C. Steinel
Submissions from 2023
New tRNA-targeting transposons that hijack phage and vesicles, Emily Dart and Nathan A. Ahlgren
Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics, Emily Dart, Jed A. Fuhrman, and Nathan A. Ahlgren
Investigating the sequence landscape in the Drosophila initiator core promoter element using an enhanced MARZ algorithm, Jacqueline Dresch, Regan D. Conrad, Daniel Klonaros, and Robert Drewell
The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing, Robert Drewell, Tayla C. Cormier, Jacob L. Steenwyk, James St Denis, Javier F. Tabima, Jacqueline Dresch, and Denis A. Larochelle
Vertical habitat stratification in Aedes triseriatus and Aedes hendersoni (Diptera: Culicidae): complications associated with sloped and flood-prone landscapes, Jamie Fitzgerald and Todd P. Livdahl
Transcriptome profile in Drosophila Kc and S2 embryonic cell lines, Daniel Klonaros, Jacqueline M. Dresch, and Robert A. Drewell
Comparative Genomic Analysis of 31 Phytophthora Genomes Reveals Genome Plasticity and Horizontal Gene Transfer, Brent A. Kronmiller, Nicolas Feau, Danyu Shen, Javier F. Tabima, Shahin S. Ali, Andrew D. Armitage, Felipe Arredondo, Bryan A. Bailey, Stephanie R. Bollmann, Angela Dale, Richard J. Harrison, Kelly Hrywkiw, Takao Kasuga, Rebecca McDougal, Charlotte F. Nellist, Preeti Panda, Sucheta Tripathy, Nari M. Williams, Wenwu Ye, Yuanchao Wang, Richard C. Hamelin, and Niklaus Grünwald
Transcriptomics of Temporal- versus Substrate-Specific Wood Decay in the Brown-Rot Fungus Fibroporia radiculosa, Byoungnam Min, Steven Ahrendt, Anna Lipzen, Cristina E. Toapanta, Robert A. Blanchette, Dan Cullen, and David Hibbett
Unraveling the functional dark matter through global metagenomics, Georgios A. Pavlopoulos, Fotis A. Baltoumas, Sirui Liu, Oguz Selvitopi, Antonio Pedro Camargo, Stephen Nayfach, Ariful Azad, Simon Roux, Lee Call, Natalia N. Ivanova, Min I. Chen, David Paez-Espino, Evangelos Karatzas, and Nathan Ahlgren
Behavioral diversity and biomechanical determinants of the outcome of a fish predator–prey interaction, Milton Q.G.A., III and Philip Bergmann
A global phylogenomic analysis of the shiitake genus Lentinula, Sean Sierra-Patev, Byoungnam Min, Miguel Naranjo-Ortiz, Brian Looney, Zachary Konkel, Jason C. Slot, Yuichi Sakamoto, Jacob L. Steenwyk, Antonis Rokas, Juan Carro, Susana Camarero, Patricia Ferreira, Gonzalo Molpeceres, Francisco J. Ruiz-Dueñas, Ana Serrano, Bernard Henrissat, Elodie Drula, Karen W. Hughes, Juan L. Mata, Noemia Kazue Ishikawa, Ruby Vargas-Isla, Shuji Ushijima, Chris A. Smith, John Donoghue, Steven Ahrendt, William Andreopoulos, Guifen He, Kurt LaButti, Anna Lipzen, Vivian Ng, Robert Riley, Laura Sandor, and David Hibbett
Phylogenomics reveals the history of host use in mosquitoes, John Soghigan, Charles Sither, Silvia Andrade Justi, Gen Morinaga, Brian K. Cassel, Christopher J. Vitek, Todd P. Livdahl, Siyang Xia, Andrea Gloria-Soria, Jeffrey R. Powell, Thomas Zavortink, Christopher M. Hardy, Nathan D. Burkett-Cadena, Lawrence E. Reeves, Richard C. Wilkerson, Robert R. Dunn, David K. Yeates, Maria Anice Sallum, Brian D. Byrd, Michelle D. Trautwein, Yvonne-Marie Linton, Michael H. Reiskind, and Brian M. Wiegmann
Rapid New Diagnostic LAMP (Loop-Mediated Isothermal Amplification) Assays to Distinguish Among the Four Lineages of Phytophthora ramorum, Kelsey L. Søndreli, Javier F. Tabima Restrepo, and Jared M. LeBoldus
Evolution of chemical-cue-mediated antipredator behavior in threespine stickleback populations experiencing northern pike predation, Dale R. Stevens, Melissa A. Graham, Christina I. Bardjis, Susan A. Foster, John A. Baker, and Kaitlyn A. Mathis
Integrating environmental complexity and the plasticity-first hypothesis to study responses to human-altered habitats, Dale R. Stevens, Matthew Wund, and Kaitlyn B. Mathis
Multiple measures of structural racism as predictors of U.S. county-level COVID-19 cases and deaths, Rosalie A. Torres Stone, Nathan A. Ahlgren, and Philip J. Bergmann
Editorial: MorphoEvoDevo: a multilevel approach to elucidate the evolution of metazoan organ systems, Andreas Wanninger, Pedro Martinez, and Néva P. Meyer
Submissions from 2022
County-level societal predictors of COVID-19 cases and deaths changed through time in the United States: A longitudinal ecological study, Philip J. Bergmann, Nathan A. Ahlgren, and Rosalie A. Torres Stone
Performance and Kinematic Differences Between Terrestrial and Aquatic Running in Anolis Sagrei, Amy Y. Cheu, Samantha A. Reed, Sara D. Mann, and Philip J. Bergmann
Coordinating tiny limbs and long bodies: Geometric mechanics of lizard terrestrial swimming, Baxi Chong, Tianyu Wang, Eva Erickson, Philip J. Bergmann, and Daniel I. Goldman
Evolutionary transition to the ectomycorrhizal habit in the genomes of a hyperdiverse lineage of mushroom-forming fungi, Brian Looney, Shingo Miyauchi, Emmanuelle Morin, Elodie Drula, Pierre Emmanuel Courty, Annegret Kohler, Alan Kuo, Kurt LaButti, Jasmyn Pangilinan, Anna Lipzen, Robert Riley, William Andreopoulos, Guifen He, Jenifer Johnson, Matt Nolan, Andrew Tritt, Kerrie W. Barry, Igor V. Grigoriev, László G. Nagy, David Hibbett, Bernard Henrissat, P. Brandon Matheny, Jesse Labbé, and Francis M. Martin
Genome Sequence of the Estuarine Synechococcus sp. Strain NB0720_010, Campbell A. MacKenzie, Marcia F. Marston, Javier F. Tabima, and Nathan A. Ahlgren
Global phylogeny of the Shiitake mushroom and related Lentinula species uncovers novel diversity and suggests an origin in the Neotropics, Nelson Menolli, Santiago Sánchez-Ramírez, Marisol Sánchez-García, Chaoqun Wang, Sean Patev, Noemia Kazue Ishikawa, Juan L. Mata, Alexandre Rafael Lenz, Ruby Vargas-Isla, Lauren Liderman, Meriel Lamb, Mitchell Nuhn, Karen W. Hughes, Yang Xiao, and David S. Hibbett
Proteome of the Wood Decay Fungus Fomitopsis pinicola Is Altered by Substrate, Grzegorz Sabat, Steven Ahrendt, Baojun Wu, Jill Gaskell, Benjamin W. Held, Cristina Toapanta, Thu V. Vuong, Anna Lipzen, Jiwei Zhang, Jonathan S. Schilling, Emma Master, Igor V. Grigoriev, Robert A. Blanchette, David S. Hibbett, Jennifer Bhatnagar, and Daniel Cullen
Evolutionary Morphogenesis of Sexual Fruiting Bodies in Basidiomycota: Toward a New Evo-Devo Synthesis, Máté Virágh, Zsolt Merényi, Árpád Csernetics, Csenge Földi, Neha Sahu, Xiao Bin Liu, David S. Hibbett, and László G. Nagy
Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes, Jingcheng Zhang, Nan Shen, Chuang Li, Xingjie Xiang, Gaolei Liu, Ying Gui, Sean Patev, David S. Hibbett, Kerrie Barry, William Andreopoulos, Anna Lipzen, Robert Riley, Guifen He, Mi Yan, Igor V. Grigoriev, Hoi Shan Kwan, Man Kit Cheung, Yinbing Bian, and Yang Xiao
Submissions from 2021
How head shape and substrate particle size affect fossorial locomotion in lizards, Philip J. Bergmann and David S. Berry
Fitting thermodynamic-based models: Incorporating parameter sensitivity improves the performance of an evolutionary algorithm, Michael J. Gaiewski, Rob Drewell, and Jacqueline M. Dresch
Linking ecomechanical models and functional traits to understand phenotypic diversity, Timothy E. Higham, Lara A. Ferry, Lars Schmitz, Duncan J. Irschick, Samuel Starko, Philip S.L. Anderson, Philip J. Bergmann, Heather A. Jamniczky, Leandro R. Monteiro, Dina Navon, Julie Messier, Emily Carrington, Stacy C. Farina, Kara L. Feilich, L. Patricia Hernandez, Michele A. Johnson, Sandy M. Kawano, Chris J. Law, Sarah J. Longo, Christopher H. Martin, Patrick T. Martone, Alejandro Rico-Guevara, Sharlene E. Santana, and Karl J. Niklas
Lentinula madagasikarensis sp. nov., a relative of shiitake mushrooms from Madagascar, B. P. Looney, B. Buyck, N. Menolli, E. Randrianjohany, and D. Hibbett
Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase Diversity, Francisco J. Ruiz-Dueñas, José M. Barrasa, Marisol Sánchez-García, Susana Camarero, Shingo Miyauchi, Ana Serrano, Dolores Linde, Rashid Babiker, Elodie Drula, Iván Ayuso-Fernández, Remedios Pacheco, Guillermo Padilla, Patricia Ferreira, Jorge Barriuso, Harald Kellner, Raúl Castanera, Manuel Alfaro, Lucía Ramírez, Antonio G. Pisabarro, Robert Riley, Alan Kuo, William Andreopoulos, Kurt Labutti, Jasmyn Pangilinan, Andrew Tritt, Anna Lipzen, Guifen He, Mi Yan, Vivian Ng, Igor V. Grigoriev, Daniel Cullen, Francis Martin, and David Hibbett
Niche partitioning of low-light adapted Prochlorococcus subecotypes across oceanographic gradients of the North Pacific Subtropical Front, Anne W. Thompson, Kathleen Kouba, and Nathan A. Ahlgren
Submissions from 2020
Genomic mosaicism underlies the adaptation of marine Synechococcus ecotypes to distinct oceanic iron niches, Nathan A. Ahlgren, Bernard Shafer Belisle, and Michael D. Lee
Genome sequences of synechococcus sp. Strain MIT S9220 and cocultured cyanophage SynMITS9220M01, B. Shafer Belisle, Andres A.Avila Paz, Angelina R. Carpenter, Tayla C. Cormier, Adam J. Lewis, Linnea S. Menin, Daniel R. Oliveira, Bukyung Song, Amy Szeto, Elizabeth I. Tchantouridze, Kayleigh A. Watson, Mary T. Yohannes, and Nathan A. Ahlgren
Convergent evolution of elongate forms in craniates and of locomotion in elongate squamate reptiles, Philip J. Bergmann, Sara D.W. Mann, Gen Morinaga, Elyse S. Freitas, and Cameron D. Siler
Locomotion and palaeoclimate explain the re-evolution of quadrupedal body form in Brachymeles lizards, Philip J. Bergmann, Gen Morinaga, Elyse S. Freitas, Duncan J. Irschick, Günter P. Wagner, and Cameron D. Siler
Using 3D-digital photogrammetry to examine scaling of the body axis in burrowing skinks, Leah DeLorenzo, Abby Vander Linden, Philip J. Bergmann, Gunter P. Wagner, Cameron D. Siler, and Duncan J. Irschick
Genetic tool development in marine protists: emerging model organisms for experimental cell biology, Drahomíra Faktorová, R. Ellen R. Nisbet, José A. Fernández Robledo, Elena Casacuberta, Lisa Sudek, Andrew E. Allen, Manuel Ares, Cristina Aresté, Cecilia Balestreri, Adrian C. Barbrook, Patrick Beardslee, Sara Bender, David S. Booth, François Yves Bouget, Chris Bowler, Susana A. Breglia, Colin Brownlee, Gertraud Burger, Heriberto Cerutti, Rachele Cesaroni, Miguel A. Chiurillo, Thomas Clemente, Duncan B. Coles, Jackie L. Collier, Elizabeth C. Cooney, Kathryn Coyne, Roberto Docampo, Christopher L. Dupont, Virginia Edgcomb, Elin Einarsson, Pía A. Elustondo, and Deborah Robertson
Long-term stability and Red Queen-like strain dynamics in marine viruses, J. Cesar Ignacio-Espinoza, Nathan A. Ahlgren, and Jed A. Fuhrman
Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits, Shingo Miyauchi, Enikő Kiss, Alan Kuo, Elodie Drula, Annegret Kohler, Marisol Sánchez-García, Emmanuelle Morin, Bill Andreopoulos, Kerrie W. Barry, Gregory Bonito, Marc Buée, Akiko Carver, Cindy Chen, Nicolas Cichocki, Alicia Clum, David Culley, Pedro W. Crous, Laure Fauchery, Mariangela Girlanda, Richard D. Hayes, Zsófia Kéri, Kurt LaButti, Anna Lipzen, Vincent Lombard, Jon Magnuson, François Maillard, Claude Murat, Matt Nolan, Robin A. Ohm, Jasmyn Pangilinan, Maíra de Freitas Pereira, Silvia Perotto, and David Hibbett
Evolution of fossorial locomotion in the transition from tetrapod to snake-like in lizards, Gen Morinaga and Philip J. Bergmann
Identifying viruses from metagenomic data using deep learning, Jie Ren, Kai Song, Chao Deng, Nathan A. Ahlgren, Jed A. Fuhrman, Yi Li, Xiaohui Xie, Ryan Poplin, and Fengzhu Sun
Fruiting body form, not nutritional mode, is the major driver of diversification in mushroom-forming fungi, Marisol Sánchez-García, Martin Ryberg, Faheema Kalsoom Khan, Torda Varga, László G. Nagy, and David S. Hibbett
Investigating cellular and molecular mechanisms of neurogenesis in Capitella teleta sheds light on the ancestor of Annelida, A. Sur, A. Renfro, P. J. Bergmann, and N. P. Meyer
A network-based integrated framework for predicting virus–prokaryote interactions, Weili Wang, Jie Ren, Kujin Tang, Emily Dart, Julio Cesar Ignacio-Espinoza, Jed A. Fuhrman, Jonathan Braun, Fengzhu Sun, and Nathan A. Ahlgren
Fungal functional ecology: bringing a trait-based approach to plant-associated fungi, Amy E. Zanne, Kessy Abarenkov, Michelle E. Afkhami, Carlos A. Aguilar-Trigueros, Scott Bates, Jennifer M. Bhatnagar, Posy E. Busby, Natalie Christian, William K. Cornwell, Thomas W. Crowther, Habacuc Flores-Moreno, Dimitrios Floudas, Romina Gazis, David Hibbett, Peter Kennedy, Daniel L. Lindner, Daniel S. Maynard, Amy M. Milo, Rolf Henrik Nilsson, Jeff Powell, Mark Schildhauer, Jonathan Schilling, and Kathleen K. Treseder
Submissions from 2019
Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes, Nathan A. Ahlgren, Clara A. Fuchsman, Gabrielle Rocap, and Jed A. Fuhrman
Multi-year dynamics of fine-scale marine cyanobacterial populations are more strongly explained by phage interactions than abiotic, bottom-up factors, Nathan A. Ahlgren, Jessica N. Perelman, Yi Chun Yeh, and Jed A. Fuhrman
The convergent evolution of snake-like forms by divergent evolutionary pathways in squamate reptiles*, Philip J. Bergmann and Gen Morinaga
Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi, Krisztina Krizsán, Éva Almási, Zsolt Merényi, Neha Sahu, Máté Virágh, Tamás Kószó, Stephen Mondo, Brigitta Kiss, Balázs Bálint, Ursula Kües, Kerrie Barry, Judit Cseklye, Botond Hegedüs, Bernard Henrissat, Jenifer Johnson, Anna Lipzen, Robin A. Ohm, István Nagy, Jasmyn Pangilinan, Juying Yan, Yi Xiong, Igor V. Grigoriev, David S. Hibbett, and László G. Nagy
Marine Synechococcus isolates representing globally abundant genomic lineages demonstrate a unique evolutionary path of genome reduction without a decrease in GC content, Michael D. Lee, Nathan A. Ahlgren, Joshua D. Kling, Nathan G. Walworth, Gabrielle Rocap, Mak A. Saito, David A. Hutchins, and Eric A. Webb
Analyzing the stability of gene expression using a simple reaction-diffusion model in an early Drosophila embryo, Gregory D. McCarthy, Robert A. Drewell, and Jacqueline M. Dresch
Angles and waves: intervertebral joint angles and axial kinematics of limbed lizards, limbless lizards, and snakes, Gen Morinaga and Philip J. Bergmann
Rapid and efficient purification of Drosophila homeodomain transcription factors for biophysical characterization, Rachel Orlomoski, Aaron Bogle, Jeanmarie Loss, Rylee Simons, Jacqueline M. Dresch, Robert A. Drewell, and Donald E. Spratt
Optimizing de novo genome assembly from PCR-amplified metagenomes, Simon Roux, Gareth Trubl, Danielle Goudeau, Nandita Nath, Estelle Couradeau, Nathan A. Ahlgren, Yuanchao Zhan, David Marsan, Feng Chen, Jed A. Fuhrman, Trent R. Northen, Matthew B. Sullivan, Virginia I. Rich, Rex R. Malmstrom, and Emiley A. Eloe-Fadrosh
Megaphylogeny resolves global patterns of mushroom evolution, Torda Varga, Krisztina Krizsán, Csenge Földi, Bálint Dima, Marisol Sánchez-García, Santiago Sánchez-Ramírez, Gergely J. Szöllősi, János G. Szarkándi, Viktor Papp, László Albert, William Andreopoulos, Claudio Angelini, Vladimír Antonín, Kerrie W. Barry, Neale L. Bougher, Peter Buchanan, Bart Buyck, Viktória Bense, Pam Catcheside, Mansi Chovatia, Jerry Cooper, Wolfgang Dämon, Dennis Desjardin, Péter Finy, József Geml, Sajeet Haridas, Karen Hughes, Alfredo Justo, Dariusz Karasiński, Ivona Kautmanova, Brigitta Kiss, Sándor Kocsubé, and David Hibbett
Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi, Baojun Wu, Jill Gaskell, Jiwei Zhang, Christina Toapanta, Steven Ahrendt, Igor V. Grigoriev, Robert A. Blanchette, Jonathan S. Schilling, Emma Master, Daniel Cullen, and David S. Hibbett
Submissions from 2018
Phylogenetic taxon definitions for Fungi, Dikarya, Ascomycota and Basidiomycota, David S. Hibbett, Meredith Blackwell, Timothy Y. James, Joseph W. Spatafora, John W. Taylor, and Rytas Vilgalys
Evolutionary dynamics of host specialization in wood-decay fungi, Franz Sebastian Krah, Claus Bässler, Christoph Heibl, John Soghigian, Hanno Schaefer, and David S. Hibbett
Contemporaneous radiations of fungi and plants linked to symbiosis, François Lutzoni, Michael D. Nowak, Michael E. Alfaro, Valérie Reeb, Jolanta Miadlikowska, Michael Krug, A. Elizabeth Arnold, Louise A. Lewis, David L. Swofford, David Hibbett, Khidir Hilu, Timothy Y. James, Dietmar Quandt, and Susana Magallón
Proposals for consideration at IMC11 to modify provisions related solely to fungi in the International Code of Nomenclature for algae, fungi, and plants, Luis A. Parra, Juan C. Zamora, David L. Hawksworth, David S. Hibbett, Paul M. Kirk, Robert Lücking, Gerhard Rambold, Konstanze Bensch, Yi Jian Yao, Vincent Robert, and Dagmar Triebel
Dynamics of Prochlorococcus Diversity and Photoacclimation During Short-Term Shifts in Water Column Stratification at Station ALOHA, Anne W. Thompson, Ger van den Engh, Nathan A. Ahlgren, Kathleen Kouba, Samantha Ward, Samuel T. Wilson, and David M. Karl
Are there general laws for digit evolution in squamates? The loss and re-evolution of digits in a clade of fossorial lizards (Brachymeles, Scincinae), Günter P. Wagner, Oliver W. Griffith, Philip J. Bergmann, Gaelle Bello-Hellegouarch, Tiana Kohlsdorf, Anjan Bhullar, and Cameron D. Siler
Substrate-specific differential gene expression and RNA editing in the brown rot fungus Fomitopsis pinicola, Baojun Wu, Jill Gaskell, Benjamin W. Held, Cristina Toapanta, Thu Vuong, Steven Ahrendt, Anna Lipzen, Jiwei Zhang, Jonathan S. Schilling, Emma Master, Igor V. Grigoriev, Robert A. Blanchette, Dan Cullen, and David S. Hibbett
Genomics and development of Lentinus tigrinus: A white-rot wood-decaying mushroom with dimorphic fruiting bodies, Baojun Wu, Zhangyi Xu, Alicia Knudson, Alexis Carlson, Naiyao Chen, Sam Kovaka, Kurt LaButti, Anna Lipzen, Christa Pennachio, Robert Riley, Wendy Schakwitz, Kiwamu Umezawa, Robin A. Ohm, Igor V. Grigoriev, Laszlo G. Nagy, John Gibbons, and David Hibbett
Submissions from 2017
Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems, Nathan A. Ahlgren, Yangyang Chen, David M. Needham, Alma E. Parada, Rohan Sachdeva, Vickie Trinh, Ting Chen, and Jed A. Fuhrman
Alignment-free d2∗ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences, Nathan A. Ahlgren, Jie Ren, Yang Young Lu, Jed A. Fuhrman, and Fengzhu Sun
It’s just sand between the toes: How particle size and shape variation affect running performance and kinematics in a generalist lizard, Philip J. Bergmann, Kyle J. Pettinelli, Marian E. Crockett, and Erika G. Schaper
Mycophagous rove beetles highlight diverse mushrooms in the Cretaceous, Chenyang Cai, Richard A.B. Leschen, David S. Hibbett, Fangyuan Xia, and Diying Huang
The folded k-spectrum kernel: A machine learning approach to detecting transcription factor binding sites with gapped nucleotide dependencies, Abdulkadir Elmas, Xiaodong Wang, and Jacqueline M. Dresch
Draft genome sequence of a monokaryotic model brown-rot fungus Postia (Rhodonia) placenta SB12, Jill Gaskell, Phil Kersten, Luis F. Larrondo, Paulo Canessa, Diego Martinez, David Hibbett, Monika Schmoll, Christian P. Kubicek, Angel T. Martinez, Jagjit Yadav, Emma Master, Jon Karl Magnuson, Debbie Yaver, Randy Berka, Kathleen Lail, Cindy Chen, Kurt LaButti, Matt Nolan, Anna Lipzen, Andrea Aerts, Robert Riley, Kerrie Barry, Bernard Henrissat, Robert Blanchette, Igor V. Grigoriev, and Dan Cullen
A revised family-level classification of the Polyporales (Basidiomycota), Alfredo Justo, Otto Miettinen, Dimitrios Floudas, Beatriz Ortiz-Santana, Elisabet Sjökvist, Daniel Lindner, Karen Nakasone, Tuomo Niemelä, Karl Henrik Larsson, Leif Ryvarden, and David S. Hibbett
Convergent body shapes have evolved via deterministic and historically contingent pathways in Lerista lizards, Gen Morinaga and Philip J. Bergmann
Genetic bases of fungal white rot wood decay predicted by phylogenomic analysis of correlated gene-phenotype evolution, Laszlo G. Nagy, Robert Riley, Philip J. Bergmann, Krisztina Krizsan, Francis M. Martin, Igor V. Grigoriev, Dan Cullen, and David Hibbett
Do the shuffle: Changes in Symbiodinium consortia throughout juvenile coral development, Hannah G. Reich, Deborah L. Robertson, and Gretchen Goodbody-Gringley
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data, Jie Ren, Nathan A. Ahlgren, Yang Young Lu, Jed A. Fuhrman, and Fengzhu Sun
Prediction of virus-host infectious association by supervised learning methods, Mengge Zhang, Lianping Yang, Jie Ren, Nathan A. Ahlgren, Jed A. Fuhrman, and Fengzhu Sun
Submissions from 2016
Nucleotide interdependency in transcription factor binding sites in the drosophila genome, Jacqueline M. Dresch, Rowan G. Zellers, Daniel K. Bork, and Robert A. Drewell
The genome of Xylona heveae provides a window into fungal endophytism, Romina Gazis, Alan Kuo, Robert Riley, Kurt LaButti, Anna Lipzen, Junyan Lin, Mojgan Amirebrahimi, Cedar N. Hesse, Joseph W. Spatafora, Bernard Henrissat, Matthieu Hainaut, Igor V. Grigoriev, and David S. Hibbett
The invisible dimension of fungal diversity, David Hibbett
Sequence-based classification and identification of Fungi, David Hibbett, Kessy Abarenkov, Urmas Kõljalg, Maarja Öpik, Benli Chai, James Cole, Qiong Wang, Pedro Crous, Vincent Robert, Thorunn Helgason, Joshua R. Herr, Paul Kirk, Shiloh Lueschow, Kerry O’Donnell, R. Henrik Nilsson, Ryoko Oono, Conrad Schoch, Christopher Smyth, Donald M. Walker, Andrea Porras-Alfaro, John W. Taylor, and David M. Geiser
Climate, decay, and the death of the coal forests, David Hibbett, Robert Blanchette, Paul Kenrick, and Benjamin Mills
Unearthing the roots of ectomycorrhizal symbioses, Francis Martin, Annegret Kohler, Claude Murat, Claire Veneault-Fourrey, and David S. Hibbett
Draft genome sequence of the white-rot fungus Obba rivulosa 3A-2, Otto Miettinen, Robert Riley, Kerrie Barry, Dan Cullen, Ronald P. de Vries, Matthieu Hainaut, Annele Hatakka, Bernard Henrissat, Kristiina Hildén, Rita Kuo, Kurt LaButti, Anna Lipzen, Miia R. Mäkelä, Laura Sandor, Joseph W. Spatafora, Igor V. Grigoriev, and David S. Hibbett
Polypores and genus concepts in Phanerochaetaceae (Polyporales, Basidiomycota), Otto Miettinen, Viacheslav Spirin, Josef Vlasák, Bernard Rivoire, Soili Stenroos, and David S. Hibbett
Thermal and moisture habitat preferences do not maximize jumping performance in frogs, Allegra Mitchell and Philip J. Bergmann
