Ecosyste.ms: Papers

10.1016/j.cell.2019.07.038

A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana
Cited by: 237
Author(s): Anna-Lena Van de Weyer, Freddy Monteiro, Oliver J. Furzer, Marc T. Nishimura, Volkan Çevik, Kamil Witek, Jonathan D. G. Jones, Jeffery L. Dangl, Detlef Weigel, Felix Bemm
Software Mentions: 23
Published: over 5 years ago

10.1016/j.cub.2020.12.047

A sex-specific switch between visual and olfactory inputs underlies adaptive sex differences in behavior
Cited by: 32
Author(s): Tetsuya Nojima, Annika Rings, Annette D. Allen, Nils Otto, Thomas A. Verschut, Jean‐Christophe Billeter, Megan C Neville, Stephen F. Goodwin
Software Mentions: 19
Published: almost 4 years ago

10.3389/fimmu.2017.00445

Integration of Immune Cell Populations, mRNA-Seq, and CpG Methylation to Better Predict Humoral Immunity to Influenza Vaccination: Dependence of mRNA-Seq/CpG Methylation on Immune Cell Populations
Cited by: 15
Author(s): Michael T. Zimmermann, Richard B. Kennedy, Diane E. Grill, Ann L. Oberg, Krista M. Goergen, Inna G. Ovsyannikova, Iana H. Haralambieva, Gregory A. Poland
Software Mentions: 16
Published: over 7 years ago

10.1371/journal.pgen.1009110

Unique genetic signatures of local adaptation over space and time for diapause, an ecologically relevant complex trait, in Drosophila melanogaster
Cited by: 45
Author(s): Priscilla A. Erickson, Cory A. Weller, Daniel Song, Alyssa Bangerter, Paul S. Schmidt, Alan O. Bergland
Software Mentions: 15
Published: about 4 years ago

10.1371/journal.pone.0240935

The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome
Cited by: 24
Author(s): Kris A. Christensen, Eric B. Rondeau, David R. Minkley, Dionne Sakhrani, Carlo A. Biagi, Anne-Marie Flores, Ruth E. Withler, Scott A. Pavey, Terry D. Beacham, Theresa Godin, Eric B. Taylor, Michael A. Russello, Robert H. Devlin, Ben F. Koop
Software Mentions: 15
Published: about 4 years ago

10.1038/srep42130

Dissecting the brown adipogenic regulatory network using integrative genomics
Cited by: 20
Author(s): Rachana Pradhan, Johannes Bues, Vincent Gardeux, Petra Schwalie, Daniel Alpern, Wanze Chen, Julie Russeil, Sunil K. Raghav, Bart Deplancke
Software Mentions: 13
Published: almost 8 years ago

10.1186/s13227-020-0147-0

Elongation during segmentation shows axial variability, low mitotic rates, and synchronized cell cycle domains in the crustacean, Thamnocephalus platyurus
Cited by: 9
Author(s): Savvas J. Constantinou, Nicole Duan, Lisa M. Nagy, Ariel D. Chipman, Terri A. Williams
Software Mentions: 13
Published: almost 5 years ago

10.1186/s12859-016-1457-z

Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq
Cited by: 55
Author(s): Claire Williams, Alyssa Baccarella, Jay Z. Parrish, Charles C. Kim
Software Mentions: 13
Published: almost 8 years ago

10.1371/journal.pone.0193437

Delineating modern variation from extinct morphology in the fossil record using shells of the Eastern Box Turtle (Terrapene carolina)
Cited by: 8
Author(s): Natasha Vitek
Software Mentions: 13
Published: almost 7 years ago

10.1111/eva.12965

Relative genomic impacts of translocation history, hatchery practices, and farm selection in Pacific oyster <i>Crassostrea gigas</i> throughout the Northern Hemisphere
Cited by: 11
Author(s): Ben J. G. Sutherland, Claire Rycroft, Anne‐Laure Ferchaud, Rob Saunders, Li Li, Sheng Liu, Amy M. Chan, Sarah P. Otto, Curtis A. Suttle, Kristina M. Miller
Software Mentions: 13
Published: over 4 years ago

10.1186/s13059-021-02293-3

Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells
Cited by: 47
Author(s): Drew Neavin, Quan Nguyen, Maciej Daniszewski, Helena Liang, Han Sheng Chiu, Yong Kiat Wee, Anne Senabouth, Samuel W. Lukowski, Duncan E. Crombie, Grace E. Lidgerwood, Damián Hernández, James C. Vickers, Anthony Cook, Nathan J. Palpant, Alice Pébay, Alex W. Hewitt, Joseph E. Powell
Software Mentions: 12
Published: almost 4 years ago

10.1186/s42523-020-00066-0

Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary
Cited by: 16
Author(s): Rebecca J. Stevick, Anton F. Post, Marta Gómez-Chiarri
Software Mentions: 11
Published: almost 4 years ago

10.1111/tpj.14784

Segmental duplications are hot spots of copy number variants affecting barley gene content
Cited by: 4
Author(s): Gianluca Bretani, Laura Rossini, Chiara Ferrandi, Joanne Russell, Robbie Waugh, Benjamin Kilian, Paolo Bagnaresi, Luigi Cattivelli, Agostino Fricano
Software Mentions: 11
Published: over 4 years ago

10.1111/mec.13636

Escape from the cryptic species trap: lichen evolution on both sides of a cyanobacterial acquisition event
Cited by: 34
Author(s): Kevin Schneider, Philipp Resl, Toby Spribille
Software Mentions: 11
Published: over 8 years ago

10.1038/s41598-020-71663-x

Discovering the indigenous microbial communities associated with the natural fermentation of sap from the cider gum Eucalyptus gunnii
Cited by: 12
Author(s): Cristián Varela, Joanna F. Sundstrom, Kathleen Cuijvers, Vladimir Jiranek, Anthony R. Borneman
Software Mentions: 10
Published: over 4 years ago

10.1038/s41598-020-64095-0

Snapshots of human anatomy, locomotion, and behavior from Late Pleistocene footprints at Engare Sero, Tanzania
Cited by: 17
Author(s): Kevin G. Hatala, William E. H. Harcourt‐Smith, Adam D. Gordon, Brian W. Zimmer, Brian G. Richmond, Briana Pobiner, David J. Green, Adam Metallo, Vince Rossi, Cynthia M. Liutkus-Pierce
Software Mentions: 10
Published: over 4 years ago

10.15252/msb.202010108

Joint cell segmentation and cell type annotation for spatial transcriptomics
Cited by: 40
Author(s): Russell Littman, Zachary Hemminger, Robert T. Foreman, Douglas Arneson, Guanglin Zhang, Fernando Gómez‐Pinilla, Xia Yang, Roy Wollman
Software Mentions: 10
Published: over 3 years ago

10.7717/peerj.10118

High-throughput analysis of adaptation using barcoded strains of<i>Saccharomyces cerevisiae</i>
Cited by: 8
Author(s): Vincent J. Fasanello, Ping Liu, Carlos A. Botero, Justin C. Fay
Software Mentions: 10
Published: about 4 years ago

10.1186/s40425-018-0422-y

33rd Annual Meeting &amp; Pre-Conference Programs of the Society for Immunotherapy of Cancer (SITC 2018)
Cited by: 36
Author(s):
Software Mentions: 9
Published: about 6 years ago

10.1523/ENEURO.0065-21.2021

Expertise Modulates Neural Stimulus-Tracking
Cited by: 0
Author(s): Geoffrey Brookshire, Heather Harden Mangelsdorf, Clara Sava-Segal, Katherine Reis, Howard C. Nusbaum, Susan Goldin‐Meadow, Daniel Casasanto
Software Mentions: 9
Published: over 3 years ago

10.3389/fmed.2021.640515

Performance of Different Diagnostic PD-L1 Clones in Head and Neck Squamous Cell Carcinoma
Cited by: 13
Author(s): Julika Ribbat‐Idel, Frederick A. Dressler, Rosemarie Krupar, Christian Watermann, F. Paulsen, Patrick Kuppler, Luise Klapper, Anne Offermann, Barbara Wollenberg, Dirk Rades, Simon Laban, Markus Reischl, Karl‐Ludwig Bruchhage, Christian Idel, Sven Perner
Software Mentions: 9
Published: over 3 years ago

10.1186/s13059-020-02141-w

Improved reference genome of the arboviral vector Aedes albopictus
Cited by: 61
Author(s): Umberto Palatini, Reem A. Masri, Luciano V. Cosme, Sergey Koren, Françoise Thibaud‐Nissen, James K. Biedler, Flávia Krsticevic, J. Spencer Johnston, Rebecca Halbach, Jacob E. Crawford, Igor Antoshechkin, Anna‐Bella Failloux, Elisa Pischedda, Michele Marconcini, Jay Ghurye, Arang Rhie, Atashi Sharma, Д. А. Карагодин, James Jenrette, Stephanie Gamez, Pascal Miesen, Patrick Masterson, Adalgisa Caccone, Maria V. Sharakhova, Zhijian Tu, Philippos Aris Papathanos, Ronald P. van Rij, Omar S. Akbari, Jeffrey R. Powell, Adam M. Phillippy, Mariangela Bonizzoni
Software Mentions: 9
Published: over 4 years ago

10.7554/eLife.50004

Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas
Cited by: 15
Author(s): A.B. Hickman, Shweta Kailasan, Pavol Genzor, Astrid D. Haase, Fred Dyda
Software Mentions: 9
Published: almost 5 years ago

10.3389/fmicb.2020.01987

Development and Analysis of a Stable, Reduced Complexity Model Soil Microbiome
Cited by: 15
Author(s): Ryan McClure, Dan Naylor, Yuliya Farris, Michelle Davison, Sarah Fansler, Kirsten Hofmockel, Janet K. Jansson
Software Mentions: 8
Published: over 4 years ago

10.1016/j.molcel.2021.03.041

DNAJC9 integrates heat shock molecular chaperones into the histone chaperone network
Cited by: 28
Author(s): Colin M. Hammond, Hongyu Bao, Ivo A. Hendriks, Massimo Carraro, Alberto García-Nieto, Yanhong Liu, Nazaret Reverón-Gómez, Christos Spanos, Liu Chen, Juri Rappsilber, Michael L. Nielsen, Dinshaw J. Patel, Hongda Huang, Anja Groth
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pone.0051609

Comparative Transcriptome Profiling of the Early Response to Magnaporthe oryzae in Durable Resistant vs Susceptible Rice (Oryza sativa L.) Genotypes
Cited by: 129
Author(s): Paolo Bagnaresi, Chiara Biselli, Luigi Orrù, Simona Urso, Laura Crispino, Pamela Abbruscato, Pietro Piffanelli, Elisabetta Lupotto, Luigi Cattivelli, Giampiero Valè
Software Mentions: 8
Published: about 12 years ago

10.7554/eLife.42448

Respiratory syncytial virus co-opts host mitochondrial function to favour infectious virus production
Cited by: 40
Author(s): Mengjie Hu, Keith E. Schulze, Reena Ghildyal, Darren C. Henstridge, Jacek L. Kolanowski, Elizabeth J. New, Yuning Hong, Alan Hsu, Philip M. Hansbro, Peter Wark, Marie A. Bogoyevitch, David A. Jans
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0246052

Transcriptomic profiling of susceptible and resistant flax seedlings after Fusarium oxysporum lini infection
Cited by: 10
Author(s): Aleksandra Boba, Kamil Kostyń, Bartosz Kozak, Iwan Zalewski, Jan Szopa, Anna Kulma
Software Mentions: 8
Published: almost 4 years ago

10.1186/s40168-017-0339-6

Metagenomic characterization of ambulances across the USA
Cited by: 29
Author(s): Niamh B. O’Hara, Harry J. Reed, Ebrahim Afshinnekoo, Donell Harvin, Nora Caplan, Gail Rosen, Brook Frye, Stephen Woloszynek, Rachid Ounit, Shawn Levy, Erin Butler, Christopher E. Mason
Software Mentions: 8
Published: about 7 years ago

10.3390/biomedicines9091253

Alterations in Circulating Monocytes Predict COVID-19 Severity and Include Chromatin Modifications Still Detectable Six Months after Recovery
Cited by: 24
Author(s): Alberto Utrero‐Rico, Cecilia González-Cuadrado, Marta Chivite-Lacaba, Óscar Cabrera-Marante, Rocío Laguna‐Goya, Patricia Almendro-Vázquez, Carmen Díaz-Pedroche, María Ruiz-Ruigómez, Antonio Lalueza, María Dolores Folgueira, Enrique Vázquez, Ana Quintas, Marcos J. Berges-Buxeda, Moisés Martín-Rodriguez, Ana Dopazo, Antonio Serrano-Hernández, Estela Paz‐Artal, Estela Paz‐Artal
Software Mentions: 8
Published: over 3 years ago

10.1534/g3.119.400373

isqg: A Binary Framework for<i>in Silico</i>Quantitative Genetics
Cited by: 1
Author(s): Fernando H. Toledo, Paulino Pérez‐Rodríguez, J. Crossa, Juan Burgueño
Software Mentions: 8
Published: over 5 years ago

10.1111/2041-210X.12490

hext , a software supporting tree‐based screens for hybrid taxa in multilocus data sets, and an evaluation of the homoplasy excess test
Cited by: 4
Author(s): Kevin Schneider, Stephan Koblmüller, Kristina M. Sefc
Software Mentions: 8
Published: about 9 years ago

10.1186/s40168-018-0468-6

Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate
Cited by: 44
Author(s): Pål Trosvik, Eric J. de Muinck, Eli Knispel Rueness, Peter J. Fashing, Evan C. Beierschmitt, Kadie R. Callingham, Jacob B. Kraus, Thomas H. Trew, Amera Moges, Addisu Mekonnen, Vivek V. Venkataraman, Nga Nguyen
Software Mentions: 8
Published: over 6 years ago

10.3389/fpls.2018.01632

Integrated QTL and eQTL Mapping Provides Insights and Candidate Genes for Fatty Acid Composition, Flowering Time, and Growth Traits in a F2 Population of a Novel Synthetic Allopolyploid Brassica napus
Cited by: 22
Author(s): Ruijuan Li, Kwangju Jeong, John Davis, Seungmo Kim, Soonbong Lee, Richard W. Michelmore, Shinje Kim, Julin Maloof
Software Mentions: 8
Published: about 6 years ago

10.1099/mgen.0.000174

The complete replicons of 16 Ensifer meliloti strains offer insights into intra- and inter-replicon gene transfer, transposon-associated loci, and repeat elements
Cited by: 19
Author(s): Matthew S. Nelson, Joseph Guhlin, Brendan Epstein, Peter Tiffin, Michael J. Sadowsky
Software Mentions: 8
Published: over 6 years ago

10.7717/peerj.8522

Detection and characterization of microRNA expression profiling and its target genes in response to canine parvovirus in Crandell Reese Feline Kidney cells
Cited by: 8
Author(s): Phongsakorn Chuammitri, Soulasack Vannamahaxay, Benjaporn Sornpet, Kidsadagon Pringproa, Prapas Patchanee
Software Mentions: 8
Published: almost 5 years ago

10.1371/journal.pgen.1009324

Virus-derived variation in diverse human genomes
Cited by: 0
Author(s): Shohei Kojima, Anselmo Jiro Kamada, Nicholas F. Parrish
Software Mentions: 8
Published: over 3 years ago

10.15252/msb.202010060

CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencing
Cited by: 11
Author(s): Liang Fang, Guipeng Li, Zhiyuan Sun, Qionghua Zhu, Huanhuan Cui, Yunfei Li, Jingwen Zhang, Weizheng Liang, Wencheng Wei, Yuhui Hu, Wei Chen
Software Mentions: 8
Published: over 3 years ago

10.1002/evl3.110

Comparative genomics of 10 new<i>Caenorhabditis</i>species
Cited by: 105
Author(s): Lewis Stevens, Marie‐Anne Félix, Toni Beltran, Christian Braendle, Carlos Caurcel, Sarah Fausett, David Fitch, Lise Frézal, Charlie Gosse, Taniya Kaur, Karin Kiontke, Matthew D. Newton, Luke M. Noble, Aurélien Richaud, Matthew V. Rockman, Walter Sudhaus, Mark Blaxter
Software Mentions: 8
Published: over 5 years ago

10.1093/molbev/msab175

Geonomics: Forward-Time, Spatially Explicit, and Arbitrarily Complex Landscape Genomic Simulations
Cited by: 10
Author(s): Drew E Terasaki Hart, Anusha P Bishop, Ian Wang
Software Mentions: 7
Published: over 3 years ago

10.1111/mec.15010

Disentangling structural genomic and behavioural barriers in a sea of connectivity
Cited by: 60
Author(s): Julia Maria Isis Barth, David Villegas‐Ríos, Carla Freitas, Even Moland, Bastiaan Star, Carl André, Halvor Knutsen, Ian Bradbury, Jan Dierking, Christoph Petereit, David Righton, Julian D. Metcalfe, Kjetill S. Jakobsen, Esben Moland Olsen, Sissel Jentoft
Software Mentions: 7
Published: almost 6 years ago

10.7554/eLife.59067

Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development
Cited by: 11
Author(s): Ryan J Geusz, Allen Wang, Joshua Chiou, Joseph J. Lancman, Nichole Wetton, Samy Kefalopoulou, Jinzhao Wang, Yunjiang Qiu, Jian Yan, Anthony Aylward, Bing Ren, Peng Dong, Kyle J. Gaulton, Maike Sander
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pone.0204076

The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly
Cited by: 62
Author(s): Kris A. Christensen, Eric B. Rondeau, David R. Minkley, Jong S. Leong, Cameron M. Nugent, Roy G. Danzmann, Moira M. Ferguson, Agnieszka Stadnik, Robert H. Devlin, Robin Muzzerall, Michael G. Edwards, William S. Davidson, Ben F. Koop
Software Mentions: 7
Published: over 6 years ago

10.1126/scitranslmed.abe9599

Plasma from patients with bacterial sepsis or severe COVID-19 induces suppressive myeloid cell production from hematopoietic progenitors in vitro
Cited by: 57
Author(s): Miguel Reyes, Michael R. Filbin, Roby P. Bhattacharyya, Abraham Sonny, Arnav Mehta, Kianna Billman, Kyle R. Kays, Mayra Pinilla-Vera, Maura Benson, Lisa A. Cosimi, Deborah T. Hung, Bruce D. Levy, Alexandra Chloé Villani, Moshe Sade-Feldman, Rebecca M. Baron, Marcia B. Goldberg, Paul C. Blainey, Nir Hacohen
Software Mentions: 7
Published: over 3 years ago

10.1186/s12915-020-0752-3

Bivalent promoter hypermethylation in cancer is linked to the H327me3/H3K4me3 ratio in embryonic stem cells
Cited by: 33
Author(s): Donnchadh S. Dunican, Heidi K. Mjoseng, Leanne Duthie, Ilya M. Flyamer, Wendy A. Bickmore, Richard R. Meehan
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pgen.1008593

Parallel and nonparallel genomic responses contribute to herbicide resistance in Ipomoea purpurea, a common agricultural weed
Cited by: 35
Author(s): Megan Van Etten, Kristin M. Lee, Shu‐Mei Chang, Regina S. Baucom
Software Mentions: 7
Published: almost 5 years ago

10.1002/ece3.4994

Sampling related individuals within ponds biases estimates of population structure in a pond‐breeding amphibian
Cited by: 23
Author(s): Kyle A. O’Connell, Kevin P. Mulder, Jose A. Maldonado, Kathleen L. Currie, Dennis M. Ferraro
Software Mentions: 7
Published: almost 6 years ago

10.1016/j.cell.2019.09.035

Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity
Cited by: 322
Author(s): Chrysothemis C. Brown, Herman Gudjonson, Yuri Pritykin, Deeksha Deep, Vincent Philippe Lavallée, Alejandra Mendoza, Rachel M. Fromme, Linas Mažutis, Charlotte E. Ariyan, Christina Leslie, Dana Pe’er, Alexander Y. Rudensky
Software Mentions: 7
Published: about 5 years ago

10.3389/fpls.2016.01446

A Developmental Transcriptome Map for Allotetraploid Arachis hypogaea
Cited by: 149
Author(s): Josh Clevenger, Ye Chu, Brian E. Scheffler, Peggy Ozias‐Akins
Software Mentions: 7
Published: about 8 years ago

10.1038/s41598-017-18435-2

Ecological plasticity in the gastrointestinal microbiomes of Ethiopian Chlorocebus monkeys
Cited by: 32
Author(s): Pål Trosvik, Eli Knispel Rueness, Eric J. de Muinck, Amera Moges, Addisu Mekonnen
Software Mentions: 7
Published: almost 7 years ago

10.1371/journal.pcbi.1008329

An extended catalogue of tandem alternative splice sites in human tissue transcriptomes
Cited by: 6
Author(s): Aleksei Mironov, Stepan Denisov, Alexander Greß, Olga V. Kalinina, Dmitri D. Pervouchine
Software Mentions: 7
Published: over 3 years ago

10.1186/s12859-018-2445-2

Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performance
Cited by: 44
Author(s): Alyssa Baccarella, Claire Williams, Jay Z. Parrish, Charles C. Kim
Software Mentions: 7
Published: about 6 years ago

10.1186/s12864-021-07744-6

The effect of methanol fixation on single-cell RNA sequencing data
Cited by: 19
Author(s): Xinlei Wang, Yu Liu, Angela Ruohao Wu
Software Mentions: 7
Published: over 3 years ago

10.1128/AEM.00646-21

Spatial and Temporal Dynamics of Prokaryotic and Viral Community Assemblages in a Lotic System (Manatee Springs, Florida)
Cited by: 8
Author(s): Kema Malki, Natalie A. Sawaya, Michael J. Tisza, Felipe H. Coutinho, Karyna Rosario, Anna J. Székely, Mya Breitbart
Software Mentions: 7
Published: over 3 years ago

10.1534/g3.120.401579

High-Quality Assemblies for Three Invasive Social Wasps from the <i>Vespula</i> Genus
Cited by: 19
Author(s): Thomas W. R. Harrop, Joseph Guhlin, Gemma M. McLaughlin, Elizabeth Permina, Peter A. Stockwell, Josh Gilligan, Marissa F. Le Lec, Monica A. M. Gruber, Oliver Quinn, Mackenzie Lovegrove, Elizabeth J. Duncan, Emily J. Remnant, Jens Van Eeckhoven, Brittany Graham, Rosemary A Knapp, Kyle W. Langford, Zev Kronenberg, Maximilian O. Press, Stephen Eacker, Erin E. Wilson Rankin, Jessica Purcell, Philip J. Lester, Peter K. Dearden
Software Mentions: 7
Published: about 4 years ago

10.1128/mSphere.00737-20

Comparative Genomics Analyses of Lifestyle Transitions at the Origin of an Invasive Fungal Pathogen in the Genus <i>Cryphonectria</i>
Cited by: 16
Author(s): Lea Stauber, Simone Prospero, Daniel Croll
Software Mentions: 7
Published: about 4 years ago

10.1186/s12863-021-00983-2

Insights into 6S RNA in lactic acid bacteria (LAB)
Cited by: 1
Author(s): Pablo G. Cataldo, Paul Klemm, Marietta Thüring, Lucila Saavedra, Elvira María Hébert, Roland K. Hartmann, Marcus Lechner
Software Mentions: 6
Published: over 3 years ago

10.3390/ijms22115814

Genomic Characterization of Cisplatin Response Uncovers Priming of Cisplatin-Induced Genes in a Resistant Cell Line
Cited by: 7
Author(s): Hadar Golan Berman, Pooja Chauhan, Shira Shalev, Hiba Hassanain, Avital Parnas, Sheera Adar
Software Mentions: 6
Published: over 3 years ago

10.1523/JNEUROSCI.2317-20.2021

Disentangling Semantic Composition and Semantic Association in the Left Temporal Lobe
Cited by: 6
Author(s): Jixing Li, Liina Pylkkänen
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0006462

Community Analysis of Chronic Wound Bacteria Using 16S rRNA Gene-Based Pyrosequencing: Impact of Diabetes and Antibiotics on Chronic Wound Microbiota
Cited by: 193
Author(s): Lance B. Price, Cindy M. Liu, Johan H. Melendez, Yelena M. Frankel, David M. Engelthaler, Maliha Aziz, Jolene R. Bowers, Rogan Rattray, Jacques Ravel, Chris Kingsley, Paul Keim, Gerald S. Lazarus, Jonathan M. Zenilman
Software Mentions: 6
Published: over 15 years ago

10.1128/JVI.00500-19

Single-Cell Virus Sequencing of Influenza Infections That Trigger Innate Immunity
Cited by: 81
Author(s): Alan D. Russell, Elizaveta Elshina, Jacob R. Kowalsky, Aartjan J.W. te Velthuis, Jesse D. Bloom
Software Mentions: 6
Published: over 5 years ago

10.1128/AEM.02111-18

Resistance Gene Carriage Predicts Growth of Natural and Clinical Escherichia coli Isolates in the Absence of Antibiotics
Cited by: 7
Author(s): Richard C. Allen, Daniel C Angst, Alex R. Hall
Software Mentions: 6
Published: almost 6 years ago

10.7554/eLife.24133

Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates
Cited by: 103
Author(s): Zachary Baker, Molly Schumer, Yuki Haba, Lisa Bashkirova, C. D. Holland, Gil G. Rosenthal, Molly Przeworski
Software Mentions: 6
Published: over 7 years ago

10.3389/fgene.2021.674783

Gene Loss, Pseudogenization in Plastomes of Genus Allium (Amaryllidaceae), and Putative Selection for Adaptation to Environmental Conditions
Cited by: 8
Author(s): Victoria A. Scobeyeva, Ilya V. Artyushin, A.A. Krinitsina, Nikitin Pavel, Antipin Mi, Sergei V. Kuptsov, Maxim S. Belenikin, Denis O. Omelchenko, Maria D. Logacheva, Е. А. Коноров, Andrei E. Samoilov, Anna S. Speranskaya
Software Mentions: 6
Published: over 3 years ago

10.7554/eLife.02535

High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species
Cited by: 111
Author(s): Molly Schumer, Rongfeng Cui, Daniel L. Powell, Rebecca Dresner, Gil G. Rosenthal, Peter Andolfatto
Software Mentions: 6
Published: over 10 years ago

10.7554/eLife.66321

Channel nuclear pore complex subunits are required for transposon silencing in Drosophila
Cited by: 10
Author(s): Marzia Munafò, Victoria R Lawless, Alessandro Passera, Serena MacMillan, Susanne Bornelöv, Irmgard U. Haussmann, Matthias Soller, Gregory J. Hannon, Benjamin Czech
Software Mentions: 6
Published: over 3 years ago

10.1007/s00439-020-02228-1

A CRISPR and high-content imaging assay compliant with ACMG/AMP guidelines for clinical variant interpretation in ciliopathies
Cited by: 5
Author(s): Liliya Nazlamova, N. Simon Thomas, Man‐Kim Cheung, Jelmer Legebeke, Jenny Lord, Reuben J. Pengelly, William Tapper, Gabrielle Wheway
Software Mentions: 6
Published: about 4 years ago

10.3389/fgene.2021.716623

Deep Sequencing of MHC-Adapted Viral Lines Reveals Complex Recombinational Exchanges With Endogenous Retroviruses Leading to High-Frequency Variants
Cited by: 1
Author(s): Earl Middlebrook, Derek L. Stark, Douglas H. Cornwall, Jason L. Kubinak, Wayne K. Potts
Software Mentions: 6
Published: over 3 years ago

10.3389/fnmol.2019.00316

Single Cell and Single Nucleus RNA-Seq Reveal Cellular Heterogeneity and Homeostatic Regulatory Networks in Adult Mouse Stria Vascularis
Cited by: 62
Author(s): Soumya Korrapati, Ian Taukulis, Rafal T. Olszewski, Madeline Pyle, Shoujun Gu, Riya Singh, C. M. Griffiths, Daniel Martin, Erich T. Boger, Robert J. Morell, Michael Hoa
Software Mentions: 6
Published: about 5 years ago

10.7554/eLife.46464

Molecular and anatomical organization of the dorsal raphe nucleus
Cited by: 120
Author(s): Kee Wui Huang, Nicole Ochandarena, Adrienne C. Philson, Minsuk Hyun, Jaclyn E Birnbaum, Marcelo Cicconet, Bernardo L. Sabatini
Software Mentions: 6
Published: over 5 years ago

10.3390/ijms21093384

A Data-Driven Review of the Genetic Factors of Pregnancy Complications
Cited by: 14
Author(s): Yury A. Barbitoff, Alexander Tsarev, Elena S. Vashukova, Evgeniia M Maksiutenko, Л. В. Коваленко, Л. Д. Белоцерковцева, Andrey S. Glotov
Software Mentions: 6
Published: over 4 years ago

10.1002/ece3.6471

Rapid generation of ecologically relevant behavioral novelty in experimental cichlid hybrids
Cited by: 12
Author(s): Anna F. Feller, Oliver M. Selz, Matthew D. McGee, Joana I. Meier, Salome Mwaiko, Ole Seehausen
Software Mentions: 6
Published: over 4 years ago

10.1002/ece3.4724

Highly flexible infection programs in a specialized wheat pathogen
Cited by: 72
Author(s): Janine Haueisen, Mareike Möller, Christoph Eschenbrenner, Jonathan Grandaubert, Heike Seybold, Holger Adamiak, Eva H. Stukenbrock
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12864-021-07571-9

Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni
Cited by: 7
Author(s): Laura Foix, Anna Nadal, Maja Zagorščak, Živa Ramšak, Anna Esteve‐Codina, Kristina Gruden, María Pla
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pgen.1008864

­­­­­­Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods
Cited by: 52
Author(s): Samuel H. Lewis, Laura Ross, Stevie A. Bain, Eleni Pahita, Stephen A. Smith, Richard Cordaux, Eric A. Miska, Boris Lenhard, Francis M. Jiggins, Peter Sarkies
Software Mentions: 6
Published: over 4 years ago

10.1128/mBio.00971-19

Evolution of Superinfection Immunity in Cluster A Mycobacteriophages
Cited by: 48
Author(s): Travis N. Mavrich, Graham F. Hatfull
Software Mentions: 6
Published: over 5 years ago

10.1093/gbe/evaa143

The Genome of the Softshell Clam Mya arenaria and the Evolution of Apoptosis
Cited by: 5
Author(s): David C. Plachetzki, M. Sabrina Pankey, Matthew D. MacManes, Michael P. Lesser, Charles W. Walker
Software Mentions: 6
Published: over 4 years ago

10.1093/gbe/evz245

The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae)
Cited by: 42
Author(s): Valerie L. Soza, Dale Lindsley, Adam Waalkes, Elizabeth Ramage, Rupali P Patwardhan, Joshua N. Burton, Andrew Adey, Akash Kumar, Ruolan Qiu, Jay Shendure, Benjamin D. Hall
Software Mentions: 6
Published: about 5 years ago

10.1186/s13073-016-0382-0

Non-coding single nucleotide variants affecting estrogen receptor binding and activity
Cited by: 5
Author(s): Amir Bahreini, Kevin M. Levine, Lucas Santana-Santos, Panayiotis V. Benos, Peilu Wang, Courtney Andersen, Steffi Oesterreich, Adrian V. Lee
Software Mentions: 6
Published: about 8 years ago

10.1038/s42003-018-0119-2

Biodiversity estimates and ecological interpretations of meiofaunal communities are biased by the taxonomic approach
Cited by: 26
Author(s): Francesca Leasi, Joseph L. Sevigny, Eric M. Laflamme, Tom Artois, Marco Curini‐Galletti, Alberto de Jesús Navarrete, Maikon Di Domênico, Freya Goetz, Jeffrey A. Hall, Rick Hochberg, Katharina M. Jörger, Ulf Jondelius, Mary Antonio Donatello Todaro, Herman H. Wirshing, Jon L. Norenburg, W. Kelley Thomas
Software Mentions: 6
Published: over 6 years ago

10.1128/mBio.02146-20

Bacteria Contribute to Plant Secondary Compound Degradation in a Generalist Herbivore System
Cited by: 20
Author(s): Charlotte B. Francoeur, Lily Khadempour, Rolando D. Moreira-Soto, Kirsten Gotting, Adam J. Book, Adrián A. Pinto‐Tomás, Ken Keefover‐Ring, Cameron R. Currie
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pcbi.1007800

MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
Cited by: 30
Author(s): Avtar Roopra
Software Mentions: 6
Published: over 4 years ago

10.3389/fpls.2021.714393

Transcriptome Profiling Reveals Differential Gene Expression of Secreted Proteases and Highly Specific Gene Repertoires Involved in Lactarius–Pinus Symbioses
Cited by: 7
Author(s): Nianwu Tang, Annie Lebreton, Wenjun Xu, Yu-Cheng Dai, Fuqiang Yu, Francis Martin
Software Mentions: 6
Published: over 3 years ago

10.1016/j.dib.2018.05.107

Integration of genome-wide mRNA and miRNA expression, and DNA methylation data of three cell lines exposed to ten carbon nanomaterials
Cited by: 8
Author(s): Giovanni Scala, Veer Singh Marwah, Pia Anneli Sofia Kinaret, Jukka Sund, Vittorio Fortino, Dario Greco
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pbio.3000365

Dissecting the transcriptome landscape of the human fetal neural retina and retinal pigment epithelium by single-cell RNA-seq analysis
Cited by: 95
Author(s): Yuqiong Hu, Xiaoye Wang, Boqiang Hu, Yunuo Mao, Yidong Chen, Liying Yan, Jun Yong, Ji Dong, Wei Yuan, Wei Wang, Lu Wen, Jie Qiao, Fuchou Tang
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pbio.2003903

Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development
Cited by: 62
Author(s): Hong Zhang, Shengqian Dou, Feng He, Junjie Luo, Liping Wei, Jian Lü
Software Mentions: 6
Published: over 6 years ago

10.1111/pbi.12834

Conversion of array‐based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (<i>Triticum aestivum</i>)
Cited by: 21
Author(s): Amanda Burridge, Paul Wilkinson, Mark Winfield, Gary Barker, Alexandra M. Allen, Jane A. Coghill, Christy Waterfall, Keith J. Edwards
Software Mentions: 6
Published: about 7 years ago

10.7717/peerj.484

The mitochondrial genome of<i>Paragonimus westermani</i>(Kerbert, 1878), the Indian isolate of the lung fluke representative of the family Paragonimidae (Trematoda)
Cited by: 29
Author(s): Devendra Kumar Biswal, Anupam Chatterjee, Alok Bhattacharya, Veena Tandon
Software Mentions: 6
Published: over 10 years ago

10.1016/j.stem.2021.04.031

Naive stem cell blastocyst model captures human embryo lineage segregation
Cited by: 139
Author(s): Akira Yanagida, Daniel Spindlow, Jennifer Nichols, Anish Dattani, Austin Smith, Ge Guo
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0152034

System-Wide Associations between DNA-Methylation, Gene Expression, and Humoral Immune Response to Influenza Vaccination
Cited by: 45
Author(s): Michael T. Zimmermann, Ann L. Oberg, Diane E. Grill, Inna G. Ovsyannikova, Iana H. Haralambieva, Richard B. Kennedy, Gregory A. Poland
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pone.0096937

Roosting and Foraging Social Structure of the Endangered Indiana Bat (Myotis sodalis)
Cited by: 35
Author(s): Alexander Silvis, Andrew B. Kniowski, Stanley D. Gehrt, W. Mark Ford
Software Mentions: 6
Published: over 10 years ago

10.1186/s12864-019-5946-0

Prediction of regulatory long intergenic non-coding RNAs acting in trans through base-pairing interactions
Cited by: 19
Author(s): Jules Deforges, Rodrigo S. Reis, Philippe Jacquet, Dominique Jacques Vuarambon, Yves Poirier
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0118867

A Deep Catalog of Autosomal Single Nucleotide Variation in the Pig
Cited by: 22
Author(s): Erica Bianco, Bruno Nevado, Sebastián E. Ramos-Onsins, Miguel Pérez‐Enciso
Software Mentions: 6
Published: almost 10 years ago

10.3389/fimmu.2019.02999

Opioids Impair Intestinal Epithelial Repair in HIV-Infected Humanized Mice
Cited by: 37
Author(s): Jingjing Meng, Santanu Banerjee, Li Zhang, Gregory M. Sindberg, Shamsudheen Moidunny, Bin Li, David J. Robbins, Mohit Girotra, Bradley J. Segura, Sundaram Ramakrishnan, Sabita Roy
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0119198

Genome-Wide Analysis of Homeobox Gene Family in Legumes: Identification, Gene Duplication and Expression Profiling
Cited by: 47
Author(s): Annapurna Bhattacharjee, Rajesh Ghangal, Rohini Garg, Mukesh Jain
Software Mentions: 5
Published: almost 10 years ago

10.3390/ani11082226

In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data
Cited by: 1
Author(s): Sazia Kunvar, Sylwia D. Czarnomska, Cino Pertoldi, Małgorzata Tokarska
Software Mentions: 5
Published: over 3 years ago

10.3389/fimmu.2018.02547

Clinical T Cell Receptor Repertoire Deep Sequencing and Analysis: An Application to Monitor Immune Reconstitution Following Cord Blood Transplantation
Cited by: 36
Author(s): Athina Soragia Gkazi, Ben Margetts, Teresa Attenborough, Lana Mhaldien, Joseph F. Standing, Theres Oakes, James Heather, John Booth, Marlène Pasquet, Robert Chiesa, Paul Veys, Nigel Klein, Benjamin M. Chain, Robin E. Callard, Stuart Adams
Software Mentions: 5
Published: about 6 years ago

10.3389/fmicb.2019.02075

Functional Characterization of a Global Virulence Regulator Hfq and Identification of Hfq-Dependent sRNAs in the Plant Pathogen Pantoea ananatis
Cited by: 14
Author(s): Gi Yoon Shin, Jeffrey K. Schachterle, Divine Yufetar Shyntum, Lucy N. Moleleki, Teresa A. Coutinho, George W. Sundin
Software Mentions: 5
Published: over 5 years ago

10.15252/msb.20167058

Mechanism for microbial population collapse in a fluctuating resource environment
Cited by: 21
Author(s): Serdar Turkarslan, Arjun V. Raman, Anne Thompson, Christina E. Arens, Mark A. Gillespie, Frederick von Netzer, Kristina L. Hillesland, Sergey Stolyar, Adrián López García de Lomana, David J Reiss, Drew Gorman‐Lewis, Grant M. Zane, Jeffrey A. Ranish, Judy D. Wall, David A. Stahl, Nitin S. Baliga
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pone.0237641

Locus of emotion influences psychophysiological reactions to music
Cited by: 7
Author(s): Julia Merrill, Diana Omigie, Melanie Wald-Fuhrmann
Software Mentions: 5
Published: over 4 years ago