pypi: custom | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1004924

The Genetic Architecture of the Genome-Wide Transcriptional Response to ER Stress in the Mouse
Cited by: 29
Author(s): Clement Y. Chow, Xiaozhu Wang, David D. Riccardi, Mariana F. Wolfner, Andrew G. Clark
Software Mentions: 4
Published: almost 10 years ago

10.1093/bioinformatics/btab263

Build a better bootstrap and the RAWR shall beat a random path to your door: phylogenetic support estimation revisited
Cited by: 1
Author(s): Wei Wang, Ahmad Hejasebazzi, Julia Zheng, Kevin J. Liu
Software Mentions: 4
Published: over 3 years ago

10.15252/embj.2019104185

Timeless couples G‐quadruplex detection with processing by <scp>DDX</scp> 11 helicase during <scp>DNA</scp> replication
Cited by: 42
Author(s): Letícia Koch Lerner, Sandro Holzer, M.L. Kilkenny, Saša Šviković, Pierre Murat, Davide Schiavone, Cara Bernadette Eldridge, Alice Bittleston, Joseph D. Maman, Dana Branzei, Katherine Stott, Luca Pellegrini, Julian E. Sale
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pgen.1002984

The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences
Cited by: 142
Author(s): Olivier Arnaiz, Nathalie Mathy, Céline Baudry, Sophie Malinsky, Jean‐Marc Aury, Cyril Denby Wilkes, Olivier Garnier, Karine Labadie, Benjamin E. Lauderdale, Anne Le Mouël, Antoine Marmignon, Mariusz Nowacki, Julie Poulain, M Prajer, Patrick Wincker, Éric Meyer, Sandra Duharcourt, Laurent Duret, Mireille Bétermier, Linda Sperling
Software Mentions: 4
Published: about 12 years ago

10.1186/1471-2164-15-1179

The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis
Cited by: 34
Author(s): Kate J. Howell, Lucy A. Weinert, Roy R. Chaudhuri, Shi-Lu Luan, Sarah Peters, Jukka Corander, David Harris, Øystein Angen, Virginia Aragón, Albert Bensaid, Susanna Williamson, Julian Parkhill, Paul R. Langford, Andrew N. Rycroft, Brendan W. Wren, Matthew T. G. Holden, Alexander W. Tucker, Duncan J. Maskell
Software Mentions: 4
Published: almost 11 years ago

10.3389/fcimb.2021.698146

L-Arabinose Transport and Metabolism in Salmonella Influences Biofilm Formation
Cited by: 9
Author(s): Erin M. Vasicek, Lindsey O’Neal, Matthew R. Parsek, James Fitch, Peter White, John S. Gunn
Software Mentions: 4
Published: over 3 years ago

10.1128/mBio.02257-16

Selective Whole-Genome Amplification Is a Robust Method That Enables Scalable Whole-Genome Sequencing of Plasmodium vivax from Unprocessed Clinical Samples
Cited by: 54
Author(s): Annie N. Cowell, Dorothy E. Loy, Sesh A. Sundararaman, Hugo O. Valdivia, Kathleen Fisch, Andrés G. Lescano, G. Christian Baldeviano, Salomón Durand, Vincent R. Gerbasi, Colin J. Sutherland, Debbie Nolder, Joseph M. Vinetz, Beatrice H. Hahn, Elizabeth A. Winzeler
Software Mentions: 4
Published: over 7 years ago

10.1186/s13287-021-02601-5

Longitudinal clonal tracking in humanized mice reveals sustained polyclonal repopulation of gene-modified human-HSPC despite vector integration bias
Cited by: 0
Author(s): Gajendra W. Suryawanshi, Hubert Arokium, Sanggu Kim, Wannisa Khamaikawin, Samantha Lin, Saki Shimizu, Koollawat Chupradit, Yoojin Lee, Yiming Xie, Xin Guan, Vasantika Suryawanshi, Angela P. Presson, Dong-Sung An, Irvin S. Y. Chen
Software Mentions: 4
Published: about 3 years ago

10.7554/eLife.52775

Nucleotide inhibition of the pancreatic ATP-sensitive K+ channel explored with patch-clamp fluorometry
Cited by: 18
Author(s): Samuel Usher, Frances M. Ashcroft, Michael C. Puljung
Software Mentions: 4
Published: almost 5 years ago

10.1016/j.ydbio.2015.04.010

Imprinted expression in cystic embryoid bodies shows an embryonic and not an extra-embryonic pattern
Cited by: 7
Author(s): Tomasz M. Kuliński, M. Rita T. Casari, Philipp M. Guenzl, D. Wenzel, Daniel Andergassen, Anastasiya Hladik, Paul Datlinger, Matthias Farlik, Hans-Christian Theussl, Josef Penninger, Sylvia Knapp, Christoph Bock, Denise P. Barlow, Quanah J. Hudson
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-015-1374-y

Sequencing, identification and mapping of primed L1 elements (SIMPLE) reveals significant variation in full length L1 elements between individuals
Cited by: 29
Author(s): Vincent A. Streva, Vallmer E Jordan, Sara B. Linker, Dale J. Hedges, Prescott L. Deininger
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-021-84044-9

Identification of candidate repurposable drugs to combat COVID-19 using a signature-based approach
Cited by: 18
Author(s): Sinead M. O’Donovan, Ali Sajid Imami, Hunter M. Eby, Nicholas Henkel, Justin Creeden, Sophie Asah, Xiaolu Zhang, Xiaojun Wu, Rawan Alnafisah, R. Travis Taylor, James Reigle, Alexander W. Thorman, Behrouz Shamsaei, Jarek Meller, Robert E. McCullumsmith
Software Mentions: 4
Published: over 3 years ago

10.1186/s12915-021-00991-9

Long-term persistence of supernumerary B chromosomes in multiple species of Astyanax fish
Cited by: 6
Author(s): Duílio Mazzoni Zerbinato de Andrade Silva, Francisco J. Ruíz-Ruano, Ricardo Utsunomia, María Martín-Peciña, Jonathan Pena Castro, Paula Paccielli Freire, Robson Francisco Carvalho, Diogo Teruo Hashimoto, Alexander Suh, Cláudio Oliveira, Fábio Porto‐Foresti, Roberto Ferreira Artoni, Fausto Foresti, Juan Pedro M. Camacho
Software Mentions: 4
Published: over 3 years ago

10.1242/dev.172916

Capacitation of human naïve pluripotent stem cells for multi-lineage differentiation
Cited by: 78
Author(s): Maria Rostovskaya, Giuliano Giuseppe Stirparo, Austin Smith
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-86148-8

Comparative in silico genome analysis of Clostridium perfringens unravels stable phylogroups with different genome characteristics and pathogenic potential
Cited by: 15
Author(s): Mostafa Y. Abdel-Glil, Prasad Thomas, Jörg Linde, Anne Busch, Lothar H. Wieler, Heinrich Neubauer, Christian Seyboldt
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pgen.1009097

Diversified regulation of circadian clock gene expression following whole genome duplication
Cited by: 9
Author(s): Alexander C. West, Marianne Iversen, Even H. Jørgensen, Simen Rød Sandve, David G. Hazlerigg, Shona H. Wood
Software Mentions: 4
Published: about 4 years ago

10.1242/dmm.045773

Zebrafish mbnl mutants model physical and molecular phenotypes of myotonic dystrophy
Cited by: 7
Author(s): Melissa N. Hinman, Jared Richardson, Rose A. Sockol, Eliza D Aronson, Sarah J. Stednitz, Katrina N. Murray, J. Andrew Berglund, Karen Guillemin
Software Mentions: 4
Published: over 3 years ago

10.1186/s12870-015-0632-0

Global analysis of uncapped mRNA changes under drought stress and microRNA-dependent endonucleolytic cleavages in foxtail millet
Cited by: 10
Author(s): Fei Yi, Jian Chen, Jingjuan Yu
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-020-80682-7

TIM29 is required for enhanced stem cell activity during regeneration in the flatworm Macrostomum lignano
Cited by: 2
Author(s): Stijn Mouton, Kirill Ustyantsev, Frank W. Beltman, Lisa Glazenburg, Eugène Berezikov
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-021-97654-0

Assessment of the effectiveness of the EUROFORGEN NAME and Precision ID Ancestry panel markers for ancestry investigations
Cited by: 8
Author(s): Ditte Truelsen, Torben Tvedebrink, Helle Smidt Mogensen, Maryam Sharafi Farzad, Muhammad Adnan Shan, Niels Morling, Vânia Pereira, Claus Børsting
Software Mentions: 4
Published: about 3 years ago

10.1186/s12870-014-0306-3

Increased sucrose levels mediate selective mRNA translation in Arabidopsis
Cited by: 22
Author(s): Magdalena Gamm, Alessia Peviani, Anne Honsel, Berend Snel, Sjef Smeekens, Johannes Hanson
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pgen.1007332

Genome-wide detection of conservative site-specific recombination in bacteria
Cited by: 37
Author(s): Ognjen Sekulović, Elizabeth M. Garrett, Jacob Bourgeois, Rita Tamayo, Aimee Shen, Andrew Camilli
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-021-04301-6

neoDL: a novel neoantigen intrinsic feature-based deep learning model identifies IDH wild-type glioblastomas with the longest survival
Cited by: 3
Author(s): Taixiang Sun, Yufei He, Wendong Li, Guang Liu, Lin Li, Lu Wang, Zixuan Xiao, Xiaohan Han, Hao Wen, Yong Liu, Yifan Chen, Haoyu Wang, Jing Li, Yubo Fan, Wei Zhang, Jing Zhang
Software Mentions: 4
Published: over 3 years ago

10.1038/s42003-019-0306-9

Mechanistic insights into the evolution of DUF26-containing proteins in land plants
Cited by: 67
Author(s): Aleksia Vaattovaara, Benjamin Brandt, Sitaram Rajaraman, Omid Safronov, Andres Veidenberg, Markéta Luklová, Jaakko Kangasjärvi, Ari Löytynoja, Michael Hothorn, Jarkko Salojärvi, Michael Wrzaczek
Software Mentions: 4
Published: almost 6 years ago

10.1016/j.cub.2017.04.057

Canine Brachycephaly Is Associated with a Retrotransposon-Mediated Missplicing of SMOC2
Cited by: 76
Author(s): Thomas W. Marchant, Edward J. Johnson, Lynn McTeir, Craig Johnson, Adam Gow, Tiziana Liuti, Dana Kuehn, Karen L. Svenson, Mairead Lesley Bermingham, Michaela Drögemüller, Marc Nussbaumer, Megan Davey, David Argyle, Roger M. Powell, Sérgio Guilherme, Johann Lang, Gert ter Haar, Tosso Leeb, Tobias Schwarz, Richard J. Mellanby, Dylan Clements, Jeffrey J. Schoenebeck
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-020-79552-z

Host mitochondrial transcriptome response to SARS-CoV-2 in multiple cell models and clinical samples
Cited by: 45
Author(s): Brendan Miller, Ana R. Silverstein, Melanie Flores, Kevin Cao, Hiroshi Kumagai, Hemal H. Mehta, Kelvin Yen, Su Jeong Kim, Pinchas Cohen
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-019-47226-0

Daphnia stressor database: Taking advantage of a decade of Daphnia ‘-omics’ data for gene annotation
Cited by: 12
Author(s): Suda Parimala Ravindran, Jennifer Lüneburg, Lisa Gottschlich, Verena Tams, Mathilde Cordellier
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1003219

Unlocking the Bottleneck in Forward Genetics Using Whole-Genome Sequencing and Identity by Descent to Isolate Causative Mutations
Cited by: 43
Author(s): Katherine Bull, Andrew Rimmer, Owen M. Siggs, Lisa A. Miosge, Carla Roots, Anselm Enders, Edward M. Bertram, Tanya L. Crockford, Belinda Whittle, Paul K. Potter, Michelle Simon, Ann Marie Mallon, Steve Brown, Bruce Beutler, Christopher C. Goodnow, Gerton Lunter, Richard J. Cornall
Software Mentions: 4
Published: almost 12 years ago

10.3389/fmicb.2017.01808

Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses
Cited by: 36
Author(s): François Thomas, Philippe Bordron, Damien Eveillard, Gurvan Michel
Software Mentions: 4
Published: about 7 years ago

10.1186/s40168-019-0650-5

Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites
Cited by: 93
Author(s): Alessio Tovaglieri, Alexandra Sontheimer-Phelps, Annelies Geirnaert, Rachelle Prantil‐Baun, Diogo M. Camacho, David B. Chou, Hossein Baharvand, Tomás de Wouters, Magdalena Kasendra, Michael Super, Mark Cartwright, Camilla A. Richmond, David T. Breault, Christophe Lacroix, Donald E. Ingber
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-017-1536-9

Network-based analysis of transcriptional profiles from chemical perturbations experiments
Cited by: 11
Author(s): Francesca Mulas, Amy Li, David H. Sherr, Stefano Monti
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-020-58969-6

Dramatic HIV DNA degradation associated with spontaneous HIV suppression and disease-free outcome in a young seropositive woman following her infection
Cited by: 2
Author(s): Philippe Colson, Catherine Dhiver, Catherine Tamalet, Jérémy Delerce, Olga O. Glazunova, Maxime Gaudin, Anthony Levasseur, Didier Raoult
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-018-27979-w

Genome-wide bisulphite-sequencing reveals organ-specific methylation patterns in chickpea
Cited by: 22
Author(s): Himanshi Bhatia, Niraj Khemka, Mukesh Jain, Rohini Garg
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-59887-3

Genomic divergence reveals unique populations among Indian Yaks
Cited by: 8
Author(s): S. Jayakumar, M R Vineeth, Tarida Marlin Surya, Kritika Singh, S. P. Dixit, S. K. Niranjan, M. S. Tantia, I. D. Gupta, Dhanalakshmi Ravikumar
Software Mentions: 4
Published: over 4 years ago

10.1038/s41418-019-0285-x

CBP and SRF co-regulate dendritic growth and synaptic maturation
Cited by: 25
Author(s): Beatriz del Blanco, Deisy Guiretti, Romana Tomasoni, María T. Lopez-Cascales, Rafael Muñoz‐Viana, Michał Lipiński, Marilyn Scandaglia, Yaiza Coca, Román Olivares, Luis M. Valor, Eloı́sa Herrera, Ángel Barco
Software Mentions: 4
Published: over 5 years ago

10.1038/srep27754

Ocular exposure to blue-enriched light has an asymmetric influence on neural activity and spatial attention
Cited by: 14
Author(s): Daniel P. Newman, Steven W. Lockley, Gerard M. Loughnane, Ana Carina Pamplona Martins, Rafael Abe, Marco T. R. Zoratti, Simon P. Kelly, Megan O'Neill, Shanthakumar M W Rajaratnam, Redmond G O’Connell, Mark A. Bellgrove
Software Mentions: 4
Published: over 8 years ago

10.1038/srep20064

Digital detection of endonuclease mediated gene disruption in the HIV provirus
Cited by: 21
Author(s): Ruth Hall Sedlak, Shu Liang, Nixon Niyonzima, Harshana S. De Silva Feelixge, Pavitra Roychoudhury, Alexander L. Greninger, Nicholas Weber, Sandrine Boissel, Andrew M. Scharenberg, Anqi Cheng, Amalia Magaret, Roger E. Bumgarner, Daniel Stone, Keith R. Jerome
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pcbi.1003107

Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples
Cited by: 125
Author(s): David R. Riley, Karsten B. Sieber, Kelly Robinson, James R. White, Ashwinkumar Ganesan, Syrus Nourbakhsh, Julie C. Dunning Hotopp
Software Mentions: 4
Published: over 11 years ago

10.1016/j.cell.2019.10.010

Discovery of Human Signaling Systems: Pairing Peptides to G Protein-Coupled Receptors
Cited by: 143
Author(s): Simon R. Foster, Alexander S. Hauser, Line Vedel, Ryan T. Strachan, Xi Ping Huang, Ariana C. Gavin, Sushrut D. Shah, Ajay P. Nayak, Linda M. Haugaard‐Kedström, Raymond B. Penn, Bryan L. Roth, Hans Bräuner‐Osborne, David E. Gloriam
Software Mentions: 4
Published: about 5 years ago

10.3390/v10100576

Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes
Cited by: 10
Author(s): Phillip Seitzer, Adrien Jeanniard, Fangrui Ma, James L. Van Etten, Marc T. Facciotti, David D. Dunigan
Software Mentions: 4
Published: about 6 years ago

10.3390/cancers13174305

The Microenvironment of Small Intestinal Neuroendocrine Tumours Contains Lymphocytes Capable of Recognition and Activation after Expansion
Cited by: 5
Author(s): Tobias Hofving, Frank Liang, Jan Ch Karlsson, Ulf Yrlid, Jonas A. Nilsson, Ola Nilsson, Lisa M. Nilsson
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.ppat.1000846

SREB, a GATA Transcription Factor That Directs Disparate Fates in Blastomyces dermatitidis Including Morphogenesis and Siderophore Biosynthesis
Cited by: 57
Author(s): Gregory M. Gauthier, Thomas D. Sullivan, Sergio S. Gallardo, T. Tristan Brandhorst, Amber J. Vanden Wymelenberg, Christina A. Cuomo, Garret Suen, Cameron R. Currie, Bruce S. Klein
Software Mentions: 4
Published: over 14 years ago

10.1186/s40462-017-0108-y

Three-dimensional space use during the bottom phase of southern elephant seal dives
Cited by: 15
Author(s): Yves Le Bras, Joffrey Jouma’a, Christophe Guinet
Software Mentions: 4
Published: about 7 years ago

10.1172/jci.insight.145346

Systemic and adipocyte transcriptional and metabolic dysregulation in idiopathic intracranial hypertension
Cited by: 39
Author(s): Connar Westgate, Hannah Botfield, Zerin Alimajstorovic, Andreas Yiangou, Mark D. Walsh, Gabrielle Smith, Rishi Singhal, James Mitchell, Olivia Grech, Keira Markey, Daniel Hebenstreit, Daniel A. Tennant, Jeremy W. Tomlinson, Susan P Mollan, Christian Ludwig, İldem Akerman, Gareth G. Lavery, Alexandra J Sinclair
Software Mentions: 4
Published: over 3 years ago

10.1038/s41597-021-00905-y

A resource to explore the discovery of rare diseases and their causative genes
Cited by: 5
Author(s): Friederike Ehrhart, Egon Willighagen, Martina Kutmon, Max van Hoften, Leopold Curfs, Chris T. Evelo
Software Mentions: 4
Published: over 3 years ago

10.1186/s13073-018-0563-0

Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing
Cited by: 25
Author(s): Annie N. Cowell, Hugo O. Valdivia, Danett K. Bishop, Elizabeth A. Winzeler
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0127103

From Glacier to Sauna: RNA-Seq of the Human Pathogen Black Fungus Exophiala dermatitidis under Varying Temperature Conditions Exhibits Common and Novel Fungal Response
Cited by: 31
Author(s): Barbara Blasi, Hakim Tafer, Donatella Tesei, Katja Sterflinger
Software Mentions: 4
Published: over 9 years ago

10.1186/s13024-021-00423-w

Methods to investigate intrathecal adaptive immunity in neurodegeneration
Cited by: 11
Author(s): Hamilton Oh, Olivia Leventhal, Divya Channappa, Victor W. Henderson, Tony Wyss‐Coray, Benoit Lehallier, David Gate
Software Mentions: 4
Published: almost 4 years ago

10.1186/gb-2013-14-12-r147

Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties
Cited by: 77
Author(s): Aurélien A. Sérandour, Gordon D. Brown, Joshua D. Cohen, Jason S. Carroll
Software Mentions: 4
Published: almost 12 years ago

10.1534/genetics.119.302757

Historical Introgressions from a Wild Relative of Modern Cassava Improved Important Traits and May Be Under Balancing Selection
Cited by: 26
Author(s): Marnin D. Wolfe, Guillaume Bauchet, A. M. C. Chan, Roberto Lozano, Punna Ramu, Chiedozie Egesi, Robert Kawuki, Peter Kulakow, Ismail Rabbi, Jean‐Luc Jannink
Software Mentions: 4
Published: almost 5 years ago

10.1186/gb-2014-15-4-r57

Evidence for the biogenesis of more than 1,000 novel human microRNAs
Cited by: 214
Author(s): Marc R. Friedländer, Esther Lizano, Anna J.S. Houben, Daniela Bezdan, Mónica Báñez-Coronel, Grzegorz Kudla, Elisabet Mateu-Huertas, Birgit Kagerbauer, Justo González, Kevin C. Chen, Emily LeProust, Eulàlia Martı́, Xavier Estivill
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12859-016-0982-0

Modeling the integration of bacterial rRNA fragments into the human cancer genome
Cited by: 5
Author(s): Karsten B. Sieber, Pawel Gajer, Julie C. Dunning Hotopp
Software Mentions: 4
Published: over 8 years ago

10.1186/s13059-018-1437-x

Vex-seq: high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency
Cited by: 63
Author(s): Scott I. Adamson, Lijun Zhan, Brenton R. Graveley
Software Mentions: 4
Published: over 6 years ago

10.1093/gigascience/giz029

An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies
Cited by: 34
Author(s): Jan Axtner, Alex Crampton‐Platt, Lisa Hörig, Azlan Mohamed, Charles C.Y. Xu, Douglas W. Yu, Andreas Wilting
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0181902

EINCR1 is an EGF inducible lincRNA overexpressed in lung adenocarcinomas
Cited by: 4
Author(s): Karol Nowicki-Osuch, Yaoyong Li, Mairi Challinor, Dave T. Gerrard, Neil A. Hanley, Andrew D. Sharrocks
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0045708

Cooperativity of Stress-Responsive Transcription Factors in Core Hypoxia-Inducible Factor Binding Regions
Cited by: 32
Author(s): Diego Villar, Amaya Ortiz-Barahona, Laura Gómez-Maldonado, Nuria Pescador, Fátima Sánchez-Cabo, Hubert Hackl, Blanca Rodriguez, Zlatko Trajanoski, Ana Dopazo, Tim Hui-Ming Huang, Pearlly S. Yan, Luis del Peso
Software Mentions: 4
Published: about 12 years ago

10.1534/g3.120.401306

Genotypic Characterization of the U.S. Peanut Core Collection
Cited by: 10
Author(s): Paul I. Otyama, R.S. Kulkarni, Kelly D. Chamberlin, Peggy Ozias‐Akins, Ye Chu, Lori M. Lincoln, Gregory E. MacDonald, Noelle L. Anglin, Sudhansu Dash, David J. Bertioli, David Fernández-Baca, Michelle A. Graham, Steven B. Cannon, Ethalinda K. S. Cannon
Software Mentions: 4
Published: about 4 years ago

10.1111/mec.13146

Heterogeneity of genetic architecture of body size traits in a free‐living population
Cited by: 69
Author(s): Camillo Bérénos, Philip A Ellis, Jill G. Pilkington, Sang Lee, Jacob Gratten, Josephine M. Pemberton
Software Mentions: 4
Published: over 9 years ago

10.1186/1471-2105-12-29

Investigating the effect of paralogs on microarray gene-set analysis
Cited by: 0
Author(s): Aline Faure, Cathal Seoighe, Nicola Mulder
Software Mentions: 4
Published: almost 14 years ago

10.3390/genes9040180

Non-Pleiotropic Coupling of Daily and Seasonal Temporal Isolation in the European Corn Borer
Cited by: 29
Author(s): Rebecca C. Levy, Genevieve M. Kozak, Erik B. Dopman
Software Mentions: 4
Published: over 6 years ago

10.1534/g3.117.300550

Genetic Loci Governing Androgenic Capacity in Perennial Ryegrass (Lolium perenne L.)
Cited by: 8
Author(s): Rachel F. Begheyn, Steven Yates, Timothy Sykes, Bruno Studer
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0228722

Iron metabolic pathways in the processes of sponge plasticity
Cited by: 8
Author(s): Alexander D. Finoshin, Kim I. Adameyko, Kirill V. Mikhailov, О. И. Кравчук, Anton Georgiev, Н. Г. Горностаев, Igor A. Kosevich, Victor S. Mikhailov, Guzel Gazizova, Elena Shagimardanova, Oleg Gusev, Yu. V. Lyupina
Software Mentions: 4
Published: over 4 years ago

10.1534/g3.120.401497

Comparative Genomic Analyses and a Novel Linkage Map for Cisco (Coregonus artedi) Provide Insights into Chromosomal Evolution and Rediploidization Across Salmonids
Cited by: 13
Author(s): Danielle M. Blumstein, Matthew A. Campbell, Matthew C. Hale, Ben J. G. Sutherland, Garrett J. McKinney, Wendylee Stott, Wesley A. Larson
Software Mentions: 4
Published: over 4 years ago

10.1590/1678-4685-GMB-2017-0164

Identification of potential target genes of USP22 via ChIP-seq and RNA-seq analysis in HeLa cells
Cited by: 5
Author(s): Zhizhong Gong, Jianyun Liu, Xin Xie, Xiaoyuan Xu, Ping Wu, Huimin Li, Yaqin Wang, Weidong Li, Jianjun Xiong
Software Mentions: 4
Published: over 6 years ago

10.1038/s41437-019-0252-9

Conservation of the genome-wide recombination rate in white-footed mice
Cited by: 8
Author(s): April Peterson, Nathan D. Miller, Bret A. Payseur
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-65322-4

Genomic analysis of the natural history of attention-deficit/hyperactivity disorder using Neanderthal and ancient Homo sapiens samples
Cited by: 17
Author(s): Paula Esteller-Cucala, Iago Maceda, Anders Børglum, Ditte Demontis, Stephen V. Faraone, Bru Cormand, Oscar Lao
Software Mentions: 4
Published: over 4 years ago

10.1093/molbev/msy158

Coalescent Analysis of Phylogenomic Data Confidently Resolves the Species Relationships in the Anopheles gambiae Species Complex
Cited by: 73
Author(s): Yuttapong Thawornwattana, Daniel A. Dalquen, Ziheng Yang
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-7-228

Genome sequence alterations detected upon passage of Burkholderia mallei ATCC 23344 in culture and in mammalian hosts
Cited by: 26
Author(s): Claudia Mabel Terenti Romero, David DeShazer, Tamara Feldblyum, Jacques Ravel, Donald E. Woods, Heenam Stanley Kim, Yan Yu, Catherine M. Ronning, William C. Nierman
Software Mentions: 3
Published: about 18 years ago

10.1371/journal.pone.0222323

Upper versus lower airway microbiome and metagenome in children with cystic fibrosis and their correlation with lung inflammation
Cited by: 16
Author(s): Mariana E. Kirst, Dawn Baker, Eric Li, Mutasim Abu-Hasan, Gary P. Wang
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0054664

Whole Genome Gene Expression Analysis Reveals Casiopeína-Induced Apoptosis Pathways
Cited by: 31
Author(s): Alejandra Idan Valencia-Cruz, Laura Uribe-Figueroa, Rodrigo Galindo‐Murillo, Karol Baca-López, Anllely Grizett Gutiérrez, Adriana Vázquez-Aguirre, Lena Ruíz-Azuara, Enrique Hernández‐Lemus, Carmen Mejía
Software Mentions: 3
Published: almost 12 years ago

10.3389/fpls.2017.00391

Phylogeny Predicts the Quantity of Antimalarial Alkaloids within the Iconic Yellow Cinchona Bark (Rubiaceae: Cinchona calisaya)
Cited by: 35
Author(s): Carla Maldonado, Christopher J. Barnes, Claus Cornett, Else Holmfred, Steen Honoré Hansen, Claes Persson, Alexandre Antonelli, Nina Rønsted
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2021.703283

Lens orientalis Contributes Quantitative Trait Loci and Candidate Genes Associated With Ascochyta Blight Resistance in Lentil
Cited by: 10
Author(s): Rama Harinath Reddy Dadu, Ido Bar, Rebecca Ford, Prabhakaran Thanjavur Sambasivam, Janine Croser, Federico M. Ribalta, Sukhjiwan Kaur, Shimna Sudheesh, Dorin Gupta
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0177742

Using NextRAD sequencing to infer movement of herbivores among host plants
Cited by: 18
Author(s): Zhen F. Fu, Brendan Epstein, Joanna L. Kelley, Qi Zheng, Alan O. Bergland, Carmen I. Castillo Carrillo, Andrew S. Jensen, Jennifer Dahan, Alexander V. Karasev, William E. Snyder
Software Mentions: 3
Published: over 7 years ago

10.3389/fonc.2020.00757

Integration of Digital Pathologic and Transcriptomic Analyses Connects Tumor-Infiltrating Lymphocyte Spatial Density With Clinical Response to BRAF Inhibitors
Cited by: 9
Author(s): Artūras Žiemys, Michelle Kim, Alexander M. Menzies, James S. Wilmott, Georgina V. Long, Richard A. Scolyer, Larry Kwong, Ashley M. Holder, Genevieve M. Boland
Software Mentions: 3
Published: over 4 years ago

10.3389/fped.2021.618009

Impact of Probiotic B. infantis EVC001 Feeding in Premature Infants on the Gut Microbiome, Nosocomially Acquired Antibiotic Resistance, and Enteric Inflammation
Cited by: 33
Author(s): Marielle Nguyen, Heaven Holdbrooks, Prasanthi K. Mishra, Maria Abrantes, Sherri Eskew, Mariajamiela Garma, Cyr-Geraurd Oca, Carrie McGuckin, Cynthia B. Hein, Ryan D. Mitchell, Sufyan Kazi, Stephanie Chew, Giorgio Casaburi, Heather K. Brown, Steven A. Frese, Bethany M. Henrick
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2164-14-666

Intronic Non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees
Cited by: 62
Author(s): Pablo Cingolani, Xiaoyi Cao, Radhika S. Khetani, Chieh Chun Chen, Melissa Coon, Alya’a Sammak, Aliccia Bollig‐Fischer, Susan Land, Yun Huang, Matthew E. Hudson, Mark D. Garfinkel, Sheng Zhong, Gene E. Robinson, Douglas M. Ruden
Software Mentions: 3
Published: about 11 years ago

10.3390/microorganisms8060915

Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellum
Cited by: 12
Author(s): Regina Rettenmaier, Martina Schneider, Bernhard Munk, Michael Lebuhn, Sebastian Jünemann, Alexander Sczyrba, Irena Maus, Vladimir V. Zverlov, Wolfgang Liebl
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-019-3091-z

doepipeline: a systematic approach to optimizing multi-level and multi-step data processing workflows
Cited by: 2
Author(s): Daniel Svensson, Rickard Sjögren, David Sundell, Andreas Sjödin, Johan Trygg
Software Mentions: 3
Published: about 5 years ago

10.3389/fnins.2017.00691

Anodal Transcranial Direct Current Stimulation Increases Bilateral Directed Brain Connectivity during Motor-Imagery Based Brain-Computer Interface Control
Cited by: 28
Author(s): Bryan Baxter, Bradley J. Edelman, Abbas Sohrabpour, Bin He
Software Mentions: 3
Published: almost 7 years ago

10.3389/fmicb.2016.00941

Diversity and Distribution of Prokaryotes within a Shallow-Water Pockmark Field
Cited by: 23
Author(s): Donato Giovannelli, Giuseppe d’Errico, Federica Fiorentino, Daniele Fattorini, Francesco Regoli, Lorenzo Angeletti, Tatjana Bakran‐Petricioli, Costantino Vetriani, Mustafa Yücel, Marco Taviani, Elena Manini
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2164-14-540

Solanum torvum responses to the root-knot nematode Meloidogyne incognita
Cited by: 38
Author(s): Paolo Bagnaresi, T. Sala, Tiziana Irdani, Cristina Scotto, Antonella Lamontanara, Massimiliano Beretta, Giuseppe Leonardo Rotino, S. Sestili, Luigi Cattivelli, E. Sabatini
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2156-16-S2-S3

Investigation of a recent rise of dual amantadine-resistance mutations in the influenza A M2 sequence
Cited by: 27
Author(s): Matthew G. Durrant, Dennis L. Eggett, David D. Busath
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0149531

Divergence Times and Phylogenetic Patterns of Sebacinales, a Highly Diverse and Widespread Fungal Lineage
Cited by: 34
Author(s): Sigisfredo Garnica, Kai Riess, Max Emil Schön, Franz Oberwinkler, Sabrina Setaro
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-020-6603-3

Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq
Cited by: 9
Author(s): Maria Luisa Martin Cerezo, Marek Kučka, Karol Zub, Yingguang Frank Chan, Jarosław Bryk
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0083504

RNA Sequencing of the Exercise Transcriptome in Equine Athletes
Cited by: 43
Author(s): Stefano Capomaccio, Nicola Vitulo, Andrea Verini-Supplizi, Gianni Barcaccia, Alessandro Albiero, Michela D’Angelo, Davide Campagna, Giorgio Valle, Michela Felicetti, Maurizio Silvestrelli, Katia Cappelli
Software Mentions: 3
Published: almost 11 years ago

10.3389/fmicb.2017.02485

Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors
Cited by: 66
Author(s): Raymond Kiu, Shabhonam Caim, Sarah Alexander, Purnima Pachori, Lindsay J. Hall
Software Mentions: 3
Published: almost 7 years ago

10.3389/fmicb.2017.01008

Cesarean or Vaginal Birth Does Not Impact the Longitudinal Development of the Gut Microbiome in a Cohort of Exclusively Preterm Infants
Cited by: 44
Author(s): Christopher J. Stewart, Nicholas D. Embleton, Elizabeth Clements, Pamela N. Luna, Daniel P. Smith, Tatiana Fofanova, Andrew Nelson, Gillian Taylor, Caroline Orr, Joseph F. Petrosino, Janet Berrington, Stephen Cummings
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2016.01759

Bacterial Genomics Reveal the Complex Epidemiology of an Emerging Pathogen in Arctic and Boreal Ungulates
Cited by: 32
Author(s): Taya Forde, Karin Orsel, Ruth N. Zadoks, Roman Biek, Layne G. Adams, Sylvia Checkley, Tracy Davison, Jeroen De Buck, Mathieu Dumond, Brett Elkin, Laura Finnegan, Bryan Macbeth, Cait Nelson, Amanda Niptanatiak, Shane Sather, Helen Schwantje, Frank van der Meer, Susan Kutz
Software Mentions: 3
Published: about 8 years ago

10.3389/fmicb.2021.631250

Adaptive Gene Content and Allele Distribution Variations in the Wild and Domesticated Populations of Saccharomyces cerevisiae
Cited by: 12
Author(s): Dayong Han, Pei‐Jie Han, Karl Rumbold, Anbessa Dabassa Koricha, Shoufu Duan, Liang Song, Junyan Shi, Kuan Li, Qiming Wang, Feng‐Yan Bai
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0236684

Distinct patterns of activity in individual cortical neurons and local networks in primary somatosensory cortex of mice evoked by square-wave mechanical limb stimulation
Cited by: 2
Author(s): Mischa V Bandet, Bin Dong, Ian R. Winship
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0049455

Comparative Analysis of Genome Sequences Covering the Seven Cronobacter Species
Cited by: 104
Author(s): Susan Joseph, Prerak Desai, Yongmei Ji, Craig Cummings, Pei-Ju Rita Shih, Lovorka Degoricija, Alain Rico, Pius Brzoska, Stephen E. Hamby, Naqash Masood, Sumyya Hariri, Hana Sonbol, Nadia Chuzhanova, Michael McClelland, Manohar R. Furtado, Stephen Forsythe
Software Mentions: 3
Published: about 12 years ago

10.3389/fmicb.2017.01695

AR-13, a Celecoxib Derivative, Directly Kills Francisella In Vitro and Aids Clearance and Mouse Survival In Vivo
Cited by: 4
Author(s): Ky V. Hoang, Haley E. Adcox, James Fitch, David Gordon, Heather M. Curry, Larry S. Schlesinger, Peter White, John S. Gunn
Software Mentions: 3
Published: about 7 years ago

10.3389/fnins.2019.00615

Overexpression of a Neuronal Type Adenylyl Cyclase (Type 8) in Sinoatrial Node Markedly Impacts Heart Rate and Rhythm
Cited by: 32
Author(s): Jack M. Moen, Michael G. Matt, Christopher Ramirez, Kirill V. Tarasov, Khalid Chakir, Yelena S. Tarasova, Yevgeniya O. Lukyanenko, Kenta Tsutsui, Oliver Monfredi, Christopher H. Morrell, Syevda Tagirova, Yael Yaniv, Thanh Huynh, Karel Pacák, Ismayil Ahmet, Edward G. Lakatta
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0216565

Faecal microbiota changes associated with the moult fast in chinstrap and gentoo penguins
Cited by: 7
Author(s): Won Young Lee, Hyunjun Cho, Min‐Cheol Kim, Binu M. Tripathi, Jin-Woo Jung, Hosung Chung, Jeong-Hoon Kim
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0074256

Gene Regulatory Networks Elucidating Huanglongbing Disease Mechanisms
Cited by: 90
Author(s): Federico Martinelli, Russell L. Reagan, Sandra L. Uratsu, My L. Phu, Ute Albrecht, Wenwei Zhao, Cristina E. Davis, Kim D. Bowman, Abhaya M. Dandekar
Software Mentions: 3
Published: about 11 years ago

10.1186/1471-2164-13-492

Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat
Cited by: 35
Author(s): Andreas W. Schreiber, Matthew Hayden, Kerrie Forrest, Stephan Kong, Peter Langridge, Ute Baumann
Software Mentions: 3
Published: almost 13 years ago

10.1007/s00335-016-9663-6

Genome characterization of the selected long- and short-sleep mouse lines
Cited by: 4
Author(s): Robin D. Dowell, Aaron Odell, Phillip A. Richmond, Daniel Malmer, Eitan Halper-Stromberg, Beth Bennett, Colin Larson, Sonia M. Leach, Richard A. Radcliffe
Software Mentions: 3
Published: about 8 years ago

10.3389/fimmu.2019.01295

miRNAs Involved in M1/M2 Hyperpolarization Are Clustered and Coordinately Expressed in Alcoholic Hepatitis
Cited by: 18
Author(s): Adam Kim, Paramananda Saikia, Laura E. Nagy
Software Mentions: 3
Published: over 5 years ago

10.1186/s12936-015-1081-9

UTR introns, antisense RNA and differentially spliced transcripts between Plasmodium yoelii subspecies
Cited by: 13
Author(s): Jian Li, Baowei Cai, Yanwei Qi, Wenting Zhao, Jianwen Liu, Rui-Xue Xu, Qiuxiang Pang, Zhi‐Yong Tao, Liu Hong, Shengfa Liu, Maarten Leerkes, Mariam Quiñones, Xin-zhuan Su
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0159177

Immunophenotypic and Ultrastructural Analysis of Mast Cells in Hermansky-Pudlak Syndrome Type-1: A Possible Connection to Pulmonary Fibrosis
Cited by: 11
Author(s): Arnold S. Kirshenbaum, Glenn Cruse, Avanti Desai, Geethani Bandara, Maarten Leerkes, Chyi‐Chia Richard Lee, Elizabeth R. Fischer, Kevin O’Brien, Bernadette R. Gochuico, Kelly D. Stone, William A. Gahl, Dean D. Metcalfe
Software Mentions: 3
Published: over 8 years ago

Projects: pypi: custom

Papers Mentioning custom 1,363