Ecosyste.ms: Papers

10.1371/journal.pntd.0008623

Population genomic evidence that human and animal infections in Africa come from the same populations of Dracunculus medinensis
Cited by: 16
Author(s): Caroline Durrant, Elizabeth A. Thiele, Nancy Holroyd, Stephen R. Doyle, Guillaume Sallé, Alan S. Tracey, Geetha Sankaranarayanan, Magda E. Lotkowska, Hayley M. Bennett, Harrison Thomas, Zahra Abdellah, Ouakou Tchindebet, Mesfin Wossen, Makoy Samuel Yibi Logora, Cheick Oumar Coulibaly, Adam Weiss, Albrecht I. Schulte‐Hostedde, Jeremy M. Foster, Christopher A. Cleveland, Michael J. Yabsley, Ernesto Ruiz‐Tiben, Matthew Berriman, Mark L. Eberhard, James A. Cotton
Software Mentions: 8
Published: almost 4 years ago

10.1590/1678-4685-GMB-2016-0230

Approaches for in silico finishing of microbial genome sequences
Cited by: 17
Author(s): Frederico Schmitt Kremer, Alan J. A. McBride, Luciano da Silva Pinto
Software Mentions: 8
Published: about 7 years ago

10.1098/rspb.2014.1371

A global model of the response of tropical and sub-tropical forest biodiversity to anthropogenic pressures
Cited by: 175
Author(s): Tim Newbold, Lawrence N. Hudson, Helen R. P. Phillips, Samantha L. L. Hill, Sara Contu, Igor Lysenko, Abigayil Blandon, Stuart H. M. Butchart, Hollie Booth, Julie Day, Adriana De Palma, Michelle L K Harrison, Lucinda Kirkpatrick, Edwin Pynegar, Alexandra Robinson, Jake E. Simpson, Georgina M. Mace, Jörn P. W. Scharlemann, Andy Purvis
Software Mentions: 7
Published: about 10 years ago

10.1186/s13072-021-00415-6

Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR
Cited by: 1
Author(s): Michael Scherer, Gilles Gasparoni, Souad Rahmouni, Tatiana I. Shashkova, Marion Arnoux, Édouard Louis, Arina Nostaeva, Diana Avalos, Emmanouil T. Dermitzakis, Yurii S. Aulchenko, Thomas Lengauer, Paul Lyons, Michel Georges, Jörn Walter
Software Mentions: 7
Published: about 3 years ago

10.1099/mgen.0.000156

Assembly of highly repetitive genomes using short reads: the genome of discrete typing unit III Trypanosoma cruzi strain 231
Cited by: 23
Author(s): Rodrigo P. Baptista, João Luís Reis-Cunha, Jeremy D. DeBarry, Égler Chiari, Jessica C. Kissinger, Daniella Castanheira Bartholomeu, Andréa Mara Macedo
Software Mentions: 6
Published: over 6 years ago

10.1186/1471-2164-15-1103

An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies
Cited by: 75
Author(s): Romain Blanc-Mathieu, Bram Verhelst, Évelyne Derelle, Stéphane Rombauts, François‐Yves Bouget, Isabelle A. Carré, Annie Château, Adam Eyre‐Walker, Nigel Grimsley, Hervé Moreau, Benoît Piégu, Éric Rivals, Wendy Schackwitz, Yves Van de Peer, Gwenaël Piganeau
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pgen.1008770

Multiple mechanisms regulate H3 acetylation of enhancers in response to thyroid hormone
Cited by: 19
Author(s): Stine M. Præstholm, Majken Siersbæk, Ronni Nielsen, Xuguang Zhu, Anthony N. Hollenberg, Sheue-yann Cheng, Lars Grøntved
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-018-26484-4

Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo
Cited by: 11
Author(s): David W. Waite, Melissa Dsouza, Yuji Sekiguchi, Philip Hugenholtz, Michael W. Taylor
Software Mentions: 5
Published: over 6 years ago

10.1098/rstb.2010.0127

Competition for land
Cited by: 406
Author(s): Pete Smith, P. J. Gregory, Detlef van Vuuren, Michael Obersteiner, Petr Havlík, Mark Rounsevell, Jeremy Woods, Elke Stehfest, Jessica Bellarby
Software Mentions: 5
Published: about 14 years ago

10.1186/1471-2164-13-531

Comparative genomic analysis of human infective Trypanosoma cruzi lineages with the bat-restricted subspecies T. cruzi marinkellei
Cited by: 57
Author(s): Oscar Franzén, Carlos Talavera-López, Stephen Ochaya, Claire E. Butler, Louisa A. Messenger, Michael D. Lewis, Martin S. Llewellyn, C. J. Marinkelle, Kevin M. Tyler, Michael A. Miles, Björn Andersson
Software Mentions: 5
Published: almost 13 years ago

10.1002/ece3.7052

Environment‐induced changes in reproductive strategies and their transgenerational effects in the three‐spined stickleback
Cited by: 3
Author(s): Náyade Álvarez‐Quintero, Alberto Velando, José C. Noguera, Sin‐Yeon Kim
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pbio.2006249

Insulin signaling and reduced glucocorticoid receptor activity attenuate postprandial gene expression in liver
Cited by: 35
Author(s): Adrija Kalviša, Majken Siersbæk, Stine M. Præstholm, Line Julie Lindorf Christensen, Ronni Nielsen, Oliver Stöhr, Sabine Vettorazzi, Jan Tuckermann, Morris F. White, Susanne Mandrup, Lars Grøntved
Software Mentions: 4
Published: almost 6 years ago

10.1038/srep43149

The hidden perils of read mapping as a quality assessment tool in genome sequencing
Cited by: 4
Author(s): Burhan Lehri, Alan M. Seddon, Andrey V. Karlyshev
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-016-2502-z

Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia
Cited by: 71
Author(s): Charles H. D. Williamson, Jason W. Sahl, Theresa J. Smith, Gary Xie, Brian Foley, Leonard A. Smith, Rafael Fernández, Miia Lindström, Hannu Korkeala, Paul Keim, Jeffrey T. Foster, Karen K. Hill
Software Mentions: 4
Published: over 8 years ago

10.12688/wellcomeopenres.15590.1

Evolutionary analysis of the most polymorphic gene family in falciparum malaria
Cited by: 56
Author(s): Thomas D. Otto, Sammy A. Assefa, Ulrike Böhme, Mandy Sanders, Dominic Kwiatkowski, Matthew Berriman, Chris Newbold
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-017-19128-6

Virtual Genome Walking across the 32 Gb Ambystoma mexicanum genome; assembling gene models and intronic sequence
Cited by: 9
Author(s): Teri Evans, Andrew D. Johnson, Matthew Loose
Software Mentions: 4
Published: almost 7 years ago

10.1038/srep16324

Revisiting the reference genomes of human pathogenic Cryptosporidium species: reannotation of C. parvum Iowa and a new C. hominis reference
Cited by: 42
Author(s): Juan Pablo Isaza, Ana Luz Galván, Víctor Polanco, Bernice Huang, Andrey V. Matveyev, Myrna G. Serrano, Patrício Manque, Gregory A. Buck, Juan F. Alzate
Software Mentions: 3
Published: about 9 years ago

10.1038/srep40366

Lessons from temporal and spatial patterns in global use of N and P fertilizer on cropland
Cited by: 151
Author(s): A. F. Bouwman, Arthur Beusen, Luis Lassaletta, Dirk van Apeldoorn, Hans van Grinsven, J. Zhang, M. K. Van
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41597-020-00669-x

Global land use for 2015–2100 at 0.05° resolution under diverse socioeconomic and climate scenarios
Cited by: 65
Author(s): Min Chen, Chris R. Vernon, Neal Graham, Mohamad Hejazi, Maoyi Huang, Yanyan Cheng, Katherine Calvin
Software Mentions: 3
Published: about 4 years ago

10.3390/ijerph15071315

A Review of Methods for Assessing the Environmental Health Impacts of an Agricultural System
Cited by: 7
Author(s): Lise Grout, Simon Hales, Nigel P. French, Michael G Baker
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pntd.0002728

Presence of Extensive Wolbachia Symbiont Insertions Discovered in the Genome of Its Host Glossina morsitans morsitans
Cited by: 63
Author(s): Corey L. Brelsfoard, George Tsiamis, Marco Falchetto, Ludvik M. Gomulski, Erich Loza Telleria, Uzma Alam, Vangelis Doudoumis, Francesca Scolari, Joshua B. Benoit, Martin Swain, Peter Takáč, Anna R. Malacrida, Kostas Bourtzis, Serap Aksoy
Software Mentions: 3
Published: over 10 years ago

10.1016/j.ejrh.2019.01.004

Modelling nutrient fluxes into the Mediterranean Sea
Cited by: 24
Author(s): Anna Malagó, F. Bouraoui, Bruna Grizzetti, Ad de Roo
Software Mentions: 3
Published: over 5 years ago

10.3390/s21041134

ALMI—A Generic Active Learning System for Computational Object Classification in Marine Observation Images
Cited by: 2
Author(s): Torben Möller, Tim Wilhelm Nattkemper
Software Mentions: 3
Published: almost 4 years ago

10.1128/JVI.03614-14

Genome Diversity of Epstein-Barr Virus from Multiple Tumor Types and Normal Infection
Cited by: 193
Author(s): Anne L. Palser, Nicholas Grayson, Rob White, Craig Corton, Samantha Correia, Mohammed Ba Abdullah, Simon J. Watson, Matthew Cotten, John R. Arrand, Paul G. Murray, Martin J. Allday, Alan B. Rickinson, Young Lw, Paul J. Farrell, Paul Kellam
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pntd.0002557

Genomic Characterisation of Invasive Non-Typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans Isolates from Malawi
Cited by: 23
Author(s): Christina Bronowski, María Fookes, Ruth Gilderthorp, Kevin E. Ashelford, Simon R. Harris, Ajib Phiri, Neil Hall, Michael A. Gordon, John Wain, C. A. Hart, Paul Wigley, Nicholas R. Thomson, Craig Winstanley
Software Mentions: 3
Published: about 11 years ago

10.1186/s13099-016-0084-6

Genome sequence of Escherichia coli NCCP15653, a group D strain isolated from a diarrhea patient
Cited by: 2
Author(s): Min Jung Kwak, Myoung Soo Kim, Soon Kyeong Kwon, Seung Hak Cho, Jihyun F. Kim
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13059-019-1813-1

IMAGE: high-powered detection of genetic effects on DNA methylation using integrated methylation QTL mapping and allele-specific analysis
Cited by: 12
Author(s): Yue Fan, Tauras P. Vilgalys, Shuang Sun, Qinke Peng, Jenny Tung, Xiang Zhou
Software Mentions: 3
Published: about 5 years ago

10.1038/sdata.2017.87

A web platform for landuse, climate, demography, hydrology and beach erosion in the Black Sea catchment
Cited by: 12
Author(s): Anthony Lehmann, Yaniss Guigoz, Nicolas Ray, Emanuele Mancosu, Karim C. Abbaspour, Elham Rouholahnejad Freund, Karin Allenbach, Andrea Bono, Marc Fasel, Ana Gago-Silva, Roger Bär, Pierre Lacroix, Gaston Giuliani
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2105-13-229

AbsIDconvert: An absolute approach for converting genetic identifiers at different granularities
Cited by: 9
Author(s): Fahim Mohammad, Robert M. Flight, Benjamin J. Harrison, Jeffrey C. Petruska, Eric C. Rouchka
Software Mentions: 3
Published: about 12 years ago

10.7554/eLife.06974

Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites
Cited by: 175
Author(s): Yong Woo, Hifzur Rahman Ansari, Thomas D. Otto, Christen M. Klinger, Martin Kolísko, Jan Michálek, Alka Saxena, Dhanasekaran Shanmugam, Annageldi Tayyrov, Alaguraj Veluchamy, Shahjahan Ali, Axel Bernal, Javier del Campo, Jaromír Cihlář, Pavel Flegontov, Sebastian G. Gornik, Eva Hajdušková, Aleš Horák, Jan Janouškovec, Nicholas J. Katris, Fred D. Mast, Diego Miranda‐Saavedra, Tobias Mourier, Raeece Naeem, Mridul Nair, Aswini K. Panigrahi, Neil D. Rawlings, Eriko Padron-Regalado, Abhinay Ramaprasad, Nadira Samad, Aleš Tomčala, Jonathan M. Wilkes, Daniel E. Neafsey, Christian Doerig, Chris Bowler, Patrick J. Keeling, David S. Roos, Joel B. Dacks, Thomas J. Templeton, Ross F. Waller, Julius Lukeš, Miroslav Oborník, Arnab Pain
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2164-6-123

XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis
Cited by: 7
Author(s): Alexander Sczyrba, Michael Beckstette, Ali H. Brivanlou, Robert Giegerich, Curtis R. Altmann
Software Mentions: 3
Published: about 19 years ago

10.1186/1471-2164-13-385

Genetic changes during a laboratory adaptive evolution process that allowed fast growth in glucose to an Escherichia coli strain lacking the major glucose transport system
Cited by: 38
Author(s): César Aguilar, Adelfo Escalante, Noemí Flores, R. Anda, Fernando Riveros-Mckay, Guillermo Gosset, Enrique Morett, Francisco Bolívar
Software Mentions: 3
Published: over 12 years ago

10.3389/fmicb.2020.01930

New Plasmodium vivax Genomes From the China-Myanmar Border
Cited by: 5
Author(s): Awtum Brashear, Adam C Huckaby, Qi Fan, Luke J Dillard, Yubing Hu, Yuling Li, Yan Zhao, Zenglei Wang, Yaming Cao, Jun Miao, Jennifer L. Guler, Liwang Cui
Software Mentions: 3
Published: over 4 years ago

10.1007/s00787-017-0972-4

Risk factors for comorbid oppositional defiant disorder in attention-deficit/hyperactivity disorder
Cited by: 26
Author(s): Siri D. S. Noordermeer, Marjolein Luman, Wouter D. Weeda, Jan K. Buitelaar, Jennifer S. Richards, Catharina A. Hartman, Pieter J. Hoekstra, Barbara Franke, Dirk J. Heslenfeld, Jaap Oosterlaan
Software Mentions: 3
Published: over 7 years ago

10.1007/s10584-019-02539-x

Biomass residues as twenty-first century bioenergy feedstock—a comparison of eight integrated assessment models
Cited by: 28
Author(s): Steef V. Hanssen, Vassilis Daioglou, Zoran J. N. Steinmann, Stefan Frank, Alexander Popp, Thierry Brunelle, Pekka Lauri, Tomoko Hasegawa, Mark A. J. Huijbregts, Detlef P. van Vuuren
Software Mentions: 3
Published: about 5 years ago

10.1186/gb-2010-11-4-r41

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps
Cited by: 274
Author(s): Isheng Jason Tsai, Thomas D. Otto, Matthew Berriman
Software Mentions: 3
Published: over 14 years ago

10.3390/pharmaceutics8020015

Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine
Cited by: 12
Author(s): Wenming Xiao, Leihong Wu, Gökhan Yavaş, Vahan Simonyan, Baitang Ning, Huixiao Hong
Software Mentions: 3
Published: over 8 years ago

10.1093/gbe/evu067

Comparative Genomics of Taphrina Fungi Causing Varying Degrees of Tumorous Deformity in Plants
Cited by: 29
Author(s): Isheng Jason Tsai, Eiji Tanaka, Hayato Masuya, Ryusei Tanaka, Y. Hirooka, Rikiya Endoh, Norio Sahashi, Taisei Kikuchi
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0108009

Genome-Based Comparative Analyses of Antarctic and Temperate Species of Paenibacillus
Cited by: 30
Author(s): Melissa Dsouza, Michael W. Taylor, Susan Turner, Jackie Aislabie
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pbio.3000467

Dynamic enhancers control skeletal muscle identity and reprogramming
Cited by: 31
Author(s): Krithika Ramachandran, Madhavi D. Senagolage, Meredith A Sommars, Christopher R. Futtner, Yasuhiro Omura, Amanda L. Allred, Grant D. Barish
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-018-4539-7

The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development
Cited by: 19
Author(s): Josiah Tad Wagner, Param Priya Singh, Amie L. Romney, Claire L. Riggs, Patrick Minx, Steven Cody Woll, Jake Roush, Wesley C. Warren, Anne Brunet, Jason E. Podrabsky
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pgen.1003868

Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection
Cited by: 71
Author(s): Nicholas J. Croucher, Andrea M. Mitchell, Katherine A. Gould, Donald Inverarity, Lars Barquist, Theresa Feltwell, María Fookes, Simon R. Harris, Janina Dordel, Susannah J. Salter, Sarah Browall, Helena Žemličková, Julian Parkhill, Staffan Normark, Birgitta Henriques‐Normark, Jason Hinds, Tim Mitchell, Stephen D. Bentley
Software Mentions: 3
Published: about 11 years ago

10.1186/s40359-019-0352-6

Enhanced cognitive processing by viewing snakes in children with autism spectrum disorder. A preliminary study
Cited by: 0
Author(s): Marine Grandgeorge, Alban Lemasson, Martine Hausberger, Hiroki Koda, Nobuo Masataka
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pntd.0001455

A Systematically Improved High Quality Genome and Transcriptome of the Human Blood Fluke Schistosoma mansoni
Cited by: 365
Author(s): Anna V. Protasio, Isheng Jason Tsai, Anne Babbage, Sarah Nichol, Martin Hunt, Martin Aslett, Nishadi De Silva, Giles Velarde, Tim Anderson, Richard Clark, Claire Davidson, G. Dillon, Nancy Holroyd, Philip T. LoVerde, Christine Lloyd, Jacquelline McQuillan, Guilherme Oliveira, Thomas D. Otto, Sophia J. Parker-Manuel, Michael A. Quail, R. A. Wilson, Adhemar Zerlotini, David W. Dunne, Matthew Berriman
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0101419

Recombinations in Staphylococcal Cassette Chromosome mec Elements Compromise the Molecular Detection of Methicillin Resistance in Staphylococcus aureus
Cited by: 49
Author(s): Grant A. Hill-Cawthorne, Lyndsey O. Hudson, Moataz Abd El Ghany, Olaf Piepenburg, Mridul Nair, Andrew Dodgson, Matthew S. Forrest, Taane G. Clark, Arnab Pain
Software Mentions: 2
Published: over 10 years ago

10.1186/s43058-020-00042-4

Is it time to RE-AIM? A systematic review of economic empowerment as HIV prevention intervention for adolescent girls and young women in sub-Saharan Africa using the RE-AIM framework
Cited by: 12
Author(s): Juliet Iwelunmor, Ucheoma Nwaozuru, Chisom Obiezu-Umeh, Florida Uzoaru, John E. Ehiri, Jami Curley, Oliver Ezechi, Collins O. Airhihenbuwa, Fred M. Ssewamala
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2164-7-227

Genomic organization and evolution of the ULBP genes in cattle
Cited by: 21
Author(s): Joshua H. Larson, Brandy M. Marron, Jonathan E. Beever, Bruce A. Roe, Harris A. Lewin
Software Mentions: 2
Published: about 18 years ago

10.1186/1471-2164-15-1131

Interspecific and intraspecific gene variability in a 1-Mb region containing the highest density of NBS-LRR genes found in the melon genome
Cited by: 15
Author(s): Víctor González, Núria Aventín, Emilio Centeno, Pere Puigdomènech
Software Mentions: 2
Published: almost 10 years ago

10.1007/s11625-017-0521-6

Assessment of mitigation strategies as tools for risk management under future uncertainties: a multi-model approach
Cited by: 10
Author(s): Shunsuke Mori, Toyoaki Washida, Atsushi Kurosawa, Toshihiko Masui
Software Mentions: 2
Published: almost 7 years ago

10.1029/2021JA029292

Multi‐Instrument Characterization of Magnetospheric Cold Plasma Dynamics in the June 22, 2015 Geomagnetic Storm
Cited by: 4
Author(s): M. Vellante, Kazue Takahashi, Alfredo Del Corpo, Irina Zhelavskaya, J. Goldstein, I. R. Mann, E. Pietropaolo, Jan Reda, B. Heilig
Software Mentions: 2
Published: over 3 years ago

10.1002/jia2.25787

HIV‐sensitive social protection for vulnerable young women in East and Southern Africa: a systematic review
Cited by: 6
Author(s): Ran van der Wal, David Loutfi, Quan Nha Hong, Isabelle Vedel, Anne Cockcroft, Mira Johri, Neil Andersson
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0052038

Semi-Automatic In Silico Gap Closure Enabled De Novo Assembly of Two Dehalobacter Genomes from Metagenomic Data
Cited by: 45
Author(s): Siu Wa Tang, Yunchen Gong, Elizabeth A. Edwards
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0101130

Brain Volumetric Correlates of Autism Spectrum Disorder Symptoms in Attention Deficit/Hyperactivity Disorder
Cited by: 22
Author(s): Laurence O’Dwyer, Colby J. Tanner, Eelco V. van Dongen, Corina U. Greven, Janita Bralten, Marcel P. Zwiers, Barbara Franke, Jaap Oosterlaan, Dirk J. Heslenfeld, Pieter J. Hoekstra, Catharina A. Hartman, Nanda Rommelse, Jan K. Buitelaar
Software Mentions: 2
Published: over 10 years ago

10.1038/s41598-017-17309-x

A Coxiella mutualist symbiont is essential to the development of Rhipicephalus microplus
Cited by: 96
Author(s): Melina Garcia Guizzo, Luís Fernando Parizi, Rodrigo Dutra Nunes, Renata Schama, Rodolpho Mattos Albano, Lucas Tirloni, Daiane P. Oldiges, Ricardo P. Vieira, Wanderson Henrique Cruz Oliveira, Milane de Souza Leite, Sergio A. Gonzales, Marisa Diana Farber, Orlando B. Martins, Itabajara da Silva Vaz, Pedro L. Oliveira
Software Mentions: 2
Published: almost 7 years ago

10.1007/s11214-019-0599-5

Explosive Magnetotail Activity
Cited by: 70
Author(s): M. I. Sitnov, J. Birn, Banafsheh Ferdousi, E. Gordeev, Yuri V. Khotyaintsev, V. G. Merkin, T. Motoba, A. Otto, E. V. Panov, P. L. Pritchett, Fulvia Pucci, J. Raeder, A. Runov, В. А. Сергеев, M. Velli, Xuzhi Zhou
Software Mentions: 2
Published: over 5 years ago

10.1074/jbc.M114.561845

Involvement of MicroRNAs in the Regulation of Muscle Wasting during Catabolic Conditions
Cited by: 120
Author(s): Ricardo Soares, Stefano Cagnin, Francesco Chemello, Matteo Silvestrin, Antonio Musarò, Cristiano De Pittà, Gerolamo Lanfranchi, Marco Sandri
Software Mentions: 2
Published: over 10 years ago

10.1186/s13012-017-0619-3

Implementation findings from a hybrid III implementation-effectiveness trial of the Diabetes Prevention Program (DPP) in the Veterans Health Administration (VHA)
Cited by: 48
Author(s): Laura J. Damschroder, Caitlin M. Reardon, Mona AuYoung, Tannaz Moin, Santanu K. Datta, Jordan B Sparks, Matthew L. Maciejewski, Nanette I. Steinle, Jane Weinreb, M. E. Hughes, Lillian F. Pinault, Xinran Xiang, Charles J. Billington, Caroline R. Richardson
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1002219

Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilus
Cited by: 340
Author(s): Taisei Kikuchi, James A. Cotton, Johnathan J. Dalzell, Koichi Hasegawa, Natsumi Kanzaki, Paul McVeigh, Takuma Takanashi, Isheng Jason Tsai, Samuel Assefa, Peter J. A. Cock, Thomas D. Otto, Martin Hunt, Adam J. Reid, Alejandro Sánchez-Flores, Kazuko Tsuchihara, Toshiro Yokoi, Mattias C. Larsson, Johji Miwa, Aaron G. Maule, Norio Sahashi, John T. Jones, Matthew Berriman
Software Mentions: 2
Published: about 13 years ago

10.1186/s12889-019-7154-x

A protocol for a cluster-randomized controlled trial testing an empowerment intervention to prevent sexual assault in upper primary school adolescents in the informal settlements of Nairobi, Kenya
Cited by: 11
Author(s): Clea Sarnquist, Jennifer L. Kang, Mary Amuyunzu-Nyamongo, Gabriel Oguda, Dorothy Otieno, Benjamin Mboya, Nancy Omondi, Duncan Kipkirui, Michael Baiocchi
Software Mentions: 2
Published: over 5 years ago

10.1186/s12859-015-0705-y

WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data
Cited by: 7
Author(s): Gregory K. Farrant, Mark Hoebeke, Frédéric Partensky, Gwendoline Andres, Matthieu Le Corre, Laurence Garczarek
Software Mentions: 2
Published: about 9 years ago

10.1007/s11121-019-01070-w

Intervention with Microfinance for AIDS and Gender Equity (IMAGE): Women’s Engagement with the Scaled-up IMAGE Programme and Experience of Intimate Partner Violence in Rural South Africa
Cited by: 7
Author(s): Louise Knight, N. Ranganathan, Tanya Abramsky, Tara Polzer-Ngwato, Lufuno Muvhango, Mpho Molebatsi, Heidi Stöckl, Shelley Lees, Charlotte Watts
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pbio.2006035

Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution
Cited by: 30
Author(s): Aude Gilabert, Thomas D. Otto, Gavin G. Rutledge, Blaise Franzon, Benjamin Ollomo, Céline Arnathau, Patrick Durand, Nancy Diamella Moukodoum, Alain-Prince Okouga, Barthélémy Ngoubangoye, Boris Makanga, Larson Boundenga, Christophe Paupy, François Renaud, Franck Prugnolle, Virginie Rougeron
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-11-395

A draft physical map of a D-genome cotton species (Gossypium raimondii)
Cited by: 47
Author(s): Lifeng Lin, Gary J. Pierce, John E. Bowers, James C. Estill, Rosana Compton, Lisa K. Rainville, Changsoo Kim, Cornelia Lemke, Junkang Rong, Haibao Tang, Xiyin Wang, Michele Braidotti, Amy H. Chen, Kristen A. Chicola, Kristi Collura, Ethan Epps, Wolfgang Golser, Corrinne E. Grover, Jennifer Ingles, Santhosh Karunakaran, Dave Kudrna, Jaime Olive, Nabila Tabassum, Eareana Um, Marina Wissotski, Yeisoo Yu, Andrea Zuccolo, Md Jamilur Rahman, Daniel G. Peterson, Rod A. Wing, Jonathan F. Wendel, Andrew H. Paterson
Software Mentions: 2
Published: over 14 years ago

10.1186/gb-2012-13-6-r56

Toward almost closed genomes with GapFiller
Cited by: 915
Author(s): Marten Boetzer, Walter Pirovano
Software Mentions: 2
Published: almost 13 years ago

10.1098/rstb.2010.0141

Managing uncertainty: a review of food system scenario analysis and modelling
Cited by: 85
Author(s): Michael Reilly, Dirk Willenbockel
Software Mentions: 2
Published: about 14 years ago

10.1186/gb-2014-15-3-r42

A comprehensive evaluation of assembly scaffolding tools
Cited by: 155
Author(s): Martin Hunt, Chris Newbold, Matthew Berriman, Thomas D. Otto
Software Mentions: 2
Published: almost 11 years ago

10.1111/gcb.14848

Projecting terrestrial biodiversity intactness with GLOBIO 4
Cited by: 75
Author(s): Aafke M. Schipper, Jelle P. Hilbers, Johan Meijer, Laura H. Antão, Ana Benítez‐López, Melinda M.J. de Jonge, Luuk H. Leemans, Eddy Scheper, Rob Alkemade, Jonathan C. Doelman, Sido D. Mylius, Elke Stehfest, Detlef P. van Vuuren, Willem Jan van Zeist, Mark A. J. Huijbregts
Software Mentions: 2
Published: about 5 years ago

10.3389/fnhum.2016.00211

Studying Autism Spectrum Disorder with Structural and Diffusion Magnetic Resonance Imaging: A Survey
Cited by: 74
Author(s): Marwa Ismail, Robert Keynton, Mahmoud Mostapha, Ahmed ElTanboly, Manuel F. Casanova, Georgy Gimel’farb, Ayman El-Baz
Software Mentions: 2
Published: over 8 years ago

10.3389/fgene.2021.575405

Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine Breed
Cited by: 5
Author(s): Simon Boitard, Cyriel Paris, Natalia Sevane, Bertrand Servin, Kenza Bazi-Kabbaj, S. Dunner
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13072-021-00392-w

Early-life undernutrition induces enhancer RNA remodeling in mice liver
Cited by: 2
Author(s): Yinyu Wang, Yiting Mao, Yiran Zhao, Xianfu Yi, Guo-Hui Ding, Chuanjin Yu, Jian‐Zhong Sheng, Xinmei Liu, Yicong Meng, He‐Feng Huang
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-244X-11-55

The impact of study design and diagnostic approach in a large multi-centre ADHD study: Part 2: Dimensional measures of psychopathology and intelligence
Cited by: 44
Author(s): Urs Müller, Philip Asherson, Tobias Banaschewski, Jan K. Buitelaar, Richard P. Ebstein, Jacques Eisenberg, Michael Gill, Iris Manor, Ana Miranda, Robert D. Oades, Herbert Roeyers, Aribert Rothenberger, Joseph A. Sergeant, Edmund Sonuga‐Barke, Margaret Thompson, Stephen V. Faraone, Hans-Christoph Steinhausen
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-244X-11-54

The impact of study design and diagnostic approach in a large multi-centre ADHD study. Part 1: ADHD symptom patterns
Cited by: 65
Author(s): Urs Müller, Philip Asherson, Tobias Banaschewski, Jan K. Buitelaar, Richard P. Ebstein, Jacques Eisenberg, Michael Gill, Iris Manor, Ana Miranda, Robert D. Oades, Herbert Roeyers, Aribert Rothenberger, Joseph A. Sergeant, Edmund Sonuga‐Barke, Margaret Thompson, Stephen V. Faraone, Hans-Christoph Steinhausen
Software Mentions: 2
Published: over 13 years ago

10.12688/wellcomeopenres.9876.1

A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes
Cited by: 101
Author(s): Sarah Auburn, Ulrike Böhme, Sascha Steinbiss, Hidayat Trimarsanto, Jessica B. Hostetler, Mandy Sanders, Qi Gao, François Nosten, Chris Newbold, Matthew Berriman, Ric N. Price, Thomas D. Otto
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0165620

Decreased Left Caudate Volume Is Associated with Increased Severity of Autistic-Like Symptoms in a Cohort of ADHD Patients and Their Unaffected Siblings
Cited by: 15
Author(s): Laurence O’Dwyer, Colby J. Tanner, Eelco V. van Dongen, Corina U. Greven, Janita Bralten, Marcel P. Zwiers, Barbara Franke, Dirk J. Heslenfeld, Jaap Oosterlaan, Pieter J. Hoekstra, Catharina A. Hartman, Wouter B. Groen, Nanda Rommelse, Jan K. Buitelaar
Software Mentions: 2
Published: about 8 years ago

10.1186/s13039-015-0158-z

Construction of BAC contig maps of homoeologous chromosomes A12 and D12 of Gossypium hirsutum L. acc. TM-1
Cited by: 0
Author(s): Yanhui Lv, Dan Ma, Wan Liang, Yuanda Lv, Wenshan Guo, Yan Hu, Tianzhen Zhang
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0121052

Genomic Characterization of Burkholderia pseudomallei Isolates Selected for Medical Countermeasures Testing: Comparative Genomics Associated with Differential Virulence
Cited by: 23
Author(s): Jason W. Sahl, Christopher John Allender, Rebecca E. Colman, Katy J. Califf, James M. Schupp, Bart J. Currie, Kristopher E. Van Zandt, H. Carl Gelhaus, Paul Keim, Apichai Tuanyok
Software Mentions: 2
Published: over 9 years ago

10.1186/s12889-015-2460-4

Systematic review of structural interventions for intimate partner violence in low- and middle-income countries: organizing evidence for prevention
Cited by: 163
Author(s): Christine Bourey, Whitney Williams, Erin Bernstein, Robert Stephenson
Software Mentions: 2
Published: about 9 years ago

10.1186/s40623-018-0843-3

Simultaneous observation of auroral substorm onset in Polar satellite global images and ground-based all-sky images
Cited by: 6
Author(s): A. Ieda, Kirsti Kauristie, Y. Nishimura, Yukinaga Miyashita, H. U. Frey, Liisa Juusola, Daniel Whiter, M. Nosé, M. O. Fillingim, F. Honary, Neil Rogers, Yoshizumi Miyoshi, Takuya Miura, T. Kawashima, S. Machida
Software Mentions: 2
Published: over 6 years ago

10.1186/s13229-021-00457-3

The Monash Autism-ADHD genetics and neurodevelopment (MAGNET) project design and methodologies: a dimensional approach to understanding neurobiological and genetic aetiology
Cited by: 4
Author(s): Rachael Knott, Beth Johnson, Jeggan Tiego, Olivia Mellahn, Amy Finlay, Kathryn Kallady, Maria Kouspos, Vishnu Priya Mohanakumar Sindhu, Ziarih Hawi, Aurina Arnatkevičiūtė, Tracey Chau, Dalia Maron, Emily Clare Mercieca, Kirsten Furley, Katrina Harris, Katrina Williams, Alexandra Ure, Alex Fornito, Kylie Megan Gray, David Coghill, Ann E. Nicholson, Dinh Phung, Eva Loth, Luke Mason, Declan Murphy, Jan K. Buitelaar, Mark A. Bellgrove
Software Mentions: 2
Published: over 3 years ago

10.1007/s11027-014-9549-4

Multi-model comparison of the economic and energy implications for China and India in an international climate regime
Cited by: 40
Author(s): Daniel Johansson, Paul L. Lucas, Matthias Weitzel, Erik O. Ahlgren, Amir Bazaz, Wenying Chen, Michel den Elzen, Joydeep Ghosh, Maria Grahn, Qiao‐Mei Liang, Sonja Peterson, Basanta K. Pradhan, Bas van Ruijven, P.R. Shukla, Detlef van Vuuren, Yi‐Ming Wei
Software Mentions: 2
Published: over 10 years ago

10.1186/s12864-019-5562-z

Genomic analysis of Leptospira interrogans serovar Paidjan and Dadas isolates from carrier dogs and comparative genomic analysis to detect genes under positive selection
Cited by: 7
Author(s): Alongkorn Kurilung, Chantisa Keeratipusana, Prapat Suriyaphol, David J. Hampson, Nuvee Prapasarakul
Software Mentions: 2
Published: over 5 years ago

10.1002/ana.25709

Robust Markers and Sample Sizes for Multicenter Trials of Huntington Disease
Cited by: 20
Author(s): P. A. Wijeratne, Eileanoir B. Johnson, Arman Eshaghi, Leon Aksman, Sarah Gregory, Hans J. Johnson, Govinda Poudel, Amrita Mohan, Cristina Sampaio, Nellie Georgiou‐Karistianis, Jane S. Paulsen, Sarah J. Tabrizi, Rachael I. Scahill, Predict-Hd Image-Hd, Track-Hd Investigators, Daniel C. Alexander
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0117850

Forecasting the Effects of Land Use Scenarios on Farmland Birds Reveal a Potential Mitigation of Climate Change Impacts
Cited by: 21
Author(s): Karine Princé, Romain Lorrillière, Morgane Barbet‐Massin, François Léger, Frédéric Jiguet
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0051759

Crop Expansion and Conservation Priorities in Tropical Countries
Cited by: 243
Author(s): Ben Phalan, Monika Bertzky, Stuart H. M. Butchart, Paul F. Donald, Jörn P. W. Scharlemann, Alison J. Stattersfield, Andrew Balmford
Software Mentions: 2
Published: almost 12 years ago

10.1002/2017EF000744

Biogeophysical Impacts of Land-Use Change on Climate Extremes in Low-Emission Scenarios: Results From HAPPI-Land
Cited by: 29
Author(s): Annette L. Hirsch, Benoît P. Guillod, Sonia I. Seneviratne, Urs Beyerle, Lena Boysen, Victor Brovkin, Edouard L. Davin, Jonathan C. Doelman, Hyungjun Kim, Dann Mitchell, Tomoko Nitta, Hideo Shiogama, Sarah Sparrow, Elke Stehfest, Detlef P. van Vuuren, Simon Wilson
Software Mentions: 2
Published: over 6 years ago

10.1186/gb-2007-8-7-r139

A high utility integrated map of the pig genome
Cited by: 134
Author(s): Sean Humphray, Carol Scott, Richard Clark, Brandy M. Marron, Clare Bender, Nick Camm, Jayne L. Davis, Andrew Jenks, Angela T. Noon, Monali Patel, Harminder Sehra, Fengtang Yang, Margarita B. Rogatcheva, Denis Milan, Patrick Chardon, G. A. Rohrer, Dan Nonneman, Pieter J. de Jong, Stacey N. Meyers, Alan Archibald, Jonathan E. Beever, Lawrence B. Schook, Jane Rogers
Software Mentions: 2
Published: almost 18 years ago

10.1093/rheumatology/keab429

A systematic review and network meta-analysis of the safety of early interventional treatments in rheumatoid arthritis
Cited by: 3
Author(s): Maryam A Adas, Victoria B Allen, Mark Yates, Katie Bechman, Benjamin D Clarke, Mark Russell, Andrew I Rutherford, Andrew Cope, Sam Norton, James Galloway
Software Mentions: 2
Published: over 3 years ago

10.1264/jsme2.ME14153

An Efficient Strategy Developed for Next-Generation Sequencing of Endosymbiont Genomes Performed Using Crude DNA Isolated from Host Tissues: A Case Study of <i>Blattabacterium cuenoti</i> Inhabiting the Fat Bodies of Cockroaches
Cited by: 13
Author(s): Yukihiro Kinjo, Seikoh Saitoh, Gaku Tokuda
Software Mentions: 1
Published: almost 10 years ago

10.1016/j.mex.2020.101155

The method for integrating dual-color fluorescence colocalization and single molecule photobleaching technology on the theophylline sensing platform
Cited by: 0
Author(s): Dong Zhang, Shi Gang Liu, Zhaodi Fu, Yu He, Wenli Gao, Xingbo Shi
Software Mentions: 1
Published: almost 5 years ago

10.1007/s10980-012-9715-6

An assessment of the impact of climate adaptation measures to reduce flood risk on ecosystem services
Cited by: 43
Author(s): Peter H. Verburg, E. Koomen, M. Hilferink, Marta Pérez‐Soba, J.P. Lesschen
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-14-829

Draft genome sequence of Xanthomonas fragariaereveals reductive evolution and distinct virulence-related gene content
Cited by: 31
Author(s): Joachim Vandroemme, Bart Cottyn, Steve Baeyen, Paul De Vos, Martine Maes
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2407-8-376

Cimetidine inhibits salivary gland tumor cell adhesion to neural cells and induces apoptosis by blocking NCAM expression
Cited by: 19
Author(s): Masakatsu Fukuda, Kaoru Kusama, Hideaki Sakashita
Software Mentions: 1
Published: almost 16 years ago

10.1186/1475-2840-11-56

Let’s prevent diabetes: study protocol for a cluster randomised controlled trial of an educational intervention in a multi-ethnic UK population with screen detected impaired glucose regulation
Cited by: 34
Author(s): Laura J. Gray, Kamlesh Khunti, S. Williams, Stephanie Goldby, Jacqui Troughton, Thomas Yates, Alastair Gray, Melanie J. Davies
Software Mentions: 1
Published: over 12 years ago

10.1186/s13021-015-0017-6

Projecting the spatiotemporal carbon dynamics of the Greater Yellowstone Ecosystem from 2006 to 2050
Cited by: 2
Author(s): Shengli Huang, Shuguang Liu, Jinxun Liu, Devendra Dahal, Claudia Young, Brian F. Davis, Terry L. Sohl, Todd J. Hawbaker, Benjamin M. Sleeter, Zhiliang Zhu
Software Mentions: 1
Published: over 9 years ago

10.1186/1750-0680-3-3

Quantifying the effectiveness of climate change mitigation through forest plantations and carbon sequestration with an integrated land-use model
Cited by: 45
Author(s): J.G. van Minnen, Bart J. Strengers, B. Eickhout, Rob Swart, Rik Leemans
Software Mentions: 1
Published: over 16 years ago

10.1002/cam4.717

Real-world treatment practice in patients with advanced melanoma in the era before ipilimumab: results from the IMAGE study
Cited by: 13
Author(s): Mark R. Middleton, S. Dalle, Joël Claveau, P. Mut, Sigrun Hallmeyer, P. Plantin, Martin Highley, Srividya Kotapati, Trong Kim Le, Jane Brokaw, Amy P. Abernethy
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-015-1220-2

Genomic and phenotypic insights into the ecology of Arthrobacter from Antarctic soils
Cited by: 71
Author(s): Melissa Dsouza, Michael W. Taylor, Susan Turner, Jackie Aislabie
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12885-021-08032-y

Long-term real-world experience with ipilimumab and non-ipilimumab therapies in advanced melanoma: the IMAGE study
Cited by: 7
Author(s): Stéphane Dalle, Laurent Mortier, Pippa Corrie, Michal Lotem, Ruth Board, Ana Arance, Frank Meiß, Patrick Terheyden, Ralf Gutzmer, B. Buysse, Kelly Oh, Jane Brokaw, Trong Kim Le, Susan D. Mathias, Julie Scotto, Jennifer Lord-Bessen, Andriy Moshyk, Srividya Kotapati, Mark R. Middleton
Software Mentions: 1
Published: over 3 years ago

10.1186/s13075-015-0736-9

Rheumatoid factor, not antibodies against citrullinated proteins, is associated with baseline disease activity in rheumatoid arthritis clinical trials
Cited by: 65
Author(s): Daniel Aletaha, Farideh Alasti, Josef S. Smolen
Software Mentions: 1
Published: about 9 years ago

10.2471/BLT.15.168252

Group-based microfinance for collective empowerment: a systematic review of health impacts
Cited by: 57
Author(s): Lois Orton, Andy Pennington, Shilpa Nayak, Amanda Sowden, Martin White, Margaret Whitehead
Software Mentions: 1
Published: over 8 years ago