pypi: stats | Projects | Ecosyste.ms: Papers

10.1186/s40168-018-0535-z

High-resolution ISR amplicon sequencing reveals personalized oral microbiome
Cited by: 30
Author(s): Chiranjit Mukherjee, Clifford J. Beall, Ann L. Griffen, Eugene J. Leys
Software Mentions: 9
Published: about 6 years ago

10.1002/ece3.6190

Friend or foe? A parasitic wasp shifts the cost/benefit ratio in a nursery pollination system impacting plant fitness
Cited by: 2
Author(s): Carmen Villacañas de Castro, Thomas S. Hoffmeister
Software Mentions: 9
Published: over 4 years ago

10.18632/aging.203379

Integration of segmented regression analysis with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues
Cited by: 8
Author(s): Margarida Ferreira, Stephany Francisco, Ana Raquel Soares, Ana Nobre, Miguel Pinheiro, Andreia Reis, Sonya Neto, Ana João Rodrigues, Nuno Sousa, Gabriela Moura, Manuel A. S. Santos
Software Mentions: 9
Published: over 3 years ago

10.1186/s12915-020-00908-y

First evidence of convergent lifestyle signal in reptile skull roof microanatomy
Cited by: 11
Author(s): Roy Ebel, Johannes Müller, Till Ramm, Christy A. Hipsley, Eli Amson
Software Mentions: 9
Published: almost 4 years ago

10.1186/s12870-019-1679-0

Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon
Cited by: 34
Author(s): Alejandro Sanz-Carbonell, Maria Carmen Marqués, Alexander Bustamante, Mario A. Fares, Guillermo Rodrigo, Gustavo Gómez
Software Mentions: 9
Published: almost 6 years ago

10.3389/fpls.2019.01717

Incorporating Local Adaptation Into Species Distribution Modeling of Paeonia mairei, an Endemic Plant to China
Cited by: 27
Author(s): Qihang Chen, Yijia Yin, Rui Zhao, Yong Yang, Jaime A. Teixeira da Silva, Xiaonan Yu
Software Mentions: 9
Published: almost 5 years ago

10.1186/1471-2105-11-503

Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering
Cited by: 54
Author(s): Eva Freyhult, Mattias Landfors, Jenny Önskog, Torgeir R. Hvidsten, Patrik Rydén
Software Mentions: 9
Published: about 14 years ago

10.1186/s13040-016-0086-4

Prediction of donor splice sites using random forest with a new sequence encoding approach
Cited by: 31
Author(s): Prabina Kumar Meher, Tanmaya Kumar Sahu, Atmakuri Ramakrishna Rao
Software Mentions: 9
Published: almost 9 years ago

10.1016/j.celrep.2019.01.041

RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types
Cited by: 510
Author(s): Gianni Monaco, Bernett Lee, Weili Xu, Seri Mustafah, You Yi Hwang, Christophe Carré, Nicolas Burdin, Lucian Visan, Michele Ceccarelli, Michael Poidinger, Alfred Zippelius, João Pedro de Magalhães, Anis Larbi
Software Mentions: 9
Published: almost 6 years ago

10.1128/mSystems.00081-18

Epstein-Barr Virus-Positive Cancers Show Altered B-Cell Clonality
Cited by: 16
Author(s): Sara R. Selitsky, David Marron, Lisle E. Mose, Joel S. Parker, Dirk P. Dittmer
Software Mentions: 9
Published: about 6 years ago

10.3390/cancers13040722

Prognostic and Predictive Value of Integrated Qualitative and Quantitative Magnetic Resonance Imaging Analysis in Glioblastoma
Cited by: 19
Author(s): Maikel Verduin, Sergey Primakov, Inge Compter, Henry C. Woodruff, Sander M. J. van Kuijk, Bram Ramaekers, Maarten te Dorsthorst, Elles G. M. Revenich, Mark ter Laan, Sjoert Pegge, Frederick J. A. Meijer, Jan Beckervordersandforth, Ernst-Jan M. Speel, Benno Küsters, Wendy W.J. de Leng, Monique M. Anten, Martijn P. G. Broen, Linda Ackermans, Olaf Schijns, Onno P.M. Teernstra, Koos E. Hovinga, Marc Vooijs, Vivianne C. G. Tjan‐Heijnen, Daniëlle Eekers, Alida A. Postma, Ann Hoeben
Software Mentions: 9
Published: almost 4 years ago

10.3389/fpls.2017.01160

Repeated Stand-Replacing Crown Fires Affect Seed Morphology and Germination in Aleppo pine
Cited by: 7
Author(s): Antonio Saracino, Alessandro Bellino, Emilia Allevato, Antonio Mingo, Stefano Conti, Sergio Rossi, Giuliano Bonanomi, Domenico Carputo, Stefano Mazzoleni
Software Mentions: 9
Published: over 7 years ago

10.2196/10076

Key Elements of mHealth Interventions to Successfully Increase Physical Activity: Meta-Regression
Cited by: 56
Author(s): Lisa V. Eckerstorfer, Norbert K. Tanzer, Claudia Vogrincic-Haselbacher, Gayannée Kedia, Hilmar Brohmer, Isabelle Dinslaken, Katja Corcoran
Software Mentions: 9
Published: about 6 years ago

10.1371/journal.pone.0224186

Studying global processing in autism and attention-deficit/hyperactivity disorder with gaze movements: The example of a copying task
Cited by: 2
Author(s): Divya Seernani, Chara Ioannou, K. Damania, Kurt P. Spindler, Holger Hill, Tom Foulsham, Nikolaos Smyrnis, Stephan Bender, Christian Fleischhaker, Monica Biscaldi, Ulrich W. Ebner‐Priemer, Christoph Klein
Software Mentions: 9
Published: over 4 years ago

10.1371/journal.pone.0240462

The origins of money: Calculation of similarity indexes demonstrates the earliest development of commodity money in prehistoric Central Europe
Cited by: 11
Author(s): Maikel H.G. Kuijpers, Cătălin Nicolae Popa
Software Mentions: 9
Published: almost 4 years ago

10.3389/fonc.2021.698856

A Novel Ferroptosis-Related Gene Model for Overall Survival Predictions of Bladder Urothelial Carcinoma Patients
Cited by: 9
Author(s): Min Zhang, Xin Zhang, Minghang Yu, Wei Zhang, Di Zhang, Song Zeng, Xi Wang, Xiaosong Hu
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pbio.2004045

A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates
Cited by: 41
Author(s): Jean-Louis Plouhinec, Sofía Medina-Ruíz, Caroline Borday, Elsa Bernard, Jean-Philippe Vert, Michael B. Eisen, Richard M. Harland, Anne H. Monsoro-Burq
Software Mentions: 9
Published: about 7 years ago

10.1002/ece3.6335

High dispersal capacity and biogeographic breaks shape the genetic diversity of a globally distributed reef‐dwelling calcifier
Cited by: 16
Author(s): Martina Prazeres, Raphaël Morard, Thomas E. Roberts, Steve S. Doo, Jamaluddin Jompa, Christiane Schmidt, Marleen Stuhr, Willem Renema, Michal Kučera
Software Mentions: 9
Published: over 4 years ago

10.3389/fninf.2021.561689

QDECR: A Flexible, Extensible Vertex-Wise Analysis Framework in R
Cited by: 13
Author(s): Sander Lamballais, Ryan L. Muetzel
Software Mentions: 9
Published: over 3 years ago

10.3390/microorganisms8010038

Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota
Cited by: 13
Author(s): Matteo Chialva, Stefano Ghignone, Mara Novero, Wael N. Hozzein, Luisa Lanfranco, Paola Bonfante
Software Mentions: 9
Published: almost 5 years ago

10.1038/s41375-020-01096-y

Copy number evolution and its relationship with patient outcome—an analysis of 178 matched presentation-relapse tumor pairs from the Myeloma XI trial
Cited by: 21
Author(s): James Croft, Sidra Ellis, Amy L. Sherborne, Kim A. Sharp, Amy Price, Matthew Jenner, Mark T. Drayson, Roger G. Owen, Sally Chown, Jindriska Lindsay, Kamaraj Karunanithi, Hannah Hunter, Walter M. Gregory, Faith E. Davies, Gareth J. Morgan, Gordon Cook, Lilit Atanesyan, Suvi Savola, David A. Cairns, Graham Jackson, Richard S. Houlston, Martin Kaiser
Software Mentions: 8
Published: almost 4 years ago

10.1186/s12864-015-2319-1

Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes
Cited by: 3
Author(s): Youko Horiuchi, Yoshiaki Harushima, Hironori Fujisawa, Takako Mochizuki, Masahiro Fujita, Hajime Ohyanagi, Nori Kurata
Software Mentions: 8
Published: almost 9 years ago

10.3389/fgene.2018.00123

Inferring Variation in Copy Number Using High Throughput Sequencing Data in R
Cited by: 15
Author(s): Brian J. Knaus, Niklaus J. Grünwald
Software Mentions: 8
Published: over 6 years ago

10.1002/1878-0261.12139

Transcription instability in high-risk neuroblastoma is associated with a global perturbation of chromatin domains
Cited by: 4
Author(s): Carlo Zanon, Gian Paolo Tonini
Software Mentions: 8
Published: about 7 years ago

10.12688/f1000research.14361.1

freesurfer: Connecting the Freesurfer software with R
Cited by: 7
Author(s): John Muschelli, Elizabeth Sweeney, Ciprian M. Crainiceanu
Software Mentions: 8
Published: over 6 years ago

10.1371/journal.pone.0183264

The transcriptional profiling of human in vivo-generated plasma cells identifies selective imbalances in monoclonal gammopathies
Cited by: 12
Author(s): Luis M. Valor, Beatriz Rodrı́guez-Bayona, Ana Ramos-Amaya, José A. Brieva, Antonio Campos‐Caro
Software Mentions: 8
Published: over 7 years ago

10.3390/ani10050889

Combination of Bacillus licheniformis and Salinomycin: Effect on the Growth Performance and GIT Microbial Populations of Broiler Chickens
Cited by: 15
Author(s): Jacek Trela, Bartosz Kierończyk, Veerle Hautekiet, Damian Józefiak
Software Mentions: 8
Published: over 4 years ago

10.1128/mSphere.00488-17

Novel ITS1 Fungal Primers for Characterization of the Mycobiome
Cited by: 68
Author(s): Mykhaylo Usyk, Christine P. Zolnik, Hitesh D. Patel, Michael H. Levi, Robert D. Burk
Software Mentions: 8
Published: almost 7 years ago

10.3758/s13420-016-0255-9

Effects of forced movements on learning: Findings from a choice reaction time task in rats
Cited by: 3
Author(s): Hidekazu Kaneko, Hiroto Sano, Yasuhisa Hasegawa, Hiroshi Tamura, Shinya Suzuki
Software Mentions: 8
Published: almost 8 years ago

10.1007/s00787-020-01535-2

Visual search in ADHD, ASD and ASD + ADHD: overlapping or dissociating disorders?
Cited by: 13
Author(s): Divya Seernani, K. Damania, Chara Ioannou, N. Penkalla, Holger Hill, Tom Foulsham, Alan Kingstone, Nicola Anderson, Giuseppe Boccignone, Stephan Bender, N. Smyrnis, Monica Biscaldi, Ulrich W. Ebner‐Priemer, Christoph Klein
Software Mentions: 8
Published: over 4 years ago

10.1093/bib/bbaa290

NetCoMi: network construction and comparison for microbiome data in R
Cited by: 165
Author(s): Stefanie Peschel, Christian L. Müller, Erika von Mutius, Anne‐Laure Boulesteix, Martin Depner
Software Mentions: 8
Published: almost 4 years ago

10.3390/foods8100488

Effect of Product Involvement on Panels’ Vocabulary Generation, Attribute Identification, and Sample Configurations in Beer
Cited by: 4
Author(s): Line Elgaard, Line Holler Mielby, Hildegarde Heymann, Derek V. Byrne
Software Mentions: 8
Published: about 5 years ago

10.3390/e23010072

Unraveling of a Strongly Correlated Dynamical Network of Residues Controlling the Permeation of Potassium in KcsA Ion Channel
Cited by: 2
Author(s): Salvatore M. Cosseddu, Eunju Julia Choe, I. A. Khovanov
Software Mentions: 8
Published: almost 4 years ago

10.1371/journal.pone.0206077

Demographic characteristics of an avian predator, Louisiana Waterthrush (Parkesia motacilla), in response to its aquatic prey in a Central Appalachian USA watershed impacted by shale gas development
Cited by: 6
Author(s): Mack W. Frantz, Petra Bohall Wood, George T. Merovich
Software Mentions: 8
Published: almost 6 years ago

10.1038/s41598-021-96160-7

Wolves, dogs and humans in regular contact can mutually impact each other’s skin microbiota
Cited by: 6
Author(s): Stefanie U. Wetzels, Cameron Strachan, Beate Conrady, Martin Wagner, Iwan Burgener, Zsófia Virányi, Evelyne Selberherr
Software Mentions: 8
Published: about 3 years ago

10.1371/journal.pone.0220926

Gut microbiome shifts with urbanization and potentially facilitates a zoonotic pathogen in a wading bird
Cited by: 50
Author(s): Maureen H. Murray, Emily W. Lankau, Anjelika D. Kidd, Catharine N. Welch, Taylor Ellison, Henry Adams, Erin K. Lipp, Sonia M. Hernández
Software Mentions: 8
Published: over 4 years ago

10.1038/s41598-021-99046-w

Using fecal immunochemical tubes for the analysis of the gut microbiome has the potential to improve colorectal cancer screening
Cited by: 7
Author(s): Kertu Liis Krigul, Oliver Aasmets, Kreete Lüll, Tõnis Org, Elin Org
Software Mentions: 8
Published: about 3 years ago

10.1038/s41598-019-50858-x

Landscape determinants of density of blacklegged ticks, vectors of Lyme disease, at the northern edge of their distribution in Canada
Cited by: 19
Author(s): Benoit Talbot, Andreea Slatculescu, Charles Thickstun, Jules K. Koffi, Patrick A. Leighton, Roman McKay, Manisha A. Kulkarni
Software Mentions: 8
Published: about 5 years ago

10.1038/s41598-019-55706-6

Tailings microbial community profile and prediction of its functionality in basins of tungsten mine
Cited by: 26
Author(s): Ana Paula Chung, Carina Coimbra, Pedro Farias, Romeu Francisco, Rita Branco, Francisco Veiga Simão, Érico Rodrigues Gomes, Alcides Pereira, Maria Cristina Vila, António Fiúza, Martin Steen Mortensen, Søren J. Sørensen, Paula V. Morais
Software Mentions: 8
Published: almost 5 years ago

10.1186/s12870-020-02739-z

Candidate genes and SNPs associated with stomatal conductance under drought stress in Vitis
Cited by: 7
Author(s): Massimiliano Trenti, Silvia Lorenzi, P. Bianchedi, Daniele Grossi, O. Failla, M. S. Grando, F. Emanuelli
Software Mentions: 8
Published: almost 4 years ago

10.1371/journal.pone.0234537

Prairie plants harbor distinct and beneficial root-endophytic bacterial communities
Cited by: 0
Author(s): Boahemaa Adu-Oppong, Scott A. Mangan, Cláudia Stein, Christopher P. Catano, Jonathan A. Myers, Gautam Dantas
Software Mentions: 8
Published: over 4 years ago

10.1038/s41598-019-44597-2

NOMePlot: analysis of DNA methylation and nucleosome occupancy at the single molecule
Cited by: 3
Author(s): Francisco Requena, Helena G Asenjo, Guillermo Barturen, Jordi Martorell-Marugán, Pedro Carmona-Sáez, David Landeira
Software Mentions: 8
Published: over 5 years ago

10.1038/s41598-020-59524-z

Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach
Cited by: 16
Author(s): Ruibo Cai, Ehsan Kayal, Catharina Alves‐de‐Souza, Estelle Bigeard, Erwan Corre, Christian Jeanthon, Dominique Marie, Betina M. Porcel, Raffaele Siano, Jeremy Szymczak, Matthias Wolf, Laure Guillou
Software Mentions: 8
Published: almost 5 years ago

10.1371/journal.pone.0206662

Predicting hospital and emergency department utilization among community-dwelling older adults: Statistical and machine learning approaches
Cited by: 15
Author(s): Aaron Jones, Andrew P. Costa, Angelina Pesevski, Paul D. McNicholas
Software Mentions: 8
Published: about 6 years ago

10.1038/s41598-019-38483-0

Metabotyping as a Stopover in Genome-to-Phenome Mapping
Cited by: 31
Author(s): Pubudu Handakumbura, Bryan Stanfill, Albert Rivas‐Ubach, Dan Fortin, John P. Vogel, Christer Jansson
Software Mentions: 8
Published: almost 6 years ago

10.1038/s41598-017-14785-z

Poly-β-hydroxybutyrate administration during early life: effects on performance, immunity and microbial community of European sea bass yolk-sac larvae
Cited by: 18
Author(s): Andrea Franke, Olivia Roth, Peter De Schryver, Till Bayer, Linsey Garcia‐Gonzalez, Sven Künzel, Peter Bossier, Joanna J. Miest, Catriona Clemmesen
Software Mentions: 8
Published: about 7 years ago

10.3390/microorganisms9020378

Differences in the Concentration of the Fecal Neurotransmitters GABA and Glutamate Are Associated with Microbial Composition among Healthy Human Subjects
Cited by: 18
Author(s): Hend Altaib, Kohei Nakamura, Mayuko Abe, Yassien Badr, Emiko Yanase, Izumi Nomura, Tomohiko Suzuki
Software Mentions: 8
Published: almost 4 years ago

10.1186/s13058-018-1022-y

Clonal relatedness in tumour pairs of breast cancer patients
Cited by: 14
Author(s): Jana Biermann, Toshima Z. Parris, Szilárd Nemes, Anna Danielsson, Hanna Engqvist, Elisabeth Werner Rönnerman, Eva Forssell-Aronsson, Anikó Kovács, Per Karlsson, Khalil Helou
Software Mentions: 8
Published: over 6 years ago

10.1038/srep30086

Random Bits Forest: a Strong Classifier/Regressor for Big Data
Cited by: 22
Author(s): Yi Wang, Li Yi, Weilin Pu, Kathryn Wen, Yin Yao Shugart, Momiao Xiong, Li Jin
Software Mentions: 8
Published: over 8 years ago

10.1002/ece3.4442

Females know better: Sex-biased habitat selection by the European wildcat
Cited by: 25
Author(s): Teresa Martins de Oliveira, Fermín Urra, José María López‐Martín, Elena Ballesteros‐Duperón, José Miguel Barea‐Azcón, Marcos Moleón, José María Gil‐Sánchez, Paulo C. Alves, Francisco Díaz‐Ruíz, Pablo Ferreras, Pedro Monterroso
Software Mentions: 8
Published: about 6 years ago

10.1002/ece3.4535

Determining social and population structures requires multiple approaches: A case study of the desert ant<i>Cataglyphis israelensis</i>
Cited by: 3
Author(s): Tali Reiner Brodetzki, Abraham Hefetz
Software Mentions: 8
Published: almost 6 years ago

10.1098/rspb.2020.1158

Parasite infection disrupts escape behaviours in fish shoals
Cited by: 3
Author(s): Nicolle Demandt, Marit Praetz, Ralf H. J. M. Kurvers, Jens Krause, Joachim Kurtz, Jörn P. Scharsack
Software Mentions: 8
Published: about 4 years ago

10.1002/ece3.6913

Changes in beta diversity and species functional traits differ between saplings and mature trees in an old‐growth forest
Cited by: 1
Author(s): David Anthony Kirk, Marie‐Hélène Brice, Michael S. W. Bradstreet, Ken A. Elliott
Software Mentions: 8
Published: almost 4 years ago

10.1002/ece3.5289

Disturbance history mediates climate change effects on subtropical forest biomass and dynamics
Cited by: 16
Author(s): Alexandre F. Souza, Solon Jonas Longhi
Software Mentions: 8
Published: over 5 years ago

10.1186/s12866-021-02222-1

Patterns of yeast diversity distribution and its drivers in rhizosphere soil of Hami melon orchards in different regions of Xinjiang
Cited by: 7
Author(s): Shanshan Zhu, Yonghui Lei, Chong Wang, Yu‐Mei Wei, Chuncheng Wang, Yanfei Sun
Software Mentions: 8
Published: over 3 years ago

10.3390/plants10081594

RNAi Suppression of LEAFY Gives Stable Floral Sterility, and Reduced Growth Rate and Leaf Size, in Field-Grown Poplars
Cited by: 5
Author(s): Amy L. Klocko, Amanda Goddard, Jeremy R. Jacobson, Anna Magnuson, S. H. Strauss
Software Mentions: 8
Published: over 3 years ago

10.3390/ani10112127

Vultures and Livestock: The Where, When, and Why of Visits to Farms
Cited by: 6
Author(s): Marina García‐Alfonso, Thijs van Overveld, Laura Gangoso, David Serrano, José A. Donázar
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.ppat.1006525

Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens
Cited by: 53
Author(s): Olaya Rendueles, Marc García-Garcerá, Bertrand Néron, Marie Touchon, Eduardo P. C. Rocha
Software Mentions: 8
Published: over 7 years ago

10.1371/journal.pbio.2002054

Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells
Cited by: 76
Author(s): Colin R. Lickwar, J. Gray Camp, Matthew Weiser, Jordan L. Cocchiaro, David M. Kingsley, Terrence S. Furey, Shehzad Z. Sheikh, John F. Rawls
Software Mentions: 8
Published: about 7 years ago

10.1002/ece3.6390

Can ancestry and morphology be used as surrogates for species niche relationships?
Cited by: 5
Author(s): Friedrich W. Keppeler, Kirk O. Winemiller
Software Mentions: 8
Published: over 4 years ago

10.7717/peerj.2436

RBioplot: an easy-to-use R pipeline for automated statistical analysis and data visualization in molecular biology and biochemistry
Cited by: 65
Author(s): Jing Zhang, Kenneth B. Storey
Software Mentions: 8
Published: about 8 years ago

10.1534/g3.114.010298

Parametric and Nonparametric Statistical Methods for Genomic Selection of Traits with Additive and Epistatic Genetic Architectures
Cited by: 132
Author(s): Réka Howard, Alicia L. Carriquiry, William D. Beavis
Software Mentions: 8
Published: over 10 years ago

10.1186/s12864-020-6653-6

Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp
Cited by: 14
Author(s): Gabriel A. Vignolle, Robert L. Mach, Astrid R. Mach-Aigner, Christian Derntl
Software Mentions: 8
Published: over 4 years ago

10.3390/cancers12010045

N-Terminal Truncated Myb with New Transcriptional Activity Produced Through Use of an Alternative MYB Promoter in Salivary Gland Adenoid Cystic Carcinoma
Cited by: 11
Author(s): Candace A. Frerich, Hailey N. Sedam, Huining Kang, Yoshitsugu Mitani, Adel K. El‐Naggar, Scott A. Ness
Software Mentions: 8
Published: almost 5 years ago

10.1186/s40168-019-0716-4

The association between pneumococcal vaccination, ethnicity, and the nasopharyngeal microbiota of children in Fiji
Cited by: 11
Author(s): Laura K. Boelsen, Eileen M. Dunne, Moana Mika, Stefanie Eggers, Cattram Nguyen, Felisita Tupou Ratu, Fiona M. Russell, E. Kim Mulholland, Markus Hilty, Catherine Satzke
Software Mentions: 8
Published: over 5 years ago

10.3389/fpsyg.2021.703892

“It All Makes Us Feel Together”: Young People's Experiences of Virtual Group Music-Making During the COVID-19 Pandemic
Cited by: 10
Author(s): Maruša Levstek, Rubie Mai Barnby, Katherine Pocock, Robin Banerjee
Software Mentions: 8
Published: over 3 years ago

10.1093/bioinformatics/bts438

iBBiG: iterative binary bi-clustering of gene sets
Cited by: 44
Author(s): Daniel Gusenleitner, Eleanor Howe, Stefan Bentink, John Quackenbush, Aedín C. Culhane
Software Mentions: 8
Published: over 12 years ago

10.1186/s40478-021-01240-4

Experimental colitis promotes sustained, sex-dependent, T-cell-associated neuroinflammation and parkinsonian neuropathology
Cited by: 26
Author(s): Madelyn C. Houser, W. Michael Caudle, Jianjun Chang, George T. Kannarkat, Yuan Yang, Sean D. Kelly, Danielle Oliver, Valerie Joers, Kathleen M. Shannon, Ali Keshavarzian, Malú G. Tansey
Software Mentions: 8
Published: over 3 years ago

10.3389/fpsyg.2017.02229

Work Engagement among Rescue Workers: Psychometric Properties of the Portuguese UWES
Cited by: 18
Author(s): Jorge Sinval, Alexandra Marqués Pinto, Cristina Queirós, João Marôco
Software Mentions: 8
Published: almost 7 years ago

10.1186/s42523-021-00111-6

Characterization of the gut microbiome in wild rocky mountainsnails (Oreohelix strigosa)
Cited by: 2
Author(s): Bridget Chalifour, Jingchun Li
Software Mentions: 8
Published: over 3 years ago

10.1038/s41598-019-50642-x

Transcriptome Sequencing of Peripheral Blood Mononuclear Cells from Elite Controller-Long Term Non Progressors
Cited by: 11
Author(s): Francisco Díez-Fuertes, Humberto Erick De La Torre Tarazona, Esther Calonge, María Pernas, María del Mar Alonso-Socas, Laura Capa, Javier García-Pérez, Anavaj Sakuntabhai, José Alcamı́
Software Mentions: 8
Published: about 5 years ago

10.1038/s42003-021-02509-z

Species diversity and food web structure jointly shape natural biological control in agricultural landscapes
Cited by: 10
Author(s): Fan Yang, Bing Liu, Zhao Yu, Kris A.G. Wyckhuys, Wopke Van der Werf, Yanhui Lu
Software Mentions: 8
Published: over 3 years ago

10.1186/s13148-021-01144-z

Whole-genome methylation analysis of testicular germ cells from cryptozoospermic men points to recurrent and functionally relevant DNA methylation changes
Cited by: 9
Author(s): Sara Di Persio, Elsa Leitão, Marius Wöste, Tobias Tekath, Jann‐Frederik Cremers, Martin Dugas, Xiaolin Liao, Gerd Meyer zu Hörste, Sabine Kliesch, Sandra Laurentino, Nina Neuhaus, Bernhard Horsthemke
Software Mentions: 8
Published: over 3 years ago

10.1186/s12877-020-01644-2

Dysbiosis, gut barrier dysfunction and inflammation in dementia: a pilot study
Cited by: 87
Author(s): Vanessa Stadlbauer, Lara Engertsberger, Irina Komarova, Nicole Feldbacher, Bettina Leber, Gerhard Pichler, Nicole Fink, Monika Scarpatetti, Walter Schippinger, Reinhold Schmidt, Angela Horvath
Software Mentions: 8
Published: over 4 years ago

10.3390/cells8080920

The Snapdragon LATE ELONGATED HYPOCOTYL Plays A Dual Role in Activating Floral Growth and Scent Emission
Cited by: 9
Author(s): Marta I. Terry, Fernando Pérez-Sánz, Pedro J. Navarro, Julia Weiß, Marcos Egea‐Cortines
Software Mentions: 8
Published: over 5 years ago

10.3389/fvets.2020.00523

Mind the Queue: A Case Study in Visualizing Heterogeneous Behavioral Patterns in Livestock Sensor Data Using Unsupervised Machine Learning Techniques
Cited by: 11
Author(s): Catherine McVey, Fushing Hsieh, Diego Manríquez, Pablo Pinedo, Kristina Horback
Software Mentions: 8
Published: over 4 years ago

10.1038/s42003-021-01658-5

Colonization and genetic diversification processes of Leishmania infantum in the Americas
Cited by: 30
Author(s): Philipp Schwabl, Mariana Côrtes Boité, Giovanni Bussotti, Arne Jacobs, Björn Andersson, Otacílio C. Moreira, Anita Leocádio Freitas-Mesquita, José Roberto Meyer‐Fernandes, Erich Loza Telleria, Yara M. Traub-Csekö, Slavica Vaselek, Tereza Leštinová, Petr Volf, Fernanda Nazaré Morgado, Renato Porrozzi, Martin S. Llewellyn, Gérald F. Späth, Elisa Cupolillo
Software Mentions: 8
Published: almost 4 years ago

10.7717/peerj.10696

Rapid relative increase of crustose coralline algae following herbivore exclusion in a reef of El Salvador
Cited by: 1
Author(s): Xochitl E. Elías Ilosvay, Johanna Segovia, Sebastian C. A. Ferse, Walter Ernesto Elias, Christian Wild
Software Mentions: 8
Published: almost 4 years ago

10.3390/cancers12113089

CT-Based Radiomics Analysis to Predict Malignancy in Patients with Intraductal Papillary Mucinous Neoplasm (IPMN) of the Pancreas
Cited by: 28
Author(s): David Tobaly, João Santinha, Riccardo Sartoris, Marco Dioguardi Burgio, Celso Matos, Jérôme Cros, Anne Couvelard, Vinciane Rebours, Alain Sauvanet, Maxime Ronot, Nikolaos Papanikolaou, Valérie Vilgrain
Software Mentions: 8
Published: about 4 years ago

10.1002/acn3.51441

Gut microbiome is associated with multiple sclerosis activity in children
Cited by: 18
Author(s): Mary Horton, Kathryn McCauley, Douglas Fadrosh, Kei E. Fujimura, Jennifer Graves, Jayne Ness, Yolanda Wheeler, Mark Gorman, Leslie Benson, Bianca Weinstock‐Guttman, Amy Waldman, Moses Rodriguez, Jan‐Mendelt Tillema, Lauren Krupp, Anita Belman, Soe Mar, Mary Rensel, Tanuja Chitnis, T. Charles Casper, John Rose, Janace Hart, Xiaorong Shao, Helen Tremlett, Susan V. Lynch, Lisa F. Barcellos, Emmanuelle Waubant
Software Mentions: 8
Published: over 3 years ago

10.3390/cancers13143621

HPV Infection Leaves a DNA Methylation Signature in Oropharyngeal Cancer Affecting Both Coding Genes and Transposable Elements
Cited by: 10
Author(s): Diego Camuzi, Luisa Aguirre Buexm, Simone De Queiroz Chaves Lourenço, Davide Degli Esposti, Cyrille Cuenin, Monique de Souza Almeida Lopes, Francesca Manara, Fazlur Rahman Talukdar, Zdenko Herceg, Luís Felipe Ribeiro Pinto, Sheila Coelho Soares-Lima
Software Mentions: 8
Published: over 3 years ago

10.3389/fonc.2020.00832

Diagnostic Value of Combinatorial Markers in Colorectal Carcinoma
Cited by: 7
Author(s): Veronika Voronova, Petr Glybochko, Andrey Svistunov, В В Фомин, Philipp Kopylov, Peter Tzarkov, А. В. Егоров, E. P. Gitel, А. А. Рагимов, Alexander Boroda, Elena Poddubskaya, Marina Sekacheva
Software Mentions: 8
Published: over 4 years ago

10.1186/1471-2105-14-133

How cyanobacteria pose new problems to old methods: challenges in microarray time series analysis
Cited by: 23
Author(s): Robert Lehmann, Rainer Machné, Jens Georg, Manuela Benary, Ilka M. Axmann, Ralf Steuer
Software Mentions: 8
Published: over 11 years ago

10.7554/eLife.19545

Splicing repression allows the gradual emergence of new Alu-exons in primate evolution
Cited by: 52
Author(s): Jan Attig, Igor Ruiz de los Mozos, Nejc Haberman, Zhen Wang, Warren Emmett, Kathi Zarnack, Julian König, Jernej Ule
Software Mentions: 8
Published: about 8 years ago

10.1186/s12917-015-0593-4

A preliminary study of the effect of closed incision management with negative pressure wound therapy over high-risk incisions
Cited by: 14
Author(s): Karen L Perry, Lynda Rutherford, D. Sajik, Mieghan Bruce
Software Mentions: 8
Published: about 9 years ago

10.3389/fonc.2019.01243

Identification of Subtype-Specific Three-Gene Signature for Prognostic Prediction in Diffuse Type Gastric Cancer
Cited by: 12
Author(s): Bowen Bao, Chunlei Zheng, Bowen Yang, Yue Jin, Kezuo Hou, Zhi Li, Xueying Zheng, Shitong Yu, Xiaojie Zhang, Yibo Fan, Xiujuan Qu, Yunpeng Liu, Xiaofang Che
Software Mentions: 8
Published: about 5 years ago

10.1136/jitc-2020-002071

HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy
Cited by: 109
Author(s): Ana Marcu, Leon Bichmann, Lèon Kuchenbecker, Daniel J. Kowalewski, Lena Katharina Freudenmann, Linus Backert, Lena Mühlenbruch, András Szolek, Maren Lübke, Philipp Wagner, Tobias Engler, Sabine Matovina, Jian Wang, Mathias Hauri-Hohl, Thierry Martin, Konstantina Kapolou, Juliane S. Walz, Julia Velz, Holger Moch, Luca Regli, Manuela Silginer, Michael Weller, Markus Löffler, Florian Erhard, Andreas Schlösser, Oliver Kohlbacher, Stefan Stevanović, Hans Georg Rammensee, Marian C. Neidert
Software Mentions: 8
Published: over 3 years ago

10.3389/fpls.2021.616975

Heterotic Patterns of Temperate and Tropical Maize by Ear Photometry
Cited by: 1
Author(s): Seth Tolley, Amritpal Singh, Mitchell R. Tuinstra
Software Mentions: 8
Published: over 3 years ago

10.1038/s41396-019-0383-2

Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots
Cited by: 596
Author(s): Samiran Banerjee, Florian Walder, Lucie Büchi, Marion Meyer, Alain Held, Andreas Gattinger, Thomas Keller, Raphaël Charles, Marcel G. A. van der Heijden
Software Mentions: 8
Published: over 5 years ago

10.1038/s41389-019-0157-8

DeepCC: a novel deep learning-based framework for cancer molecular subtype classification
Cited by: 119
Author(s): Feng Gao, Wei Wang, Miaomiao Tan, Lina Zhu, Yuchen Zhang, Evelyn Fessler, Louis Vermeulen, Xin Wang
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pgen.1008754

Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei
Cited by: 24
Author(s): Shan Jiang, Katherine Williams, Xiangduo Kong, Weihua Zeng, Nam Viet Nguyen, Xinyi Ma, Rabi Tawil, Kyoko Yokomori, A Mortazavi
Software Mentions: 8
Published: over 4 years ago

10.1038/s41598-021-92658-2

Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP
Cited by: 10
Author(s): Abhijeet Singh, Bettina Müller, Anna Schnürer
Software Mentions: 8
Published: over 3 years ago

10.3389/fmicb.2021.644828

The Cheese Production Facility Microbiome Exhibits Temporal and Spatial Variability
Cited by: 12
Author(s): Jared Johnson, Chris Curtin, Joy Waite‐Cusic
Software Mentions: 8
Published: over 3 years ago

10.1093/gigascience/giz003

Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise
Cited by: 21
Author(s): Stefan Prost, Ellie E. Armstrong, Johan A. A. Nylander, Gregg W.C. Thomas, Alexander Suh, Bent Petersen, Love Dalén, Brett W. Benz, Mozes P. K. Blom, Eleftheria Palkopoulou, Per G. P. Ericson, Martin Irestedt
Software Mentions: 8
Published: almost 6 years ago

10.1038/s41598-020-75541-4

Stromal microenvironment promoted infiltration in esophageal adenocarcinoma and squamous cell carcinoma: a multi-cohort gene-based analysis
Cited by: 6
Author(s): Jiali Li, Zhao-Yi Zeng, Xueping Jiang, Nannan Zhang, Yanping Gao, Yuan Luo, Wenjie Sun, Shuying Li, Jiangbo Ren, Yan Gong, Conghua Xie
Software Mentions: 8
Published: about 4 years ago

10.3390/ijms21103591

Examining Short-Term Responses to a Long-Term Problem: RNA-Seq Analyses of Iron Deficiency Chlorosis Tolerant Soybean
Cited by: 8
Author(s): Adrienne N. Moran Lauter, Lindsay Rutter, Dianne Cook, Jamie A. O’Rourke, Michelle A. Graham
Software Mentions: 8
Published: over 4 years ago

10.3390/insects12080701

Anthonomus rubi on Strawberry Fruit: Its Biology, Ecology, Damage, and Control from an IPM Perspective
Cited by: 5
Author(s): Lorenzo Tonina, Giulia Zanettin, Paolo Miorelli, Simone Puppato, Andrew G. S. Cuthbertson, A. Grassi
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pone.0245029

Experimental warming influences species abundances in a Drosophila host community through direct effects on species performance rather than altered competition and parasitism
Cited by: 8
Author(s): Mélanie Thierry, Nicholas A. Pardikes, Chia‐Hua Lue, Owen T. Lewis, Jan Hrček
Software Mentions: 8
Published: almost 4 years ago

10.3390/jcm9113569

Seroprevalence of SARS-CoV-2 IgG Antibodies in Corsica (France), April and June 2020
Cited by: 11
Author(s): Lisandru Capai, Nazlı Ayhan, Shirley Masse, Jean Canarelli, Stéphane Priet, Marie-Hélène Simeoni, Rémi N. Charrel, Xavier de Lamballerie, Alessandra Falchi
Software Mentions: 8
Published: about 4 years ago

10.3389/fimmu.2018.00462

Analyzing Immunoglobulin Repertoires
Cited by: 77
Author(s): Neha Chaudhary, Duane R. Wesemann
Software Mentions: 8
Published: over 6 years ago

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