cran: plot3D | Projects | Ecosyste.ms: Papers

10.7554/eLife.53350

The natverse, a versatile toolbox for combining and analysing neuroanatomical data
Cited by: 128
Author(s): Alexander Shakeel Bates, James D. Manton, Sridhar R. Jagannathan, Marta Costa, Philipp Schlegel, Torsten Rohlfing, Gregory Jefferis
Software Mentions: 17
Published: over 4 years ago

10.3389/fcell.2020.596679

Development and Validation of a Combined Ferroptosis and Immune Prognostic Classifier for Hepatocellular Carcinoma
Cited by: 77
Author(s): Yang Liu, Xi Zhang, Junjun Zhang, Juan Tan, Jie Li, Zewen Song
Software Mentions: 16
Published: almost 4 years ago

10.15252/msb.20209498

Developmental function and state transitions of a gene expression oscillator in <i>Caenorhabditis elegans</i>
Cited by: 43
Author(s): Milou W.M. Meeuse, Yannick P Hauser, Lucas J Morales Moya, Gert‐Jan Hendriks, Jan Eglinger, Guy Bogaarts, Charisios D. Tsiairis, Helge Großhans
Software Mentions: 14
Published: over 4 years ago

10.1371/journal.pone.0184652

The evolution of Lachancea thermotolerans is driven by geographical determination, anthropisation and flux between different ecosystems
Cited by: 48
Author(s): Ana Hranilović, Marina Bely, Isabelle Masneuf‐Pomarède, Vladimir Jiranek, Warren Albertin
Software Mentions: 12
Published: about 7 years ago

10.7554/eLife.66738

Subventricular zone/white matter microglia reconstitute the empty adult microglial niche in a dynamic wave
Cited by: 15
Author(s): Lindsay A. Hohsfield, Allison R. Najafi, Yasamine Ghorbanian, Neelakshi Soni, Joshua Crapser, Dario X. Figueroa Velez, Shan Jiang, Sarah E Royer, Sung Jin Kim, Caden M Henningfield, Aileen J. Anderson, Sunil Gandhi, A Mortazavi, Matthew A. Inlay, Kim N. Green
Software Mentions: 12
Published: about 3 years ago

10.1038/s41408-019-0199-3

Deciphering the chronology of copy number alterations in Multiple Myeloma
Cited by: 35
Author(s): Anıl Aktaş Samur, Stéphane Minvielle, Masood A. Shammas, Mariateresa Fulciniti, Florence Magrangeas, Paul G. Richardson, Philippe Moreau, Michel Attal, Kenneth C. Anderson, Giovanni Parmigiani, Hervé Avet‐Loiseau, Nikhil C. Munshi, Mehmet K. Samur
Software Mentions: 11
Published: over 5 years ago

10.18632/aging.203257

Characterization of ferroptosis signature to evaluate the predict prognosis and immunotherapy in glioblastoma
Cited by: 14
Author(s): Xiaopeng Zhu, Yuxiang Zhou, Yangqian Ou, Zebo Cheng, Deqing Han, Zhou Chu, Sian Pan
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pone.0204990

Blaunet: An R-based graphical user interface package to analyze Blau space
Cited by: 4
Author(s): Michael Genkin, Cheng Wang, George Berry, Matthew E. Brashears
Software Mentions: 9
Published: about 6 years ago

10.1186/s12859-017-1936-x

Software for rapid time dependent ChIP-sequencing analysis (TDCA)
Cited by: 1
Author(s): Mike Myschyshyn, Marco Farren-Dai, Tien-Jui Chuang, David J. Vocadlo
Software Mentions: 9
Published: almost 7 years ago

10.1186/s12859-020-03669-1

TRIP - T cell receptor/immunoglobulin profiler
Cited by: 11
Author(s): Maria Th. Kotouza, Katerina Gemenetzi, Chrysi Galigalidou, Elisavet Vlachonikola, Nikolaos Pechlivanis, Andreas Agathangelidis, Raphael Sandaltzopoulos, Pericles A. Mitkas, Kostas Stamatopoulos, Anastasia Chatzidimitriou, Fotis Psomopoulos
Software Mentions: 9
Published: about 4 years ago

10.1371/journal.pone.0177276

Succinct workflows for circulating tumor cells after enrichment: From systematic counting to mutational profiling
Cited by: 11
Author(s): Vernon G. Wong, Josephine Mun Yee Ko, Chi-Tat Lam, Maria Li Lung
Software Mentions: 9
Published: over 7 years ago

10.1371/journal.pone.0253847

TeamTree analysis: A new approach to evaluate scientific production
Cited by: 2
Author(s): Frank W. Pfrieger
Software Mentions: 8
Published: over 3 years ago

10.7554/eLife.65228

Egr2 induction in spiny projection neurons of the ventrolateral striatum contributes to cocaine place preference in mice
Cited by: 8
Author(s): Diptendu Mukherjee, Ben J. Gonzales, Reut Ashwal-Fluss, Hagit Turm, Maya Groysman, Ami Citri
Software Mentions: 8
Published: over 3 years ago

10.7717/peerj.11983

Identifying transcript 5′ capped ends in <i>Plasmodium falciparum</i>
Cited by: 2
Author(s): Philip Shaw, Jittima Piriyapongsa, Pavita Kaewprommal, Chayaphat Wongsombat, Chadapohn Chaosrikul, Krirkwit Teeravajanadet, Manon Boonbangyang, Chairat Uthaipibull, Sumalee Kamchonwongpaisan, Sissades Tongsima
Software Mentions: 8
Published: about 3 years ago

10.3389/fpsyg.2018.02358

East Asian Young and Older Adult Perceptions of Emotional Faces From an Age- and Sex-Fair East Asian Facial Expression Database
Cited by: 13
Author(s): Yu-Zhen Tu, Dai-Jie Lin, Atsunobu Suzuki, Joshua Oon Soo Goh
Software Mentions: 7
Published: almost 6 years ago

10.3389/fpsyg.2018.02232

Analyzing Multivariate Dynamics Using Cross-Recurrence Quantification Analysis (CRQA), Diagonal-Cross-Recurrence Profiles (DCRP), and Multidimensional Recurrence Quantification Analysis (MdRQA) – A Tutorial in R
Cited by: 50
Author(s): Sebastian Wallot, G. G. Leonardi
Software Mentions: 6
Published: almost 6 years ago

10.1007/s00125-019-05032-3

Clinical and genetic correlates of islet-autoimmune signatures in juvenile-onset type 1 diabetes
Cited by: 19
Author(s): Laura A. Claessens, Joris Wesselius, Menno van Lummel, Sandra Laban, Flip Mulder, Dick Mul, Tanja Nikolić, Henk‐Jan Aanstoot, Bobby P. C. Koeleman, Bart O. Roep
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pone.0221487

AdequacyModel: An R package for probability distributions and general purpose optimization
Cited by: 36
Author(s): Pedro Rafael Diniz Marinho, Rodrigo B. Silva, Marcelo Bourguignon, Gauss M. Cordeiro, Saralees Nadarajah
Software Mentions: 6
Published: about 5 years ago

10.1038/srep26454

GBIQ: a non-arbitrary, non-biased method for quantification of fluorescent images
Cited by: 2
Author(s): Youichirou Ninomiya, Wei Zhao, Yumiko Saga
Software Mentions: 6
Published: over 8 years ago

10.1038/s41598-021-94258-6

Ecological plasticity to ions concentration determines genetic response and dominance of Anopheles coluzzii larvae in urban coastal habitats of Central Africa
Cited by: 7
Author(s): Neil Michel Longo-Pendy, Billy Téné-Fossog, Robert E. Tawedi, Ousman Akone‐Ella, Céline Toty, Nil Rahola, Jean‐Jacques Braun, Nicolás Berthet, Pierre Kengne, Carlo Costantini, Diégo Ayala
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-019-40910-1

Phosphorus source driving the soil microbial interactions and improving sugarcane development
Cited by: 25
Author(s): Thiago Gumière, Alain N. Rousseau, Diogo Paes da Costa, Alice de Souza Cassetari, Simone Raposo Cotta, Fernando Dini Andreote, Silvio José Gumière, Paulo Sérgio Pavinato
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0238304

Investigation of gene-gene interactions in cardiac traits and serum fatty acid levels in the LURIC Health Study
Cited by: 5
Author(s): Jiayan Zhou, Kristin Passero, Nicole Palmiero, Bertram Müller‐Myhsok, Marcus E. Kleber, Winfried Maerz, Molly A. Hall
Software Mentions: 5
Published: about 4 years ago

10.3390/genes11020216

Repetitive DNA Restructuring Across Multiple Nicotiana Allopolyploidisation Events Shows a Lack of Strong Cytoplasmic Bias in Influencing Repeat Turnover
Cited by: 6
Author(s): Steven Dodsworth, Maïté S. Guignard, Oscar Alejandro Pérez‐Escobar, Monika Struebig, Mark W. Chase, Andrew R. Leitch
Software Mentions: 4
Published: over 4 years ago

10.3390/cancers12092433

Oncogenic Orphan Nuclear Receptor NR4A3 Interacts and Cooperates with MYB in Acinic Cell Carcinoma
Cited by: 11
Author(s): David Y. Lee, Kathryn J. Brayer, Yoshitsugu Mitani, Eric A Burns, Pulivarthi H. Rao, Diana Bell, Michelle D. Williams, Renata Ferrarotto, Kristen B. Pytynia, Adel K. El‐Naggar, Scott A. Ness
Software Mentions: 4
Published: about 4 years ago

10.1002/ece3.2794

Synergistic effects of floral phytochemicals against a bumble bee parasite
Cited by: 46
Author(s): Evan C. Palmer‐Young, Ben M. Sadd, Rebecca E. Irwin, Lynn S. Adler
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2018.01002

Water Masses and Depth Structure Prokaryotic and T4-Like Viral Communities Around Hydrothermal Systems of the Nordic Seas
Cited by: 6
Author(s): Sven Le Moine Bauer, Anne Stensland, Frida Lise Daae, Ruth‐Anne Sandaa, Ingunn H. Thorseth, Ida Helene Steen, Helge K. Dahle
Software Mentions: 4
Published: over 6 years ago

10.1186/s13014-018-1072-4

Real-time intra-fraction motion management in breast cancer radiotherapy: analysis of 2028 treatment sessions
Cited by: 42
Author(s): D. Reitz, Carl Ganter, S. Schönecker, Montserrat Pazos, P. Freislederer, Maximilian Niyazi, Ute Ganswindt, Filippo Alongi, M. J. Reiner, Claus Belka, Stefanie Corradini
Software Mentions: 4
Published: over 6 years ago

10.1186/s13014-020-01572-w

Stability and reproducibility of 6013 deep inspiration breath-holds in left-sided breast cancer
Cited by: 24
Author(s): D. Reitz, Franziska Walter, S. Schönecker, P. Freislederer, Montserrat Pazos, Maximilian Niyazi, Guillaume Landry, Filippo Alongi, Edwin Bölke, Christiane Matuschek, M. J. Reiner, Claus Belka, Stefanie Corradini
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-018-25604-4

Transcriptomic integration of D4R and MOR signaling in the rat caudate putamen
Cited by: 8
Author(s): Alejandra Valderrama-Carvajal, Haritz Irizar, Belén Gago, Haritz Jiménez-Urbieta, Kjell Fuxé, María C. Rodríguez‐Oroz, David Otaegui, Alicia Rivera
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-31640-x

Cell type-resolved human lung lipidome reveals cellular cooperation in lung function
Cited by: 28
Author(s): Jennifer Kyle, Gérémy Clair, Gautam Bandyopadhyay, Ravi S. Misra, Erika Zink, Kent Bloodsworth, Anil Shukla, Yina Du, Jacquelyn Lillis, Jason Myers, John M. Ashton, Timothy Bushnell, Matthew Cochran, Gail H. Deutsch, Erin Baker, James P. Carson, Thomas J. Mariani, Yan Xu, Jeffrey A. Whitsett, Gloria S. Pryhuber, Charles Ansong
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms21041543

A High Resolution Melting Analysis-Based Genotyping Toolkit for the Peach (Prunus persica) Chilling Requirement
Cited by: 9
Author(s): Li-Dek Chou, Shih-Jie Huang, Chen Yu Hsieh, Ming-Te Lu, Chia-Wei Song, Fu-Chiun Hsu
Software Mentions: 4
Published: over 4 years ago

10.1155/2020/2948292

Commonality and Specificity of Acupuncture Point Selections
Cited by: 15
Author(s): Ye-Seul Lee, Yeonhee Ryu, Da-Eun Yoon, Cheol-Han Kim, Geesoo Hong, Ye-Chae Hwang, Younbyoung Chae
Software Mentions: 3
Published: over 4 years ago

10.1002/ece3.3058

Semi‐supervised determination of pseudocryptic morphotypes using observer‐free characterizations of anatomical alignment and shape
Cited by: 19
Author(s): Natasha Vitek, Carly L. Manz, Tingran Gao, Jonathan I. Bloch, Suzanne G. Strait, Douglas Boyer
Software Mentions: 3
Published: over 7 years ago

10.1093/jxb/eraa086

Novel routes towards bioplastics from plants: elucidation of the methylperillate biosynthesis pathway from Salvia dorisiana trichomes
Cited by: 12
Author(s): E. Jongedijk, Sebastian Müller, Aalt D. J. van Dijk, Elio Schijlen, Antoine Champagne, Marc Boutry, Mark Levisson, Sander van der Krol, Harro J. Bouwmeester, Jules Beekwilder
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-021-97862-8

Regional heterogeneity in coral species richness and hue reveals novel global predictors of reef fish intra-family diversity
Cited by: 2
Author(s): Kieran Cox, Mackenzie B. Woods, T. E. Reimchen
Software Mentions: 3
Published: about 3 years ago

10.3389/fnbeh.2017.00219

Community Violence Exposure and Conduct Problems in Children and Adolescents with Conduct Disorder and Healthy Controls
Cited by: 25
Author(s): Linda Kersten, Noortje Vriends, Martin Steppan, Nora Maria Raschle, Martin Praetzlich, Helena Oldenhof, Robert Vermeiren, Lucres M. C. Jansen, Kathrin Ackermann, Anka Bernhard, Anne Martinelli, Karen González-Madruga, Ignazio Puzzo, Anita M. Wells, Jack C. Rogers, Roberta Clanton, Rosalind Baker, Liam Grisley, Sarah Baumann, Malou Gundlach, Gregor Kohls, Miguel Ángel González‐Torres, Eva Sesma-Pardo, Roberta Dochnal, Helen Lazaratou, Zacharias Kalogerakis, Aitana Bigorra, Areti Smaragdi, Réka Siklósi, Dimitris Dikeos, Amaia Hervás, Aranzazu Fernández‐Rivas, Stéphane A. De Brito, Kerstin Konrad, Beate Herpertz‐Dahlmann, Graeme Fairchild, Christine M. Freitag, Arne Popma, Meinhard Kieser, Christina Stadler
Software Mentions: 3
Published: almost 7 years ago

10.1038/srep43558

Serum snoRNAs as biomarkers for joint ageing and post traumatic osteoarthritis
Cited by: 41
Author(s): M.M. Steinbusch, Yongxiang Fang, Peter Milner, Peter Clegg, David A. Young, Tim J. M. Welting, Mandy J. Peffers
Software Mentions: 2
Published: over 7 years ago

10.1186/s13075-020-02161-8

Higher interferon score and normal complement levels may identify a distinct clinical subset in children with systemic lupus erythematosus
Cited by: 20
Author(s): Alessandra Tesser, Luciana Martins de Carvalho, Paula Sandrin-Garcia, Alessia Pin, Serena Pastore, Andrea Taddio, L Roberti, Rosane Gomes de Paula Queiróz, Virgínia Paes Leme Ferriani, Sérgio Crovella, Alberto Tommasini
Software Mentions: 2
Published: over 4 years ago

10.3390/ani11010161

Widespread Presence of Domestic Dogs on Sandy Beaches of Southern Chile
Cited by: 11
Author(s): Esteban I Cortés, Juan G. Navedo, Eduardo A. Silva‐Rodríguez
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0223339

In vivo clearance of nanoparticles by transcytosis across alveolar epithelial cells
Cited by: 21
Author(s): Pascal Detampel, Anutosh Ganguly, Sara Tehranian, Francis Green, Santiswarup Singha, Pere Santamaría, Ayodeji Jeje, Clifford S. Cho, Björn Petri, Matthias Amrein
Software Mentions: 2
Published: about 5 years ago

10.1186/s40425-018-0327-9

Radiation and PD-(L)1 treatment combinations: immune response and dose optimization via a predictive systems model
Cited by: 77
Author(s): Yuri Kosinsky, Simon J. Dovedi, Kirill Peskov, Veronika Voronova, Lulu Chu, Helen Tomkinson, Nidal Al‐Huniti, Donald R. Stanski, Gabriel Helmlinger
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0171781

Interpretation of metabolic memory phenomenon using a physiological systems model: What drives oxidative stress following glucose normalization?
Cited by: 9
Author(s): Veronika Voronova, Kirill Zhudenkov, Gabriel Helmlinger, Kirill Peskov
Software Mentions: 2
Published: over 7 years ago

10.1002/ece3.3902

Direct effects of warming increase woody plant abundance in a subarctic wetland
Cited by: 11
Author(s): Lindsay G. Carlson, Karen H. Beard, Peter B. Adler
Software Mentions: 2
Published: over 6 years ago

10.1016/j.jaac.2015.10.013

Positive Attributes Buffer the Negative Associations Between Low Intelligence and High Psychopathology With Educational Outcomes
Cited by: 15
Author(s): Maurício Scopel Hoffmann, Ellen Leibenluft, Argyris Stringaris, P Laporte, Pedro Mário Pan, Ary Gadelha, Gisele Gus Manfro, Eurípedes Constantino Miguel, Luís Augusto Rohde, Giovanni Abrahão Salum
Software Mentions: 1
Published: almost 9 years ago

10.3390/cells8030262

Untangling Extracellular Proteasome-Osteopontin Circuit Dynamics in Multiple Sclerosis
Cited by: 8
Author(s): Chiara Dianzani, Domizia Vecchio, Nausicaa Clemente, Annalisa Chiocchetti, Filippo Martinelli Boneschi, Daniela Galimberti, Umberto Dianzani, Cristoforo Comi, Michele Mishto, Juliane Liepe
Software Mentions: 1
Published: over 5 years ago

10.1590/1678-4685-GMB-2017-0157

Cytotaxonomic study of the Chilean endemic complex Alstroemeria magnifica Herb. (Alstroemeriaceae)
Cited by: 4
Author(s): Carlos M. Baeza, Víctor L. Finot, Eduardo Ruíz, Pedro Carrasco, Patricio Novoa, Marcelo Rosas, Óscar Toro‐Núñez
Software Mentions: 1
Published: over 6 years ago

10.1590/2175-8239-JBN-2020-0138

Racial differences in the relationship between high-normal 25-hydroxy vitamin d and parathyroid hormone levels in early stage chronic kidney disease
Cited by: 0
Author(s): Marquita B. Winder, Darius L. Mason, Janani Rangaswami, Arif Asif, Tushar J. Vachharajani, Roy Mathew
Software Mentions: 1
Published: over 3 years ago

Projects: cran: plot3D

Papers Mentioning plot3D 47