cran: SAM | Projects | Ecosyste.ms: Papers

10.1186/1471-2164-11-26

1,25 dihydroxyvitamin D-mediated orchestration of anticancer, transcript-level effects in the immortalized, non-transformed prostate epithelial cell line, RWPE1
Cited by: 80
Author(s): Pavlo L. Kovalenko, Zhentao Zhang, Min Cui, S. Clinton, James C. Fleet
Software Mentions: 4
Published: over 16 years ago

10.3390/s140101155

A Methodology to Assess the Accuracy with which Remote Data Characterize a Specific Surface, as a Function of Full Width at Half Maximum (FWHM): Application to Three Italian Coastal Waters
Cited by: 12
Author(s): Rosa Maria Cavalli, Mattia Betti, Alessandra Campanelli, Annalisa Di Cicco, Daniela Guglietta, Pierluigi Penna, Viviana Piermattei
Software Mentions: 4
Published: over 12 years ago

10.7554/eLife.51109

Herpes simplex viral nucleoprotein creates a competitive transcriptional environment facilitating robust viral transcription and host shut off
Cited by: 47
Author(s): Sarah E Dremel, Neal A. DeLuca
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2105-7-335

AMDA: an R package for the automated microarray data analysis
Cited by: 35
Author(s): Mattia Pelizzola, Norman Pavelka, Maria Foti, Paola Ricciardi‐Castagnoli
Software Mentions: 4
Published: almost 20 years ago

10.1038/s41598-021-82731-1

Mating system evolution and genetic structure of diploid sexual populations of Cyrtomium falcatum in Japan
Cited by: 0
Author(s): Ryōsuke Imai, Yoshiaki Tsuda, Atsushi Ebihara, Sadamu Matsumoto, Ayumi Tezuka, Atsushi J. Nagano, Ryo Ootsuki, Yasuyuki Watano
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-70757-w

Circadian regulation of chemotherapy-induced peripheral neuropathic pain and the underlying transcriptomic landscape
Cited by: 17
Author(s): Hee Kee Kim, Sun Yeul Lee, Nobuya Koike, Eunju Kim, Marvin Wirianto, Mark J. Burish, Kazuhiro Yagita, Hyun Kyoung Lee, Zheng Chen, Jin Mo Chung, Salahadin Abdi, Seung Hee Yoo
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.0030087

Whole-Genome Cartography of Estrogen Receptor α Binding Sites
Cited by: 414
Author(s): Chin-Yo Lin, Vinsensius B. Vega, Jane S. Thomsen, Tao Zhang, Say Li Kong, Ming Xie, King-Wah Chiu, Leonard Lipovich, Daniel H. Barnett, Fabio Stossi, A. Yeo, Joshy George, Vladimir A. Kuznetsov, Yew Kok Lee, Tze Howe Charn, Nallasivam Palanisamy, Lance D. Miller, Edwin Cheung, Benita S. Katzenellenbogen, Yijun Ruan, Guillaume Bourque, Chia Lin Wei, Edison T. Liu
Software Mentions: 4
Published: about 19 years ago

10.1038/s41598-021-91807-x

Amino acid-enriched plant-based RUTF treatment was not inferior to peanut-milk RUTF treatment in restoring plasma amino acid levels among patients with oedematous or non-oedematous malnutrition
Cited by: 3
Author(s): Wataru Sato, Chie Furuta, Peter Akomo, Paluku Bahwere, Steve Collins, Kate Sadler, Chrissy Banda, Elizabeth Maganga, Sylvester Kathumba, Hitoshi Murakami
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-015-1635-9

Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection
Cited by: 72
Author(s): James E. Koltes, Eric R. Fritz-Waters, Christopher J. Eisley, Igseo Choi, Hua Bao, Arun Kommadath, Nick V. L. Serão, Nicholas Boddicker, Samuel M. Abrams, Martine Schroyen, Hyelee Loyd, Christopher K. Tuggle, Graham Plastow, Leluo Guan, Paul Stothard, Joan K. Lunney, Peng Liu, Susan Carpenter, Raymond R. R. Rowland, Jack C. M. Dekkers, James M. Reecy
Software Mentions: 4
Published: about 11 years ago

10.1186/1471-2105-7-533

Effect of various normalization methods on Applied Biosystems expression array system data
Cited by: 44
Author(s): Cátálin Bárbácioru, Yulei Wang, Roger D. Canales, Yongming Sun, David Keys, Felix Hon-Wai Chan, Karen Poulter, Raymond R. Samaha
Software Mentions: 4
Published: over 19 years ago

10.1371/journal.pcbi.1009078

lra: A long read aligner for sequences and contigs
Cited by: 50
Author(s): Jimin Ren, Mark Chaisson
Software Mentions: 4
Published: almost 5 years ago

10.1021/acssynbio.0c00637

Construction of DNA Tools for Hyperexpression in Marchantia Chloroplasts
Cited by: 8
Author(s): Eftychios Frangedakis, Fernando Guzman Chavez, Marius Rebmann, Kasey Markel, Ying Yu, Artemis Perraki, Sze Wai Tse, Yang Liu, Jenna Rever, Susanna Sauret-Güeto, Bernard Goffinet, Harald Schneider, Jim Haseloff
Software Mentions: 4
Published: almost 5 years ago

10.1186/1471-2164-14-425

Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing
Cited by: 47
Author(s): Shanrong Zhao, Kurt Prenger, Lance Smith, Thomas Messina, Huiying Fan, Edward P. Jaeger, S. A. Stephens
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.pone.0056657

Significance and Suppression of Redundant IL17 Responses in Acute Allograft Rejection by Bioinformatics Based Drug Repositioning of Fenofibrate
Cited by: 15
Author(s): Silke Roedder, Naoyuki Kimura, Homare Okamura, Szu‐Chuan Hsieh, Yongquan Gong, Minnie M. Sarwal
Software Mentions: 4
Published: over 13 years ago

10.1038/s41598-019-48692-2

Efficient and specific oligo-based depletion of rRNA
Cited by: 41
Author(s): Amelie J. Kraus, Benedikt G. Brink, T. Nicolai Siegel
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-019-49915-2

RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat
Cited by: 52
Author(s): Mir Asif Iquebal, Pradeep Sharma, Rahul Singh Jasrotia, Sarika Jaiswal, Amandeep Kaur, Monika Saroha, U. B. Angadi, Sonia Sheoran, Rajender Singh, Gyanendra Singh, Anil Rai, Ruchi Tiwari, Dinesh Kumar
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.60833

Novel LOTUS-domain proteins are organizational hubs that recruit C. elegans Vasa to germ granules
Cited by: 9
Author(s): Patricia Giselle Cipriani, Olivia Bay, John Zinno, Michelle Gutwein, Hin Hark Gan, Vinay K. Mayya, George Chung, Jia‐Xuan Chen, Hala Fahs, Yu Guan, Thomas F. Duchaîne, Matthias Selbach, Fabio Piano, Kristin C. Gunsalus
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12711-016-0257-2

Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production
Cited by: 31
Author(s): Harald Olsen, Tim Martin Knutsen, Anna Lewandowska-Sabat, Harald Grove, Torfinn Nome, Mathias Tiedemann Svendsen, Mariann Árnyasi, Marte Sodeland, Kristil Kindem Sundsaasen, Sandra Rinne Dahl, B. Heringstad, Hanne Hellerud Hansen, I. Olsaker, Matthew Kent, Sigbjørn Lien
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-019-52395-z

Environmental and ecological factors mediate taxonomic composition and body size of polyplacophoran assemblages along the Peruvian Province
Cited by: 6
Author(s): Christian M. Ibáñez, Melany Waldisperg, Felipe I. Torres, Sergio A. Carrasco, Javier Sellanes, M. Cecilia Pardo‐Gandarillas, Julia D. Sigwart
Software Mentions: 3
Published: over 6 years ago

10.3390/v11010033

A Comprehensive RNA-seq Analysis of Human Bocavirus 1 Transcripts in Infected Human Airway Epithelium
Cited by: 5
Author(s): Wei Zou, Min Xiong, Xuefeng Deng, John F. Engelhardt, Ziying Yan, Jianming Qiu
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-53901-z

Blood transcriptome analysis in a buck-ewe hybrid and its parents
Cited by: 1
Author(s): Clemens Falker‐Gieske, C. Knorr, Jens Tetens
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2105-12-382

Mulcom: a multiple comparison statistical test for microarray data in Bioconductor
Cited by: 5
Author(s): Claudio Isella, Tommaso Renzulli, Davide Corà, Enzo Medico
Software Mentions: 3
Published: over 14 years ago

10.1186/s12859-017-1831-5

SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines
Cited by: 8
Author(s): Jérôme Audoux, Mikaël Salson, Christophe Grosset, Sacha Beaumeunier, Jean-Marc Holder, Thérèse Commes, Philippe Naveilhan
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-019-45898-2

Transcriptional landscape of soybean (Glycine max) embryonic axes during germination in the presence of paclobutrazol, a gibberellin biosynthesis inhibitor
Cited by: 19
Author(s): Rajesh Kumar Gazara, Eduardo Alves Gamosa de Oliveira, B. Calderan Rodrigues, Rodrigo Nunes da Fonseca, Antônia Elenir Amâncio Oliveira, Thiago M. Venancio
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-020-59541-y

Chronic circadian misalignment accelerates immune senescence and abbreviates lifespan in mice
Cited by: 78
Author(s): Hitoshi Inokawa, Yasuhiro Umemura, Akihiro Shimba, Eiryo Kawakami, Nobuya Koike, Yoshiki Tsuchiya, Masaru Ohashi, Yoichi Minami, Guangwei Cui, T. Asahi, Ryutaro Ono, Yuh Sasawaki, Eiichi Konishi, Seung-Hee Yoo, Chen Zheng, Satoshi Teramukai, Koichi Ikuta, Kazuhiro Yagita
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-41625-z

Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data
Cited by: 12
Author(s): Lázaro Betancourt, Krzysztof Pawłowski, Jonatan Eriksson, Attila Marcell Szász, Shamik Mitra, Indira Pla, Charlotte Welinder, Henrik Ekedahl, Per Broberg, Roger Appelqvist, Maria Yakovleva, Y. Sugita, Kenichi Miharada, Christian Ingvar, Lotta Lundgren, Bo Baldetorp, Håkan Olsson, Melinda Rezeli, Elisabet Wieslander, Péter Horvatovich, Johan Malm, Göran Jönsson, György Markó-Varga
Software Mentions: 3
Published: about 7 years ago

10.1186/s12859-020-03726-9

IonCRAM: a reference-based compression tool for ion torrent sequence files
Cited by: 2
Author(s): Moustafa Shokrof, Mohamed Abouelhoda
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-43141-6

CRISPR-Cas9 Editing in Maize: Systematic Evaluation of Off-target Activity and Its Relevance in Crop Improvement
Cited by: 62
Author(s): Joshua K. Young, Gina Zastrow-Hayes, Stéphane Deschamps, Sergei Svitashev, Mindaugas Zaremba, Ananta Acharya, Sushmitha Paulraj, Brooke D. Peterson-Burch, Chris Schwartz, Vesna Djukanovic, Brian Lenderts, Lanie Feigenbutz, Limin Wang, Clara M. Alarcon, Virginijus Šikšnys, Gregory D. May, N. Doane Chilcoat, Sandeep Kumar
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-39880-1

MicroRNAs from saliva of anopheline mosquitoes mimic human endogenous miRNAs and may contribute to vector-host-pathogen interactions
Cited by: 25
Author(s): Bruno Arcà, Alessio Colantoni, Carmine Fiorillo, Francesco Severini, Vladimír Beneš, Marco Di Luca, Raffaele Calogero, Fabrizio Lombardo
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-015-2112-1

Sequencing-based high throughput mutation detection in bread wheat
Cited by: 12
Author(s): Gaganjot Sidhu, Amita Mohan, Ping Zheng, Amandeep Kaur Dhaliwal, Dorrie Main, Kulvinder S. Gill
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2105-7-237

Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation
Cited by: 37
Author(s): Jamie A. Lee, Robert S. Sinkovits, Dennis Mock, Eva L Rab, Jennifer Cai, Peng Yang, Brian Saunders, Robert C. Hsueh, Sangdun Choi, Shankar Subramaniam, Richard H. Scheuermann
Software Mentions: 3
Published: about 20 years ago

10.1038/s41598-019-43512-z

Melanoma proteomics suggests functional differences related to mutational status
Cited by: 9
Author(s): Lucía Trilla-Fuertes, Angelo Gámez‐Pozo, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Mariana Díaz-Almirón, Claudia Fortes, María Ferrer-Gómez, Rocío López-Vacas, Verónica Parra Blanco, Iván Márquez-Rodas, Ainara Soria, Juan Ángel Fresno Vara, Enrique Espinosa
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-018-23641-7

Unbiased Strain-Typing of Arbovirus Directly from Mosquitoes Using Nanopore Sequencing: A Field-forward Biosurveillance Protocol
Cited by: 43
Author(s): Joseph A. Russell, Brittany Campos, Jennifer Stone, Erik M. Blosser, Nathan D. Burkett‐Cadena, Jonathan L. Jacobs
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-21484-w

Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias
Cited by: 56
Author(s): Raga Krishnakumar, Anupama Sinha, Sara W. Bird, Harikrishnan Jayamohan, Harrison Edwards, Joseph S. Schoeniger, Kamlesh D. Patel, Steven S. Branda, Michael Bartsch
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-31064-7

Unique Molecular Identifiers reveal a novel sequencing artefact with implications for RNA-Seq based gene expression analysis
Cited by: 33
Author(s): Johnny A. Sena, Giulia Galotto, Nico Devitt, Melanie C. Connick, Jennifer L. Jacobi, Pooja Umale, Luis Vidali, Callum J. Bell
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-017-14418-5

Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis
Cited by: 10
Author(s): Emiko Yoshida, Yasuhisa Terao, Noriko Hayashi, Kaoru Mogushi, Atsushi Arakawa, Yuji Tanaka, Yoshiaki Ito, Hiroko Ohmiya, Yoshihide Hayashizaki, Satoru Takeda, Masayoshi Itoh, Hideya Kawaji
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-017-04786-3

sRNA and cis-antisense sRNA identification in Staphylococcus aureus highlights an unusual sRNA gene cluster with one encoding a secreted peptide
Cited by: 25
Author(s): Julie Bronsard, Gaëtan Pascreau, Mohamed Sassi, Tony Mauro, Yoann Augagneur, Brice Felden
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-018-31093-2

Population level mitogenomics of long-lived bats reveals dynamic heteroplasmy and challenges the Free Radical Theory of Ageing
Cited by: 23
Author(s): David Jebb, Nicole M. Foley, Conor V. Whelan, Frédéric Touzalin, Sébastien J. Puechmaille, Emma C. Teeling
Software Mentions: 3
Published: over 7 years ago

10.1186/s12859-018-2319-7

BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs
Cited by: 21
Author(s): Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier
Software Mentions: 3
Published: over 7 years ago

10.1186/s12859-020-03665-5

SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles
Cited by: 11
Author(s): Zhenhua Yu, Fang Du, Rongjun Ban, Yuanwei Zhang
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-017-02824-8

High-resolution promoter map of human limbal epithelial cells cultured with keratinocyte growth factor and rho kinase inhibitor
Cited by: 8
Author(s): Masahito Yoshihara, Yuzuru Sasamoto, Ryuhei Hayashi, Yuki Ishikawa, Motokazu Tsujikawa, Yoshihide Hayashizaki, Masayoshi Itoh, Hideya Kawaji, Kohji Nishida
Software Mentions: 3
Published: almost 9 years ago

10.18632/aging.103184

Plasma proteomic profiling of young and old mice reveals cadherin-13 prevents age-related bone loss
Cited by: 14
Author(s): Yong Ryoul Yang, Mohammad Humayun Kabir, Jin Hee Park, Jae-Il Park, Jae Sook Kang, Shinyeong Ju, Yeo Jin Shin, Seung Min Lee, Jaemin Lee, Seokho Kim, Kwang-Pyo Lee, Soo Young Lee, Cheolju Lee, Kideok D. Kwon
Software Mentions: 3
Published: about 6 years ago

10.1002/mgg3.1503

Identification of common differentially expressed genes in Turner (45,X) and Klinefelter (47,XXY) syndromes using bioinformatics analysis
Cited by: 5
Author(s): María Carolina Manotas, Juan M. Calderón, Liliana López‐Kleine, Fernando Suárez‐Obando, Olga Moreno, Alejandra Rojas
Software Mentions: 3
Published: over 5 years ago

10.3390/molecules24030631

Stratification of Breast Cancer by Integrating Gene Expression Data and Clinical Variables
Cited by: 8
Author(s): Zongzhen He, Junying Zhang, Xiguo Yuan, Jianing Xi, Zhaowen Liu, Yuanyuan Zhang
Software Mentions: 3
Published: over 7 years ago

10.15252/msb.20188584

Path‐seq identifies an essential mycolate remodeling program for mycobacterial host adaptation
Cited by: 49
Author(s): Eliza J.R. Peterson, Rebeca Bailo, Alissa C. Rothchild, Mario L. Arrieta-Ortiz, Amardeep Kaur, Min Pan, Dat Mai, Abrar A. Abidi, Charlotte Cooper, Alan Aderem, Apoorva Bhatt, Nitin S. Baliga
Software Mentions: 3
Published: over 7 years ago

10.3390/v12070782

High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics
Cited by: 4
Author(s): Sílvia Inês Sardi, Renata Carvalho, Luis Gustavo Carvalho Pacheco, João Fernando Lourenço de Almeida, Emilia M M D A Belitardo, Carina S. Pinheiro, Gúbio Soares Campos, Eric Roberto Guimarães Rocha Aguiar
Software Mentions: 3
Published: almost 6 years ago

10.1002/prot.25697

Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13
Cited by: 142
Author(s): Jie Hou, Tai Tsun Wu, Renzhi Cao, Jianlin Cheng
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2105-12-411

EPEPT: A web service for enhanced P-value estimation in permutation tests
Cited by: 5
Author(s): Theo Knijnenburg, Jake Lin, Hector Rovira, John P. Boyle, Ilya Shmulevich
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.ppat.1009175

Escalation in the host-pathogen arms race: A host resistance response corresponds to a heightened bacterial virulence response
Cited by: 5
Author(s): Qi Wang, Nadia Shakoor, Adam Boyher, Kira M. Veley, Jeffrey C. Berry, Todd C. Mockler, Rebecca Bart
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.ppat.1006510

Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection
Cited by: 50
Author(s): Gustavo H. Kijak, Eric Sanders‐Buell, Agnès‐Laurence Chenine, Michael A. Eller, Nilu Goonetilleke, Rasmi Thomas, Sivan Leviyang, Elizabeth A. Harbolick, Meera Bose, Phuc Pham, Celina Oropeza, Kultida Poltavee, Anne Marie O’Sullivan, Erik Billings, Mélanie Merbah, Margaret C. Costanzo, Joanna Warren, Bonnie M. Slike, Hui Li, Kristina K. Peachman, Will Fischer, Feng Gao, Claudia Cicala, James Arthos, Leigh Anne Eller, Robert J. O’Connell, Samuel Sinei, Lucas Maganga, Hannah Kibuuka, Sorachai Nitayaphan, Mangala Rao, Mary Marovich, Shelly J. Krebs, Morgane Rolland, Bette T. Korber, George M. Shaw, Nelson L. Michael, Merlin L. Robb, Sodsai Tovanabutra, Jerome H. Kim
Software Mentions: 3
Published: almost 9 years ago

10.1186/1476-4598-12-140

Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations
Cited by: 53
Author(s): Ângela Aguirres Fachel, Ana Carolina Tahira, Santiago A. Vilella-Arias, Vinicius Maracaja‐Coutinho, Etel Rp Gimba, Giselle Maria Vignal, Franz Campos, Eduardo M. Reis, Sérgio Verjovski-Almeida
Software Mentions: 3
Published: over 12 years ago

10.1016/j.mcpro.2021.100125

Affinity Proteomics and Deglycoproteomics Uncover Novel EDEM2 Endogenous Substrates and an Integrative ERAD Network
Cited by: 6
Author(s): Cristian V. A. Munteanu, Gabriela Chirițoiu, Marioara Chirițoiu, Simona Ghenea, Andrei-José Petrescu, Ștefana M. Petrescu
Software Mentions: 3
Published: over 5 years ago

10.1029/2019RG000686

Spaceborne Cloud and Precipitation Radars: Status, Challenges, and Ways Forward
Cited by: 65
Author(s): Alessandro Battaglia, Pavlos Kollias, Ranvir Dhillon, Richard Roy, Simone Tanelli, Katia Lamer, Mircea Grecu, Matthew Lebsock, Daniel Watters, Kamil Mróz, Gerald M. Heymsfield, Lihua Li, Katsuko Furukawa
Software Mentions: 3
Published: almost 6 years ago

10.1093/jxb/erx010

Gene expression atlas of pigeonpea and its application to gain insights into genes associated with pollen fertility implicated in seed formation
Cited by: 48
Author(s): Lekha T. Pazhamala, Shilp Purohit, Rachit K. Saxena, Vanika Garg, L. Krishnamurthy, Jérôme Verdier, Rajeev K. Varshney
Software Mentions: 3
Published: over 9 years ago

10.1120/jacmp.v17i3.6370

2016 AAPM Spring Clinical Meeting - Abstracts
Cited by: 0
Author(s):
Software Mentions: 3
Published: about 10 years ago

10.1093/jxb/erx349

Transfer of a starch phenotype from wild wheat to bread wheat by deletion of a locus controlling B-type starch granule content
Cited by: 21
Author(s): Tansy Chia, Nikolai M Adamski, Benedetta Saccomanno, Andrew J. Greenland, Alastair Nash, Cristóbal Uauy, Kay Trafford
Software Mentions: 3
Published: almost 9 years ago

10.1029/2020MS002138

Clouds and Convective Self‐Aggregation in a Multimodel Ensemble of Radiative‐Convective Equilibrium Simulations
Cited by: 69
Author(s): Allison A. Wing, Catherine L. Stauffer, Tobias Becker, Kevin A. Reed, Min‐Seop Ahn, Nathan Arnold, Sandrine Bony, Mark Branson, G. H. Bryan, Jean‐Pierre Chaboureau, Stephan R. de Roode, Gayatri Kulkarni, Cathy Hohenegger, I‐Kuan Hu, Fredrik Jansson, Todd R. Jones, Marat Khairoutdinov, Dae Hyun Kim, Zane Martin, Shuhei Matsugishi, Brian Medeiros, Hiroaki Miura, Yumin Moon, Sebastian K. Müller, Tomoki Ohno, Max Popp, Thara Prabhakaran, David A. Randall, Rosimar Ríos-Berríos, Nicolas Rochetin, Romain Roehrig, David M. Romps, James H. Ruppert, Masaki Satoh, Levi G. Silvers, Martin S. Singh, Björn Stevens, Lorenzo Tomassini, Chiel C. van Heerwaarden, Shuguang Wang, Ming Zhao
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12862-019-1353-z

Origin and diversification of the plasminogen activation system among chordates
Cited by: 26
Author(s): Andrés Chana-Muñoz, Agnieszka Jendroszek, Malene Sønnichsen, Tobias Wang, Michael Ploug, Jan K. Jensen, Peter A. Andreasen, Christian Berthou, Frank Panitz
Software Mentions: 3
Published: over 7 years ago

10.1007/s13361-016-1544-4

Prognostic Metabolite Biomarkers for Soft Tissue Sarcomas Discovered by Mass Spectrometry Imaging
Cited by: 37
Author(s): Sha Lou, Benjamin Balluff, Arjen H.G. Cleven, Judith V.M.G. Bovée, Liam A. McDonnell
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.ppat.1003341

Differences in Gastric Carcinoma Microenvironment Stratify According to EBV Infection Intensity: Implications for Possible Immune Adjuvant Therapy
Cited by: 132
Author(s): Michael J. Strong, Guiyin Xu, Joseph Coco, Carl Baribault, Dass S. Vinay, Michelle Lacey, Amy L. Strong, Teresa A. Lehman, Michael Seddon, Zhen Lin, Monica Concha, Melody Baddoo, MaryBeth Ferris, Kenneth F. Swan, Deborah E. Sullivan, Matthew E. Burow, Christopher M. Taylor, Erik K. Flemington
Software Mentions: 3
Published: about 13 years ago

10.1038/s41598-017-02329-4

Expression Profiling of mRNAs and Long Non-Coding RNAs in Aged Mouse Olfactory Bulb
Cited by: 11
Author(s): Ming Wang, Wei Liu, Jian Jiao, Jingyun Li, Chengshuo Wang, Luo Zhang
Software Mentions: 3
Published: about 9 years ago

10.3390/microorganisms9030584

Implications of Tributyrin on Gut Microbiota Shifts Related to Performances of Weaning Piglets
Cited by: 15
Author(s): Francesco Miragoli, Vania Patrone, Aldo Prandini, Samantha Sigolo, Matteo Dell’Anno, Luciana Rossi, Alice Senizza, L. Morelli, Maria Luisa Callegari
Software Mentions: 3
Published: about 5 years ago

10.3390/genes12071064

Genetic and Transcriptomic Analysis Reveal the Molecular Basis of Photoperiod-Regulated Flowering in Xishuangbanna Cucumber (Cucumis sativus L. var. xishuangbannesis Qi et Yuan)
Cited by: 7
Author(s): Zhen Tian, Molly Jahn, Xiaodong Qin, Hesbon Ochieng Obel, Fan Yang, Ji Li, Jinfeng Chen
Software Mentions: 3
Published: almost 5 years ago

10.1590/1678-4685-GMB-2017-0075

Differential gene expression profiles in peripheral blood in Northeast Chinese Han people with acute myocardial infarction
Cited by: 16
Author(s): Fan Lin, Heyu Meng, Xudong Guo, Xiangdong Li, F. Meng
Software Mentions: 3
Published: over 8 years ago

10.3390/genes11091000

Comparative Transcriptome Analysis of Pine Trees Treated with Resistance-Inducing Substances against the Nematode Bursaphelenchus xylophilus
Cited by: 6
Author(s): Jung–Wook Park, Hee Won Jeon, Hyejung Jung, Hyun‐Hee Lee, Junheon Kim, Ae Ran Park, Namgyu Kim, Gil Soo Han, Jin-Cheol Kim, Young-Su Seo
Software Mentions: 3
Published: almost 6 years ago

10.3390/genes11111290

Platinum-Quality Mitogenome Haplotypes from United States Populations
Cited by: 14
Author(s): Cassandra R. Taylor, Kevin M. Kiesler, Kimberly Sturk-Andreaggi, J. Ring, Walther Parson, Moses S. Schanfield, Peter M. Vallone, Charla Marshall
Software Mentions: 3
Published: over 5 years ago

10.1186/s12862-019-1522-0

RADseq population genomics confirms divergence across closely related species in blue coral (Heliopora coerulea)
Cited by: 11
Author(s): Akira Iguchi, Yuki Yoshioka, Zac H. Forsman, Ingrid S. Knapp, Robert J. Toonen, Yuki Hongo, Satoshi Nagai, Nina Yasuda
Software Mentions: 3
Published: over 6 years ago

10.3390/genes11010053

SparkRA: Enabling Big Data Scalability for the GATK RNA-seq Pipeline with Apache Spark
Cited by: 7
Author(s): Zaid Al-Ars, Saiyi Wang, Hamid Mushtaq
Software Mentions: 3
Published: over 6 years ago

10.3390/genes10010009

Reference Genomes from Distantly Related Species Can Be Used for Discovery of Single Nucleotide Polymorphisms to Inform Conservation Management
Cited by: 44
Author(s): Stephanie J. Galla, Natalie Forsdick, Liz Brown, Marc P. Hoeppner, Michael Knapp, Richard F. Maloney, Roger Moraga, Anna W. Santure, Tammy E. Steeves
Software Mentions: 3
Published: over 7 years ago

10.1186/gb-2007-8-5-r79

An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data
Cited by: 42
Author(s): Michał Okoniewski, Timothy Yates, Siân Dibben, Crispin Miller
Software Mentions: 3
Published: over 19 years ago

10.1534/g3.116.032839

Transcriptome Analysis Reveals that Vitamin A Metabolism in the Liver Affects Feed Efficiency in Pigs
Cited by: 31
Author(s): Yi‐Fang Zhao, Ye Hou, Fei Liu, An Liu, Jing Lü, Changzhi Zhao, Yu Luan, Yuanxin Miao, Shuhong Zhao, Xinyun Li
Software Mentions: 3
Published: over 9 years ago

10.1186/1472-6815-14-9

Combined examination of sequence and copy number variations in human deafness genes improves diagnosis for cases of genetic deafness
Cited by: 23
Author(s): Haiying Ji, Jingqiao Lü, Jianjun Wang, Huawei Li, Xiaobo Lin
Software Mentions: 3
Published: over 11 years ago

10.1111/1751-7915.13863

Transcriptome analysis reveals the roles of nitrogen metabolism and sedoheptulose bisphosphatase pathway in methanol‐dependent growth of Corynebacterium glutamicum
Cited by: 4
Author(s): Liwen Fan, Yu Wang, Jin Qian, Ning Gao, Zhihui Zhang, Xiaomeng Ni, Letian Sun, Qianqian Yuan, Ping Zheng, Jibin Sun
Software Mentions: 3
Published: almost 5 years ago

10.1534/g3.111.000240

Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences
Cited by: 1,474
Author(s): Julian M. Catchen, Angel Amores, Paul A. Hohenlohe, William A. Cresko, John H. Postlethwait
Software Mentions: 3
Published: almost 15 years ago

10.1534/g3.116.028290

Transcriptomic Analysis Identifies Candidate Genes and Gene Sets Controlling the Response of Porcine Peripheral Blood Mononuclear Cells to Poly I:C Stimulation
Cited by: 10
Author(s): Jiying Wang, Yanping Wang, Huaizhong Wang, Haifei Wang, Jianfeng Liu, Ying Wu, Jianfeng Guo
Software Mentions: 3
Published: about 10 years ago

10.3389/fpsyg.2021.622433

Understanding the Multidimensional and Dynamic Nature of Facial Expressions Based on Indicators for Appraisal Components as Basis for Measuring Drivers' Fear
Cited by: 2
Author(s): Meng Zhang, Klas Ihme, Uwe Drewitz, Meike Jipp
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-16-S18-S16

Identification of aberrant gene expression associated with aberrant promoter methylation in primordial germ cells between E13 and E16 rat F3 generation vinclozolin lineage
Cited by: 23
Author(s): Y-h. Taguchi
Software Mentions: 3
Published: over 10 years ago

10.3758/s13421-020-01082-w

The simultaneous recognition of multiple words: A process analysis
Cited by: 4
Author(s): Anne Voormann, Mikhail S. Spektor, Karl Christoph Klauer
Software Mentions: 3
Published: about 5 years ago

10.3389/fpls.2019.01624

Gene Expression Profiling of the Shoot Meristematic Tissues in Woodland Strawberry Fragaria vesca
Cited by: 8
Author(s): Yongping Li, Jia Feng, Laichao Cheng, Cheng Dai, Qi Gao, Zhongchi Liu, Chunying Kang
Software Mentions: 3
Published: over 6 years ago

10.1186/s40168-017-0341-z

Associations among dietary non-fiber carbohydrate, ruminal microbiota and epithelium G-protein-coupled receptor, and histone deacetylase regulations in goats
Cited by: 39
Author(s): Hong Shen, Zhongyan Lu, Zhihui Xu, Zhan Chen, Zongzhuan Shen
Software Mentions: 3
Published: over 8 years ago

10.3389/fpsyt.2021.685656

Metabolic Profiling Indicates Diversity in the Metabolic Physiologies Associated With Maternal Postpartum Depressive Symptoms
Cited by: 4
Author(s): Emma Bränn, Christina J. Malavaki, Emma Fransson, Maria-Konstantina Ioannidi, Hanna Henriksson, Fotios C. Papadopoulos, George P. Chrousos, Maria I. Klapa, Alkistis Skalkidou
Software Mentions: 3
Published: almost 5 years ago

10.3389/fvets.2019.00308

A Pine Enhanced Biochar Does Not Decrease Enteric CH4 Emissions, but Alters the Rumen Microbiota
Cited by: 24
Author(s): Stephanie A. Terry, Gabriel de Oliveira Ribeiro, Robert J. Gruninger, A. V. Chaves, K. A. Beauchemin, E. K. Okine, Tim A. McAllister
Software Mentions: 3
Published: over 6 years ago

10.1534/g3.119.400431

Dynamic Patterns of Transcript Abundance of Transposable Element Families in Maize
Cited by: 25
Author(s): Sarah N. Anderson, Michelle C. Stitzer, Peng Zhou, Jeffrey Ross‐Ibarra, Cory D. Hirsch, Nathan M. Springer
Software Mentions: 3
Published: over 6 years ago

10.26508/lsa.201800082

Mitochondrial ubiquinone–mediated longevity is marked by reduced cytoplasmic mRNA translation
Cited by: 12
Author(s): Marte Molenaars, Georges E. Janssens, Toon Santermans, Marco Lezzerini, Rob Jelier, Alyson W. MacInnes, Riekelt H. Houtkooper
Software Mentions: 3
Published: almost 8 years ago

10.3389/fpls.2018.01962

Early Detection of Magnaporthe oryzae-Infected Barley Leaves and Lesion Visualization Based on Hyperspectral Imaging
Cited by: 23
Author(s): Ruiqing Zhou, Juanjuan Jin, Qing-Mian Li, Zhen-Zhu Su, Xinjie Yu, Yu Tang, Shaoming Luo, Yong He, Yuanyuan Liu
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2016.01528

Invasive Shrub Mapping in an Urban Environment from Hyperspectral and LiDAR-Derived Attributes
Cited by: 29
Author(s): Curtis M. Chance, Nicholas C. Coops, Andrew Plowright, Thoreau Rory Tooke, Andreas Christen, Neal W. Aven
Software Mentions: 3
Published: over 9 years ago

10.3390/ani11071863

Differential Expression and Functional Analysis of CircRNA in the Ovaries of Low and High Fecundity Hanper Sheep
Cited by: 8
Author(s): Aiju Liu, Xiaoyong Chen, Menghe Liu, Limeng Zhang, Xiaofei Ma, Shujun Tian
Software Mentions: 3
Published: almost 5 years ago

10.1186/2049-3002-2-13

Loss of HSulf-1 promotes altered lipid metabolism in ovarian cancer
Cited by: 27
Author(s): Debarshi Roy, Susmita Mondal, Chen Wang, Xiaoping He, Ashwani Khurana, Shailendra Giri, Robert Hoffmann, Deok‐Beom Jung, Sung Hyun Kim, Eduardo N. Chini, Juliana Camacho Periera, Clifford D.L. Folmes, Andrea Mariani, Sean C. Dowdy, Jamie N. Bakkum-Gamez, Shaun M. Riska, Ann L. Oberg, Edward D. Karoly, Lauren N. Bell, Jeremy Chien, Viji Shridhar
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12859-018-2592-5

IMOS: improved Meta-aligner and Minimap2 On Spark
Cited by: 7
Author(s): Mostafa Hadadian Nejad Yousefi, Maziar Goudarzi, Seyed Abolfazl Motahari
Software Mentions: 3
Published: over 7 years ago

10.3389/fgene.2021.622886

Familial Psychosis Associated With a Missense Mutation at MACF1 Gene Combined With the Rare Duplications DUP3p26.3 and DUP16q23.3, Affecting the CNTN6 and CDH13 Genes
Cited by: 3
Author(s): Josep Pol-Fuster, Francesca Cañellas, Laura Ruiz-Guerra, Aina Medina-Dols, Bàrbara Bisbal-Carrió, Víctor J. Asensio, Bernat Ortega-Vila, Diego M. Marzese, Carme Vidal, Carmen Sofia Pedro dos Santos, Jerònia Lladó, Gabriel Olmos, Damián Heine-Suñer, Konstantin Strauch, Antònia Flaquer, Cristòfol Vives-Bauzà
Software Mentions: 3
Published: about 5 years ago

10.1186/bcr3020

Genomic and phenotypic analysis of BRCA2mutated breast cancers reveals co-occurring changes linked to progression
Cited by: 22
Author(s): Olafur A. Stefansson, Jón G. Jonasson, Katrín Ólafsdóttir, Hörður Bjarnason, Óskar T. Jóhannsson, Sigrídur K. Bödvarsdóttir, Sigrı́dur Valgeirsdóttir, Jórunn E. Eyfjörd
Software Mentions: 3
Published: over 14 years ago

10.1186/s12859-020-3491-0

Enhancing fragment-based protein structure prediction by customising fragment cardinality according to local secondary structure
Cited by: 6
Author(s): Jad Abbass, Jean‐Christophe Nebel
Software Mentions: 3
Published: about 6 years ago

10.3389/fgene.2019.01260

Joint Transcriptomic Analysis of Lung Cancer and Other Lung Diseases
Cited by: 8
Author(s): Beatriz Andrea Otálora‐Otálora, Mauro Florez, Liliana López‐Kleine, Alejandra Cañas Arboleda, Diana Urrego, Alejandra Rojas
Software Mentions: 3
Published: over 6 years ago

10.3390/metabo11090627

Comparative Untargeted Metabolomic Profiling of Induced Mitochondrial Fusion in Pancreatic Cancer
Cited by: 0
Author(s): Nathalie Nguyen, Meifang Yu, Vinit Y. Reddy, Ariana Carolina Acevedo-Diaz, Enzo C. Mesarick, Joseph Abi Jaoude, Min Yuan, John M. Asara, Cullen M. Taniguchi
Software Mentions: 3
Published: over 4 years ago

10.3389/fphar.2019.01690

SAMbinder: A Web Server for Predicting S-Adenosyl-L-Methionine Binding Residues of a Protein From Its Amino Acid Sequence
Cited by: 3
Author(s): Piyush Agrawal, Gaurav Mishra, Gajendra P. S. Raghava
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2016.01020

Low Temperature and Short-Term High-CO2 Treatment in Postharvest Storage of Table Grapes at Two Maturity Stages: Effects on Transcriptome Profiling
Cited by: 30
Author(s): Raquel Rosales, Irene Romero, Carlos Fernández-Caballero, M. Isabel Escribano, Carmen Merodio, Marı́a T. Sanchez-Ballesta
Software Mentions: 3
Published: almost 10 years ago

10.1186/1471-2105-11-73

BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets
Cited by: 11
Author(s): Mark Alston, John Seers, Jay C. D. Hinton, Sacha Lucchini
Software Mentions: 3
Published: over 16 years ago

10.3389/fgene.2014.00031

Multi-genome alignment for quality control and contamination screening of next-generation sequencing data
Cited by: 21
Author(s): James Hadfield, Matthew Eldridge
Software Mentions: 3
Published: over 12 years ago

10.3389/fgene.2014.00043

Quality assessment and control of tissue specific RNA-seq libraries of Drosophila transgenic RNAi models
Cited by: 12
Author(s): Andreia J. Amaral, Francisco Brito, Tamar Chobanyan, S. Yoshikawa, Takakazu Yokokura, David Van Vactor, Margarida Gama‐Carvalho
Software Mentions: 3
Published: about 12 years ago

10.3389/fpsyg.2020.00953

Global Image Properties Predict Ratings of Affective Pictures
Cited by: 17
Author(s): Christoph Redies, Maria Grebenkina, Mahdi Mohseni, Ali Kaduhm, Christian Dobel
Software Mentions: 3
Published: about 6 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566