cran: SAM | Projects | Ecosyste.ms: Papers

10.1038/s41598-019-51645-4

Predicting low-concentration effects of pesticides
Cited by: 17
Author(s): Matthias Liess, Sebastian Henz, Saskia Knillmann
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2105-11-205

Predicting conserved protein motifs with Sub-HMMs
Cited by: 9
Author(s): Kevin Horan, Christian R. Shelton, Thomas Girke
Software Mentions: 3
Published: over 16 years ago

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: almost 7 years ago

10.1186/1471-2164-14-337

Integrative genomic analysis of CREB defines a critical role for transcription factor networks in mediating the fed/fasted switch in liver
Cited by: 48
Author(s): Logan J. Everett, John Le Lay, Sabina Lukovac, Diana Bernstein, David J. Steger, Mitchell A. Lazar, Klaus H. Kaestner
Software Mentions: 3
Published: over 13 years ago

10.1186/s12859-021-03955-6

IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner
Cited by: 2
Author(s): Ana Maria Martins Alves Vasconcelos, Maria Beatriz Carmo, Beatriz Quintino Ferreira, Inês Viegas, Margarida Gama‐Carvalho, António E. N. Ferreira, Andreia J. Amaral
Software Mentions: 3
Published: over 5 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: almost 7 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: over 7 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: over 7 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: over 7 years ago

10.1186/1471-2105-14-S14-S17

mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis
Cited by: 17
Author(s): Cory B. Giles, G. Reshmi, Mikhail G. Dozmorov, Jonathan D. Wren
Software Mentions: 3
Published: almost 13 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

10.1038/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: about 8 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: about 8 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: about 8 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: about 12 years ago

10.1186/1471-2105-7-286

SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology
Cited by: 53
Author(s): Bruz Marzolf, Eric W. Deutsch, Patrick Moss, D. S. Campbell, Michael H. Johnson, Timothy Galitski
Software Mentions: 3
Published: over 20 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: over 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

10.1186/s12859-021-04068-w

RiboA: a web application to identify ribosome A-site locations in ribosome profiling data
Cited by: 2
Author(s): Danying Shao, Nabeel Ahmed, Nishant Soni, Edward P. O’Brien
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-14-371

Microarray and deep sequencing cross-platform analysis of the mirRNome and isomiR variation in response to epidermal growth factor
Cited by: 34
Author(s): Franc Llorens, Manuela Hummel, Lorena Pantano, Xavier Pastor, Ana Vivancos, Ester Castillo, Heidi Mattlin, Anna Ferrer, Matthew Ingham, María Noguera, Robert Kofler, Juliane C. Dohm, Raquel Pluvinet, Mònica Bayés, Heinz Himmelbauer, José Antonio del Río, Eulàlia Martı́, Lauro Sumoy
Software Mentions: 3
Published: over 13 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: over 5 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: about 7 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: about 9 years ago

10.1186/s12859-018-2315-y

bioSyntax: syntax highlighting for computational biology
Cited by: 2
Author(s): Artem Babaian, Anicet Ebou, Alyssa Fegen, Ho Yin Jeffrey Kam, Gherman Novakovsky, Jasper Wong, Dylan Aïssi, Yao Li
Software Mentions: 3
Published: about 8 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: over 9 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: 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: almost 15 years ago

10.1186/1471-2105-12-13

A Platform for Processing Expression of Short Time Series (PESTS)
Cited by: 16
Author(s): Ayan Sinha, Marianthi Markatou
Software Mentions: 3
Published: over 15 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: almost 9 years ago

10.1186/s12859-017-1705-x

An evaluation of copy number variation detection tools for cancer using whole exome sequencing data
Cited by: 121
Author(s): Fatima Zare, Michelle Dow, Nicholas J. Monteleone, Abdelrahman Hosny, Sheida Nabavi
Software Mentions: 3
Published: over 9 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: about 6 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: over 9 years ago

10.1186/bcr2632

Expression levels of uridine 5'-diphospho-glucuronosyltransferase genes in breast tissue from healthy women are associated with mammographic density
Cited by: 37
Author(s): Vilde Drageset Haakensen, Margarethe Biong, Ole Christian Lingjærde, Marit Muri Holmen, Jan Ole Frantzen, Ying Chen, Dina Navjord, Linda Romundstad, Torben Lüders, Ida K. Bukholm, Hiroko Kato Solvang, Vessela N. Kristensen, Giske Ursin, Anne‐Lise Børresen‐Dale, Åslaug Helland
Software Mentions: 3
Published: about 16 years ago

10.1186/1752-0509-7-S2-S9

Identifying novel glioma associated pathways based on systems biology level meta-analysis
Cited by: 10
Author(s): Yangfan Hu, Jinquan Li, Wenying Yan, Jiajia Chen, Yin Li, Guang Hu, Bairong Shen
Software Mentions: 3
Published: over 13 years ago

10.1186/s40478-016-0338-z

A comprehensive next generation sequencing-based virome assessment in brain tissue suggests no major virus - tumor association
Cited by: 54
Author(s): Michael J. Strong, Eugene Blanchard, Zhen Lin, Cindy A. Morris, Melody Baddoo, Christopher M. Taylor, Marcus L. Ware, Erik K. Flemington
Software Mentions: 3
Published: about 10 years ago

10.1186/bcr3672

A genomic analysis of mouse models of breast cancer reveals molecular features ofmouse models and relationships to human breast cancer
Cited by: 71
Author(s): Daniel P. Hollern, Eran R. Andrechek
Software Mentions: 3
Published: over 12 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: almost 5 years ago

10.1186/1471-2105-13-42

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community
Cited by: 142
Author(s): Konstantinos Krampis, Tim Booth, Brad Chapman, Brijesh K. Tiwari, Mesude Bicak, Dawn Field, Karen E. Nelson
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.ppat.1005943

Cathelicidin Insufficiency in Patients with Fatal Leptospirosis
Cited by: 21
Author(s): Janet C. Lindow, Elsio A. Wunder, Stephen J. Popper, Jinsoo Min, Praveen Mannam, Anup Srivastava, Yi Yao, Kathryn P. Hacker, Khadir Raddassi, Patty J Lee, Ruth R. Montgomery, Albert C. Shaw, José E. Hagan, Guilherme C. Araújo, Nívison Nery, David A. Relman, Charles C. Kim, Mitermayer Galvão dos Reis, Albert I. Ko
Software Mentions: 3
Published: almost 10 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: about 9 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

10.3390/microorganisms9091845

High Throughput Analysis Reveals Changes in Gut Microbiota and Specific Fecal Metabolomic Signature in Hematopoietic Stem Cell Transplant Patients
Cited by: 3
Author(s): Soumaya Kouidhi, Nessrine Souai, Oumaima Zidi, Ahmed Mosbah, Amel Lakhal, Tarek Ben Othmane, Dorra Belloumi, Farhat Ben Ayed, Elias Asimakis, Panagiota Stathopoulou, Ameur Chérif, George Tsiamis
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2105-10-300

RCMAT: a regularized covariance matrix approach to testing gene sets
Cited by: 8
Author(s): Phillip D. Yates, Mark Reimers
Software Mentions: 3
Published: almost 17 years ago

10.1186/1471-2164-14-471

Analysis and annotation of the hexaploid oat seed transcriptome
Cited by: 60
Author(s): Juan J. Gutiérrez-González, Zheng Jin Tu, David F. Garvin
Software Mentions: 3
Published: about 13 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: about 9 years ago

10.1186/1752-0509-8-S1-S5

Detection of type 2 diabetes related modules and genes based on epigenetic networks
Cited by: 6
Author(s): Liu Hui, Tongtong Wang, Hongbo Liu, Yanjun Wei, Guofeng Zhao, Jianzhong Su, Qiong Wu, Hong Qiao, Yan Zhang
Software Mentions: 3
Published: over 12 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

10.1371/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: over 13 years ago

10.1186/1471-2105-9-415

BATS: a Bayesian user-friendly software for Analyzing Time Series microarray experiments
Cited by: 53
Author(s): Claudia Angelini, Luisa Cutillo, Daniela De Canditiis, Margherita Mutarelli, Marianna Pensky
Software Mentions: 3
Published: almost 18 years ago

10.1038/s41598-021-90243-1

Metabolomics and computational analysis of the role of monoamine oxidase activity in delirium and SARS-COV-2 infection
Cited by: 17
Author(s): Miroslava Čuperlović-Culf, Emma Cunningham, Hossen Teimoorinia, Anuradha Surendra, Xiaobei Pan, Steffany A. L. Bennett, Mijin Jung, Bernadette McGuiness, Anthony Peter Passmore, David Beverland, Brian D. Green
Software Mentions: 3
Published: over 5 years ago

10.1073/pnas.1921055117

ASY1 acts as a dosage-dependent antagonist of telomere-led recombination and mediates crossover interference in Arabidopsis
Cited by: 54
Author(s): Christophe Lambing, Pallas Kuo, Andrew J. Tock, Stephanie D. Topp, Ian Henderson
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-018-5017-y

Genome wide transcriptome analysis provides bases on colonic mucosal immune system development affected by colostrum feeding strategies in neonatal calves
Cited by: 6
Author(s): Zhixiong He, Albert J. Fischer, Yang Song, M.A. Steele, Le Luo Guan
Software Mentions: 3
Published: about 8 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: almost 10 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: about 6 years ago

10.1120/jacmp.v17i3.6370

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

10.1186/1472-6807-11-16

Molecular modeling and in silico characterization of Mycobacterium tuberculosis TlyA: Possible misannotation of this tubercle bacilli-hemolysin
Cited by: 27
Author(s): Nelson E. Arenas, Luz Mary Salazar, Carlos Y. Soto, Carolina Vizcaíno, Manuel Elkín Patarroyo, Arley Gómez
Software Mentions: 3
Published: over 15 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

10.1186/1471-2105-8-195

Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips
Cited by: 20
Author(s): Andrew Harrison, Caroline Johnston, Christine A. Orengo
Software Mentions: 3
Published: over 19 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

10.3390/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: almost 6 years ago

10.3390/s17040777

A Review of Wetland Remote Sensing
Cited by: 247
Author(s): Meng Guo, Jing Li, Chunlei Sheng, Jiawei Xu, Li Wu
Software Mentions: 3
Published: over 9 years ago

10.3390/s18020474

Design and Implementation of Cloud-Centric Configuration Repository for DIY IoT Applications
Cited by: 37
Author(s): Shabir Ahmad, Hang Lei, Do‐Hyeun Kim
Software Mentions: 3
Published: over 8 years ago

10.3390/s18124330

Variational Pansharpening for Hyperspectral Imagery Constrained by Spectral Shape and Gram–Schmidt Transformation
Cited by: 10
Author(s): Z. J. Huang, Qihao Chen, Xiuguo Liu
Software Mentions: 3
Published: almost 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: about 6 years ago

10.1186/1471-2164-13-355

Dose-dependent effects of small-molecule antagonists on the genomic landscape of androgen receptor binding
Cited by: 7
Author(s): Zhou Zhu, Minmin Shi, Wenyue Hu, Heather Estrella, Jon Engebretsen, Tim Nichols, David M. Briere, Natilie Hosea, Gerrit Los, Paul A. Rejto, Andrea Fanjul
Software Mentions: 3
Published: over 14 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

10.1186/1471-2105-14-S9-S1

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets
Cited by: 84
Author(s): Xiao Xu, Yuanhao Zhang, Jennie L. Williams, Eric Antoniou, W. Richard McCombie, Song Wu, Wei Zhu, Nicholas O. Davidson, Paula Denoya, Ellen Li
Software Mentions: 3
Published: over 13 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: about 5 years ago

10.3390/genes3030545

Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows
Cited by: 47
Author(s): Federica Torri, Ivo D. Dinov, Alen Zamanyan, Sam Hobel, Alex Genco, Petros Petrosyan, Andrew P. Clark, Zhizhong Liu, Paul Eggert, Jonathan Pierce, James A. Knowles, Joseph Ames, Carl Kesselman, Arthur W. Toga, Steven G. Potkin, Marquis P. Vawter, Fabìo Macciardi
Software Mentions: 3
Published: about 14 years ago

10.1186/1756-0500-3-298

KC-SMARTR: An R package for detection of statistically significant aberrations in multi-experiment aCGH data
Cited by: 22
Author(s): Jorma J. de Ronde, Christiaan Klijn, Arno Velds, Henne Holstege, Marcel J. T. Reinders, Jos Jonkers, Lodewyk Wessels
Software Mentions: 3
Published: almost 16 years ago

10.1186/1756-0500-1-80

Advanced spot quality analysis in two-colour microarray experiments
Cited by: 10
Author(s): Mikalai M. Yatskou, Eugene Novikov, Guillaume Vetter, Arnaud Muller, Emmanuel Barillot, Laurent Vallar, Evelyne Friederich
Software Mentions: 3
Published: over 18 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

10.3390/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: about 6 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

10.1002/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: over 7 years ago

10.7554/eLife.32920

Association mapping from sequencing reads using k-mers
Cited by: 82
Author(s): Atif Rahman, Ingileif B. Hallgrímsdóttir, Michael B. Eisen, Lior Pachter
Software Mentions: 3
Published: over 8 years ago

10.1534/g3.118.200417

Development of Diagnostic SNP Markers To Monitor Hybridization Between Sika Deer (Cervus nippon) and Wapiti (Cervus elaphus)
Cited by: 3
Author(s): Hengxing Ba, Zhipeng Li, Yumei Yang, Chunyi Li
Software Mentions: 2
Published: about 8 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 11 years ago

10.1534/g3.118.200481

Genomics-Assisted Identification and Characterization of the Genetic Variants Underlying Differential Nitrogen Use Efficiencies in Allotetraploid Rapeseed Genotypes
Cited by: 12
Author(s): Yingpeng Hua, Ting Zhou, Qiong Liao, Haixing Song, Chunyun Guan, Zhenhua Zhang
Software Mentions: 2
Published: about 8 years ago

10.1186/s12859-019-2996-x

Magic-BLAST, an accurate RNA-seq aligner for long and short reads
Cited by: 178
Author(s): Grzegorz M. Boratyn, Jean Thierry‐Mieg, Danielle Thierry-Mieg, Ben Busby, Thomas Madden
Software Mentions: 2
Published: about 7 years ago

10.1186/s12859-020-3428-7

LCQS: an efficient lossless compression tool of quality scores with random access functionality
Cited by: 2
Author(s): Jiabing Fu, Bixin Ke, Sujun Dong
Software Mentions: 2
Published: over 6 years ago

10.1534/g3.118.200171

RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding
Cited by: 28
Author(s): Emily Humble, Kanchon K. Dasmahapatra, Alvaro Martinez-Barrio, Inês Gregório, Jaume Forcada, Ann-Christin Polikeit, Simon Goldsworthy, Michael E. Goebel, Jörn Kalinowski, Jochen B. W. Wolf, Joseph I. Hoffman
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2164-12-384

Temperature stress differentially modulates transcription in meiotic anthers of heat-tolerant and heat-sensitive tomato plants
Cited by: 96
Author(s): Craita E. Bita, Sara Zenoni, Wim H. Vriezen, Celestina Mariani, Mario Pezzotti, Tom Geräts
Software Mentions: 2
Published: about 15 years ago

10.1128/AEM.01808-20

Mapping the Efficacy and Mode of Action of Ethylzingerone [4-(3-Ethoxy-4-Hydroxyphenyl) Butan-2-One] as an Active Agent against Burkholderia Bacteria
Cited by: 1
Author(s): Laura Rushton, Ahmad Khodr, Florence Ménard-Szczebara, Jean‐Yves Maillard, Sylvie Cupferman, Eshwar Mahenthiralingam
Software Mentions: 2
Published: almost 6 years ago

10.1534/g3.118.200134

Programmable Single and Multiplex Base-Editing in Bombyx mori Using RNA-Guided Cytidine Deaminases
Cited by: 14
Author(s): Yufeng Li, Sanyuan Ma, Le Sun, Tong Zhang, Jiasong Chang, Wei Lu, Xiaoxu Chen, Yue Liu, Xiaogang Wang, Run Shi, Ping Zhao, Qingyou Xia
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-018-4475-6

Novel read density distribution score shows possible aligner artefacts, when mapping a single chromosome
Cited by: 6
Author(s): Fedor Naumenko, Irina Abnizova, Nathan Beka, Mikhail A. Genaev, Yuriy L. Orlov
Software Mentions: 2
Published: over 8 years ago

10.1534/g3.116.036673

Genome Report: Identification and Validation of Antigenic Proteins from Pajaroellobacter abortibovis Using De Novo Genome Sequence Assembly and Reverse Vaccinology
Cited by: 8
Author(s): Bryan T. Welly, Michael R. Miller, Jeffrey L Stott, M Blanchard, Alma Islas–Trejo, Sean O’Rourke, Amy Young, Juan F. Medrano, Alison L. Van Eenennaam
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-8-452

Gene expression analysis reveals early changes in several molecular pathways in cerebral malaria-susceptible mice versus cerebral malaria-resistant mice
Cited by: 55
Author(s): Nicolas Nf Delahaye, Nicolas Coltel, Denis Puthier, Mathieu Barbier, P. Benech, Florence Joly, Fuad Fa Iraqi, Georges E. Grau, Catherine Nguyen, Pascal Rihet
Software Mentions: 2
Published: almost 19 years ago

10.1186/1471-2105-14-310

A method to identify differential expression profiles of time-course gene data with Fourier transformation
Cited by: 12
Author(s): Jaehee Kim, R. Todd Ogden, Haseong Kim
Software Mentions: 2
Published: almost 13 years ago

10.1534/g3.115.017921

Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon
Cited by: 33
Author(s): Yizhou Wang, Kristina M. Smith, John W. Taylor, Michael Freitag, Jason E. Stajich
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2229-10-14

SoyDB: a knowledge database of soybean transcription factors
Cited by: 105
Author(s): Zheng Wang, Marc Libault, Trupti Joshi, Babu Valliyodan, Henry T. Nguyen, Dong Xu, Gary Stacey, Jianlin Cheng
Software Mentions: 2
Published: over 16 years ago

10.1186/1742-9994-10-9

Habitat productivity constrains the distribution of social spiders across continents – case study of the genus Stegodyphus
Cited by: 26
Author(s): Marija Majer, Jens‐Christian Svenning, Trine Bilde
Software Mentions: 2
Published: over 13 years ago

10.3389/fvets.2021.732129

Identification of Multiple Blastocystis Subtypes in Domestic Animals From Colombia Using Amplicon-Based Next Generation Sequencing
Cited by: 49
Author(s): Adriana Higuera, Giovanny Herrera, Paula Andrea Jiménez, Diego García-Corredor, Martín Orlando Pulido-Medellín, Diana María Bulla-Castañeda, Juan Carlos Pinilla, Darwin A. Moreno-Pérez, Jenny G. Maloney, Mónica Santı́n, Juan David Ramírez
Software Mentions: 2
Published: about 5 years ago

10.3389/fpsyg.2015.01232

Microtiming in Swing and Funk affects the body movement behavior of music expert listeners
Cited by: 34
Author(s): Lorenz Kilchenmann, Olivier Senn
Software Mentions: 2
Published: about 11 years ago

10.3389/fpsyg.2021.707809

The Effectiveness of Facial Expression Recognition in Detecting Emotional Responses to Sound Interventions in Older Adults With Dementia
Cited by: 4
Author(s): Ying Liu, Zixuan Wang, Ge Yu
Software Mentions: 2
Published: about 5 years ago

10.3389/fpsyg.2018.00657

Physiological Response to Facial Expressions in Peripersonal Space Determines Interpersonal Distance in a Social Interaction Context
Cited by: 55
Author(s): Alice Cartaud, Gennaro Ruggiero, Laurent Ott, Tina Iachini, C. Yann
Software Mentions: 2
Published: over 8 years ago

10.3389/fpsyg.2017.01709

Rhythmic Density Affects Listeners' Emotional Response to Microtiming
Cited by: 9
Author(s): Olivier Senn, Claudia Bullerjahn, Lorenz Kilchenmann, Richard von Georgi
Software Mentions: 2
Published: almost 9 years ago

10.1186/1471-2105-14-S7-S11

WEP: a high-performance analysis pipeline for whole-exome data
Cited by: 42
Author(s): Mattia D’Antonio, Paolo D’Onorio De Meo, Daniele Paoletti, B Elmi, Matteo Pallocca, Nico Sanna, Ernesto Picardi, Graziano Pesole, Tiziana Castrignanò
Software Mentions: 2
Published: over 13 years ago

10.3389/fpsyt.2021.633102

Spouse-Appraised Memory Functioning Predicts Memory Decline Better Than Subjective Memory Complaints in Community Dwelling Older Adults at Genetic Risk for Alzheimer's Disease
Cited by: 3
Author(s): Youssef Bellaali, John L. Woodard, Bernard Hanseeuw, Adrian Ivanoiu
Software Mentions: 2
Published: over 5 years ago

10.3389/fpsyg.2019.01835

Augmented Reality in Educational Inclusion. A Systematic Review on the Last Decade
Cited by: 79
Author(s): Jairo Quintero, Silvia Baldiris, Rainer Rubira, Jhoni Cerón, Gloria Velez
Software Mentions: 2
Published: about 7 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566