Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: cran: SAM

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/SAM

Sparse Additive Modelling
9 versions
Latest release: over 3 years ago
4 dependent packages
341 downloads last month

Papers Mentioning SAM 4,566

10.1186/s40168-019-0679-5
Chemotherapy-induced oral mucositis is associated with detrimental bacterial dysbiosis
Cited by: 117
Author(s): Bo-Young Hong, Takanori Sobue, Linda Choquette, Amanda K. Dupuy, Angela Thompson, Joseph A. Burleson, Andrew L. Salner, Peter K. Schauer, Pujan Joshi, Evan Fox, Dong-Guk Shin, George M. Weinstock, Linda D. Strausbaugh, Anna Dongari-Bagtzoglou, Douglas E. Peterson, Patricia I. Diaz
Software Mentions: 1
Published: over 5 years ago
10.1186/s40168-020-00956-0
Polinton-like viruses are abundant in aquatic ecosystems
Cited by: 27
Author(s): Christopher M. Bellas, Rubén Sommaruga
Software Mentions: 1
Published: almost 4 years ago
10.3390/microorganisms8010133
Inter-Versus Intra-Host Sequence Diversity of pH1N1 and Associated Clinical Outcomes
Cited by: 2
Author(s): Hebah A. Al-Khatib, Muna Al Maslamani, Peter Coyle, Iain Thompson, Elmoubasher Farag, Asmaa A. Al Thani, Hadi M. Yassine
Software Mentions: 1
Published: almost 5 years ago
10.12669/pjms.335.12990
Vitamin D supplementation improves FEV1 in patients of Bronchial Asthma
Cited by: 8
Author(s): Muhammad Zafar Majeed Babar, Mazhar Hussain, Sadia Majeed
Software Mentions: 1
Published: about 7 years ago
10.1017/S0031182016001797
Rumen fluke (<i>Calicophoron daubneyi</i>) on Welsh farms: prevalence, risk factors and observations on co-infection with<i>Fasciola hepatica</i>
Cited by: 44
Author(s): Rhys Aled Jones, Peter M. Brophy, Erik T. Mitchell, H. Williams
Software Mentions: 1
Published: about 8 years ago
10.1186/1756-3305-5-162
Analysis of Babesia bovis infection-induced gene expression changes in larvae from the cattle tick, Rhipicephalus (Boophilus) microplus
Cited by: 22
Author(s): Andrew M. Heekin, Felix D. Guerrero, Kylie G. Bendele, Leo Saldivar, Glen A. Scoles, Cedric Gondro, Vishvanath Nene, Appolinaire Djikeng, Kelly A. Brayton
Software Mentions: 1
Published: over 12 years ago
10.1186/s13071-015-0914-2
Phlebotomus papatasi SP15: mRNA expression variability and amino acid sequence polymorphisms of field populations
Cited by: 16
Author(s): Marcelo Ramalho-Ortigão, Iliano V. Coutinho-Abreu, Valdir Queiroz Balbino, Carlos Alberto Santiago Figueirêdo, Rami Mukbel, Hussan Dayem, Hanafi A. Hanafi, Shabaan S. El-Hossary, Emad El Din Y. Fawaz, Mahmoud N. Abo‐Shehada, David F. Hoel, Gwen Stayback, Mariha Wadsworth, Douglas A. Shoue, Jenica Abrudan, Neil F. Lobo, Andrew R. Mahon, Scott J. Emrich, Shaden Kamhawi, Frank H. Collins, Mary Ann McDowell
Software Mentions: 1
Published: over 9 years ago
10.1186/s13071-018-2816-6
Molecular and morphological characterisation of Pharyngostrongylus kappa Mawson, 1965 (Nematoda: Strongylida) from Australian macropodid marsupials with the description of a new species, P. patriciae n. sp.
Cited by: 1
Author(s): Tanapan Sukee, Ian Beveridge, Abdul Jabbar
Software Mentions: 1
Published: over 6 years ago
10.1186/s13071-016-1544-z
The persistence and ecological impacts of a cyanobacterium genetically engineered to express mosquitocidal Bacillus thuringiensis toxins
Cited by: 0
Author(s): Irene Ketseoglou, Gustav Bouwer
Software Mentions: 1
Published: over 8 years ago
10.1186/s13071-019-3578-5
Redescription and molecular characterisation of the fish ectoparasite Anilocra capensis Leach, 1818 (Isopoda: Cymothoidae), with description of six new species of Anilocra Leach, 1818 from Africa
Cited by: 13
Author(s): Rachel L. Welicky, Nico J. Smit
Software Mentions: 1
Published: over 5 years ago
10.1186/1756-3305-6-276
The ovarian transcriptome of the cattle tick, Rhipicephalus (Boophilus) microplus, feeding upon a bovine host infected with Babesia bovis
Cited by: 24
Author(s): Andrew M. Heekin, Felix D. Guerrero, Kylie G. Bendele, Leo Saldivar, Glen A. Scoles, Scot E. Dowd, Cedric Gondro, Vishvanath Nene, Appolinaire Djikeng, Kelly A. Brayton
Software Mentions: 1
Published: about 11 years ago
10.1080/20010001.2018.1516072
Evaluation of aging, diabetes mellitus, and skin wounds by scanning acoustic microscopy with protease digestion
Cited by: 5
Author(s): Katsutoshi Miura, Kensuke Yamashita
Software Mentions: 1
Published: almost 7 years ago
10.20411/pai.v6i2.461
Lack of Atorvastatin Effect on Monocyte Gene Expression and Inflammatory Markers in HIV-1- infected ART-suppressed Individuals at Risk of non-AIDS Comorbidities
Cited by: 1
Author(s): Anjana Yadav, Andrew V. Kossenkov, Louise C. Showe, Sarah J. Ratcliffe, Grace Choi, Luis J. Montaner, Pablo Tebas, Pamela A. Shaw, Ronald G. Collman
Software Mentions: 1
Published: over 3 years ago
10.1007/s12253-020-00865-5
Metabolic Parameters as Predictors for Progression Free and Overall Survival of Patients with Metastatic Colorectal Cancer
Cited by: 6
Author(s): Zsuzsanna Németh, W. Wijker, Zsolt Lengyel, Erika Hitre, Katalin Borbély
Software Mentions: 1
Published: over 4 years ago
10.7717/peerj.49
A new 12-gene diagnostic biomarker signature of melanoma revealed by integrated microarray analysis
Cited by: 55
Author(s): Wanting Liu, Yonghong Peng, Desmond J. Tobin
Software Mentions: 1
Published: over 11 years ago
10.7717/peerj.788
Loss of CITED1, an MITF regulator, drives a phenotype switch<i>in vitro</i>and can predict clinical outcome in primary melanoma tumours
Cited by: 19
Author(s): Jill Howlin, Helena Cirenajwis, Barbara Lettiero, Johan Staaf, Martin Lauss, Lao H. Saal, Åke Borg, Sofia K. Gruvberger-Saal, Göran Jönsson
Software Mentions: 1
Published: over 9 years ago
10.7717/peerj.9338
URMAP, an ultra-fast read mapper
Cited by: 7
Author(s): Robert C. Edgar
Software Mentions: 1
Published: over 4 years ago
10.7717/peerj.8349
Multiple genome pattern analysis and signature gene identification for the Caucasian lung adenocarcinoma patients with different tobacco exposure patterns
Cited by: 1
Author(s): Yanmei Dong, Li-da Qin, Yifan Tong, Qian He, Ling Wang, Kai Song
Software Mentions: 1
Published: almost 5 years ago
10.7717/peerj.6116
Elevational patterns of the percentages of plant genera with tropical and temperate affinities in Nepal
Cited by: 1
Author(s): Yunyun Lai, Jianmeng Feng
Software Mentions: 1
Published: almost 6 years ago
10.7717/peerj.808
Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space
Cited by: 33
Author(s): Richard Wilton, Tamás Budavàri, Ben Langmead, Sarah J. Wheelan, Steven L. Salzberg, Alexander S. Szalay
Software Mentions: 1
Published: over 9 years ago
10.7717/peerj.7314
Mitochondrial DNA in human identification: a review
Cited by: 56
Author(s): António Amorim, Teresa Fernandes, Nuno Taveira
Software Mentions: 1
Published: over 5 years ago
10.7717/peerj.3932
Influence of current climate, historical climate stability and topography on species richness and endemism in Mesoamerican geophyte plants
Cited by: 39
Author(s): Victoria Sosa, Israel Loera
Software Mentions: 1
Published: about 7 years ago
10.7717/peerj.4061
Levels of detail analysis of microwave scattering from human head models for brain stroke detection
Cited by: 10
Author(s): Awais Munawar Qureshi, Zartasha Mustansar
Software Mentions: 1
Published: about 7 years ago
10.7717/peerj.1743
Effects of personal relevance and simulated darkness on the affective appraisal of a virtual environment
Cited by: 8
Author(s): Alexander Toet, J.M. Houtkamp, Paul E. Vreugdenhil
Software Mentions: 1
Published: over 8 years ago
10.7717/peerj.2636
Elevational pattern of bird species richness and its causes along a central Himalaya gradient, China
Cited by: 38
Author(s): Xinyuan Pan, Zhifeng Ding, Yiming Hu, Jiankun Liang, Yongjie Wu, Xingfeng Si, Guo Ming-fang, Huijian Hu, Kazutaka Jin
Software Mentions: 1
Published: about 8 years ago
10.7717/peerj.438
Continental variation in wing pigmentation in<i>Calopteryx</i>damselflies is related to the presence of heterospecifics
Cited by: 12
Author(s): Christopher Hassall
Software Mentions: 1
Published: over 10 years ago
10.7717/peerj.990
Profiling and initial validation of urinary microRNAs as biomarkers in IgA nephropathy
Cited by: 33
Author(s): Nannan Wang, Rongfa Bu, Zhi-Yu Duan, Xueguang Zhang, Pu Chen, Zuoxiang Li, Jie Wu, Guangyan Cai, Xiangmei Chen
Software Mentions: 1
Published: over 9 years ago
10.7717/peerj.380
Effect of nutrition survey ‘cleaning criteria’ on estimates of malnutrition prevalence and disease burden: secondary data analysis
Cited by: 40
Author(s): Sonya Crowe, Andrew Seal, Carlos Grijalva-Eternod, Marko Kerac
Software Mentions: 1
Published: over 10 years ago
10.7717/peerj.11642
A new HSI denoising method via interpolated block matching 3D and guided filter
Cited by: 1
Author(s): Ping Xu, Bingqiang Chen, Jingcheng Zhang, Lei Xue, Lei Zhu
Software Mentions: 1
Published: over 3 years ago
10.7717/peerj.7591
Negative emotional state slows down movement speed: behavioral and neural evidence
Cited by: 8
Author(s): Xiawen Li, Guanghui Zhang, Changle Zhou, Xiaochun Wang
Software Mentions: 1
Published: about 5 years ago
10.7717/peerj.3850
Historical dynamics and current environmental effects explain the spatial distribution of species richness patterns of New World monkeys
Cited by: 4
Author(s): Paulo Vallejos-Garrido, Reinaldo Rivera, Oscar Inostroza‐Michael, Enrique Rodríguez‐Serrano, Cristián E. Hernández
Software Mentions: 1
Published: about 7 years ago
10.3390/pharmacy6030077
An Evidence-Based Procedure for Self-Management of Medication in Hospital: Development and Validation of the SelfMED Procedure
Cited by: 8
Author(s): Toke Vanwesemael, Tinne Dilles, Bart Van Rompaey, Koen Boussery
Software Mentions: 1
Published: over 6 years ago
10.1098/rsta.2013.0040
The ocean's role in polar climate change: asymmetric Arctic and Antarctic responses to greenhouse gas and ozone forcing
Cited by: 110
Author(s): John Marshall, Kyle C. Armour, J.W. Scott, Yavor Kostov, Ute Hausmann, David Ferreira, Theodore G. Shepherd, Cecilia M. Bitz
Software Mentions: 1
Published: over 10 years ago
10.1098/rsta.2018.0148
Assessing the scales in numerical weather and climate predictions: will exascale be the rescue?
Cited by: 49
Author(s): Philipp Neumann, Peter Dueben, Panagiotis Adamidis, Péter Bauer, Matthias Brück, Luis Kornblueh, Daniel Klocke, Björn Stevens, Nils Wedi, Joachim Biercamp
Software Mentions: 1
Published: almost 6 years ago
10.14814/phy2.13726
Physiological culture conditions alter myotube morphology and responses to atrophy treatments: implications for in vitro research on muscle wasting
Cited by: 7
Author(s): Élodie Archer-Lahlou, Cathy Lan, R. Thomas Jagoe
Software Mentions: 1
Published: over 6 years ago
10.1002/PHY2.8
Elevated pulmonary arterial pressure and altered expression of<i>Ddah1</i>and<i>Arg1</i>in mice lacking cavin-1/PTRF
Cited by: 30
Author(s): Karl Swärd, Mardjaneh Karbalaei Sadegh, Masataka Mori, Jonas Erjefält, Catarina Rippe
Software Mentions: 1
Published: over 11 years ago
10.1186/s40814-021-00883-3
Posttraumatic stress disorder intervention for people with severe mental illness in a low-income country primary care setting: a randomized feasibility trial protocol
Cited by: 1
Author(s): Lauren C. Ng, Eyerusalem Getachew Serba, Benyam Worku Dubale, Abebaw Fekadu, Charlotte Hanlon
Software Mentions: 1
Published: over 3 years ago
10.1111/pbi.13002
Time-specific and pleiotropic quantitative trait loci coordinately modulate stem growth in<i>Populus</i>
Cited by: 30
Author(s): Qingzhang Du, Xiaohui Yang, Jianbo Xie, Mingyang Quan, Xiao Liang, Wenjie Lu, Jiaxing Tian, Chenrui Gong, Jinhui Chen, Bai-Lian Li, Deqiang Zhang
Software Mentions: 1
Published: about 6 years ago
10.1111/pbi.13030
Resequencing of <i>cv</i> CRI‐12 family reveals haplotype block inheritance and recombination of agronomically important genes in artificial selection
Cited by: 18
Author(s): Xuke Lu, Xiaoqiong Fu, Delong Wang, Junyi Wang, Xiugui Chen, Meirong Hao, Junjuan Wang, Kyle A. Gervers, Lixue Guo, Shuai Wang, Zujun Yin, Weili Fan, Chunwei Shi, Xiaoge Wang, Jun Peng, Chao Chen, Ruifeng Cui, Na Shu, Binglei Zhang, Mingge Han, Xin Zhao, Mingchun Mu, John Z. Yu, Wuwei Ye
Software Mentions: 1
Published: almost 6 years ago
10.1111/pbi.12826
Assembly and analysis of aqingkereference genome demonstrate its close genetic relation to modern cultivated barley
Cited by: 48
Author(s): Fei Dai, Xiaolei Wang, Xiaoqi Zhang, Zhonghua Chen, Eviatar Nevo, Gulei Jin, Dezhi Wu, Chengdao Li, Guoping Zhang
Software Mentions: 1
Published: about 7 years ago
10.1111/pbi.12704
A novel functional gene associated with cold tolerance at the seedling stage in rice
Cited by: 56
Author(s): Junliang Zhao, Shaohong Zhang, Jingfang Dong, Ting Yang, Xingxue Mao, Qing Liu, Xiaofei Wang, Bin Liu
Software Mentions: 1
Published: over 7 years ago
10.1111/pbi.13203
A high‐throughput BAC end analysis protocol ( <scp>BAC</scp> ‐anchor) for profiling genome assembly and physical mapping
Cited by: 4
Author(s): Xiaohui Yang, Yan Yu, Jian Ling, Jiantao Guan, Xuewu Guo, Dan Dong, Liping Jin, Sanwen Huang, Jun Li, Guangcun Li
Software Mentions: 1
Published: over 5 years ago
10.1111/pbi.13138
Strong gene activation in plants with genome‐wide specificity using a new orthogonal <scp>CRISPR</scp>/Cas9‐based programmable transcriptional activator
Cited by: 70
Author(s): Sara Selma, Joan Miquel Bernabé‐Orts, Marta Vázquez‐Vilar, Borja Diego-Martin, María Ajenjo, Victor García‐Carpintero, Antonio Granell, Diego Orzáez
Software Mentions: 1
Published: over 5 years ago
10.1111/pbi.13420
Genomic prediction of maize microphenotypes provides insights for optimizing selection and mining diversity
Cited by: 15
Author(s): Xiaoqing Yu, Samuel Leiboff, Xianran Li, Tingting Guo, Natalie Ronning, Xiaoyu Zhang, Gary J. Muehlbauer, Marja C.P. Timmermans, Patrick S. Schnable, Michael J. Scanlon, Jianming Yu
Software Mentions: 1
Published: over 4 years ago
10.1002/pld3.317
Quantification of gray mold infection in lettuce using a bispectral imaging system under laboratory conditions
Cited by: 1
Author(s): Clifton G. Scarboro, Stephanie M. Ruzsa, Colleen J. Doherty, Michael W. Kudenov
Software Mentions: 1
Published: over 3 years ago
10.1002/pld3.306
A cellular expression map of epidermal and subepidermal cell layer‐enriched transcription factor genes integrated with the regulatory network in Arabidopsis shoot apical meristem
Cited by: 2
Author(s): Shivani Bhatia, Harish Kumar, Monika Mahajan, Manisha Yadav, Prince Saini, Shalini Yadav, Shivani Sahu, Jayesh Kumar Sundaram, Ram Kishor Yadav
Software Mentions: 1
Published: over 3 years ago
10.1186/s13007-017-0198-y
Improved classification accuracy of powdery mildew infection levels of wine grapes by spatial-spectral analysis of hyperspectral images
Cited by: 63
Author(s): Uwe Knauer, Andrea Matros, Tijana Petrović, T Zanker, Eileen S. Scott, Udo Seiffert
Software Mentions: 1
Published: over 7 years ago
10.1186/s13007-019-0521-x
Sensory assessment of Cercospora beticola sporulation for phenotyping the partial disease resistance of sugar beet genotypes
Cited by: 13
Author(s): E. C. Oerke, Marlene Leucker, Ulrike Steiner
Software Mentions: 1
Published: about 5 years ago
10.1186/s13007-021-00719-4
Heritable gene editing using FT mobile guide RNAs and DNA viruses
Cited by: 26
Author(s): Jianfeng Lei, Peng Dai, Yue Li, Wanqi Zhang, Guantong Zhou, Chao Liu, Xiaodong Liu
Software Mentions: 1
Published: almost 4 years ago
10.1186/1746-4811-8-3
Hyperspectral imaging for small-scale analysis of symptoms caused by different sugar beet diseases
Cited by: 257
Author(s): Anne-Katrin Mahlein, Ulrike Steiner, Christian Hillnhütter, H. W. Dehne, E. C. Oerke
Software Mentions: 1
Published: almost 13 years ago
10.34133/2021/9765952
Classification of Rice Yield Using UAV-Based Hyperspectral Imagery and Lodging Feature
Cited by: 15
Author(s): Jian Wang, Bizhi Wu, Markus V. Kohnen, Daqi Lin, Changcai Yang, Xiaowei Wang, Ailing Qiang, Wei Liu, Jian Kang, Hua Li, Jing Shen, Tianhao Yao, Jun Su, Bangyu Li, Lianfeng Gu
Software Mentions: 1
Published: almost 4 years ago
10.3390/plants10040771
Mapping of Genetic Locus for Leaf Trichome Formation in Chinese Cabbage Based on Bulked Segregant Analysis
Cited by: 6
Author(s): Rujia Zhang, Yiming Ren, Huiyuan Wu, Yang Yu, Mengguo Yuan, Haonan Liang, Changwei Zhang
Software Mentions: 1
Published: over 3 years ago
10.3390/plants10091935
Genetic Loci Associated with Resistance to Zucchini Yellow Mosaic Virus in Squash
Cited by: 6
Author(s): Swati Shrestha, Vincent Njung’e Michael, Yuqing Fu, Geoffrey Meru
Software Mentions: 1
Published: about 3 years ago
10.3390/plants9081052
Comparative Microbiome Study of Mummified Peach Fruits by Metagenomics and Metatranscriptomics
Cited by: 11
Author(s): Yeonhwa Jo, Chang–Gi Back, Hoseong Choi, Won Kyong Cho
Software Mentions: 1
Published: over 4 years ago
10.3390/plants4030356
Senescence Meets Dedifferentiation
Cited by: 7
Author(s): Yemima Givaty Rapp, Vanessa Ransbotyn, Gideon Grafi
Software Mentions: 1
Published: over 9 years ago
10.3390/plants10040751
Nanoimpact in Plants: Lessons from the Transcriptome
Cited by: 11
Author(s): Susana García-Sánchez, Michal Gala, Gabriel Žoldák
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pbio.1002031
Selective Modulation of Interhemispheric Functional Connectivity by HD-tACS Shapes Perception
Cited by: 242
Author(s): Randolph F. Helfrich, Hannah Knepper, Guido Nolte, Daniel Strüber, Stefan Rach, Christoph S. Herrmann, Till R. Schneider, Andreas K. Engel
Software Mentions: 1
Published: almost 10 years ago
10.1371/journal.pbio.0060255
Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System
Cited by: 548
Author(s): Daniel J. Hogan, Daniel P. Riordan, André P. Gerber, Daniel Herschlag, Patrick O. Brown
Software Mentions: 1
Published: about 16 years ago
10.1371/journal.pbio.1000569
Epigenetic Regulation of Learning and Memory by Drosophila EHMT/G9a
Cited by: 185
Author(s): Jamie M. Kramer, Korinna Kochinke, Merel A. W. Oortveld, Hendrik Marks, Daniela Krämer, Eiko K. de Jong, Zoltán Asztalos, J. Timothy Westwood, Hendrik G. Stunnenberg, Marla B. Sokolowski, Krystyna Keleman, Huiqing Zhou, Hans van Bokhoven, Annette Schenck
Software Mentions: 1
Published: almost 14 years ago
10.1371/journal.pbio.3001153
Avoiding organelle mutational meltdown across eukaryotes with or without a germline bottleneck
Cited by: 29
Author(s): David M. Edwards, Ellen C. Røyrvik, Joanna M. Chustecki, Konstantinos Giannakis, Robert C. Glastad, Arunas L. Radzvilavicius, Iain G. Johnston
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pbio.1001653
Unisexual and Heterosexual Meiotic Reproduction Generate Aneuploidy and Phenotypic Diversity De Novo in the Yeast Cryptococcus neoformans
Cited by: 146
Author(s): Ming-Jiu Ni, Marianna Feretzaki, Wenjun Li, Anna Floyd-Averette, Piotr A. Mieczkowski, Fred S. Dietrich, Joseph Heitman
Software Mentions: 1
Published: about 11 years ago
10.1371/journal.pbio.1001845
Toxoplasma Effector MAF1 Mediates Recruitment of Host Mitochondria and Impacts the Host Response
Cited by: 145
Author(s): Lena Pernas, Yaw Adomako‐Ankomah, Anjali J. Shastri, Sarah E. Ewald, Moritz Treeck, Jon P. Boyle, John C. Boothroyd
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pbio.0040002
Conserved and Variable Functions of the σE Stress Response in Related Genomes
Cited by: 438
Author(s): Virgil A. Rhodius, Won Chul Suh, Gen Nonaka, Joyce F. West, Carol A. Gross
Software Mentions: 1
Published: almost 19 years ago
10.1371/journal.pbio.0030187
Determination of Stromal Signatures in Breast Carcinoma
Cited by: 183
Author(s): Robert B. West, Dimitry S.A. Nuyten, Subbaya Subramanian, Torsten O. Nielsen, Christopher L. Corless, Brian P. Rubin, Kelli Montgomery, Shirley Zhu, Rajiv M. Patel, Tina Hernandez‐Boussard, John R. Goldblum, Patrick O. Brown, Marc J. van de Vijver, Matt van de Rijn
Software Mentions: 1
Published: over 19 years ago
10.1371/journal.pbio.1001100
Defining the Specificity of Cotranslationally Acting Chaperones by Systematic Analysis of mRNAs Associated with Ribosome-Nascent Chain Complexes
Cited by: 130
Author(s): Marta del Álamo, Daniel J. Hogan, Sebastian Pechmann, Véronique Albanèse, Patrick O. Brown, Judith Frydman
Software Mentions: 1
Published: over 13 years ago
10.1371/journal.pcbi.0030160
Automated Protein Subfamily Identification and Classification
Cited by: 107
Author(s): D. Brown, Nandini Krishnamurthy, Kimmen Sjölander
Software Mentions: 1
Published: over 17 years ago
10.1371/journal.pcbi.0030247
Comparative Genomics Search for Losses of Long-Established Genes on the Human Lineage
Cited by: 102
Author(s): Jingchun Zhu, J. Zachary Sanborn, Mark Diekhans, Craig B. Lowe, Tom H. Pringle, David Haussler
Software Mentions: 1
Published: almost 17 years ago
10.1371/journal.pcbi.1003017
Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci
Cited by: 38
Author(s): Emily Chambers, Wendy A. Bickmore, Colin A. Semple
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pcbi.1007523
Mathematical modeling of plant cell fate transitions controlled by hormonal signals
Cited by: 6
Author(s): Filip Z. Klawe, Thomas Stiehl, Peter Bastian, Christophe Gaillochet, Jan U. Lohmann, Anna Marciniak‐Czochra
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pcbi.1000069
A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation
Cited by: 283
Author(s): Sean R. Eddy
Software Mentions: 1
Published: over 16 years ago
10.1371/journal.pcbi.1002621
Single Nucleotide Polymorphisms Can Create Alternative Polyadenylation Signals and Affect Gene Expression through Loss of MicroRNA-Regulation
Cited by: 43
Author(s): Laurent F. Thomas, Pål Sætrom
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pcbi.0030208
Meta-Analysis of Drosophila Circadian Microarray Studies Identifies a Novel Set of Rhythmically Expressed Genes
Cited by: 106
Author(s): Kevin P. Keegan, Snehasis Pradhan, Ji-Ping Z Wang, Ravi Allada
Software Mentions: 1
Published: about 17 years ago
10.1371/journal.pcbi.1004493
Steering Evolution with Sequential Therapy to Prevent the Emergence of Bacterial Antibiotic Resistance
Cited by: 145
Author(s): Daniel Nichol, Peter Jeavons, Alexander G. Fletcher, Robert A. Bonomo, Philip K. Maini, Jerome L. Paul, Robert A. Gatenby, Alexander R.A. Anderson, Jacob G. Scott
Software Mentions: 1
Published: about 9 years ago
10.1371/journal.pcbi.1002129
A Systems Biology Approach Identifies Molecular Networks Defining Skeletal Muscle Abnormalities in Chronic Obstructive Pulmonary Disease
Cited by: 71
Author(s): Nahid Turan, Susana G. Kalko, Anna Stincone, Kim Clarke, Ayesha Sabah, Katherine Howlett, S. John Curnow, Diego A. Rodríguez, Marta Cascante, Laura P. O’Neill, Stuart Egginton, Josep Roca, Francesco Falciani
Software Mentions: 1
Published: about 13 years ago
10.1371/journal.pcbi.1005744
The logic of the floral transition: Reverse-engineering the switch controlling the identity of lateral organs
Cited by: 6
Author(s): Jean-Louis Dinh, Etienne Farcot, Charlie Hodgman
Software Mentions: 1
Published: about 7 years ago
10.1371/journal.pcbi.1000274
A Factor Graph Nested Effects Model To Identify Networks from Genetic Perturbations
Cited by: 35
Author(s): Charles J. Vaske, Carrie D. House, Truong Luu, Bryan Frank, Chen Hsiang Yeang, Norman H. Lee, Joshua M. Stuart
Software Mentions: 1
Published: almost 16 years ago
10.1371/journal.pcbi.1002195
Accelerated Profile HMM Searches
Cited by: 4,510
Author(s): Sean R. Eddy
Software Mentions: 1
Published: about 13 years ago
10.1371/journal.pcbi.1002564
Coding Conspecific Identity and Motion in the Electric Sense
Cited by: 51
Author(s): Na Yu, Ginette J. Hupé, Charles J. Garfinkle, John E. Lewis, André Longtin
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pcbi.1000730
Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor Metastasis
Cited by: 141
Author(s): Younghee Lee, Xinan Yang, Yong Huang, Huiying Fan, Qingbei Zhang, Youngfei Wu, Jiànróng Lǐ, Rifat Hasina, Chao Cheng, Mark W. Lingen, Mark Gerstein, Ralph R. Weichselbaum, H. Rosie Xing, Yves A. Lussier
Software Mentions: 1
Published: over 14 years ago
10.1371/journal.pcbi.1003069
The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch
Cited by: 24
Author(s): Wei Huang, Joohyun Kim, Shantenu Jha, Fareed Aboul‐ela
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pcbi.1004344
Inferring the Clonal Structure of Viral Populations from Time Series Sequencing
Cited by: 0
Author(s): Donatien Fotso Chedom, Pablo R. Murcia, Chris Greenman
Software Mentions: 1
Published: about 9 years ago
10.1371/journal.pcbi.0030003
Using Phylogeny to Improve Genome-Wide Distant Homology Recognition
Cited by: 6
Author(s): Sanne Abeln, Carlo Teubner, Charlotte M. Deane
Software Mentions: 1
Published: almost 18 years ago
10.1371/journal.pgen.1007075
How well do you know your mutation? Complex effects of genetic background on expressivity, complementation, and ordering of allelic effects
Cited by: 45
Author(s): Christopher H. Chandler, Sudarshan Chari, Alycia Kowalski, Lin Choi, David C. Tack, Michael DeNieu, William Pitchers, Anne Sonnenschein, Leslie Marvin, Kristen Hummel, Christian Marier, Andrew Victory, Cody K. Porter, Anna Mammel, Julie Holms, Gayatri Sivaratnam, Ian Dworkin
Software Mentions: 1
Published: about 7 years ago
10.1371/journal.pgen.1004097
CEP-1, the Caenorhabditis elegans p53 Homolog, Mediates Opposing Longevity Outcomes in Mitochondrial Electron Transport Chain Mutants
Cited by: 57
Author(s): Aiswarya Baruah, Hung‐Hao Chang, Mathew Hall, Jie Yuan, Sarah Gordon, Erik C. Johnson, Ludmila Shtessel, Callista Yee, Siegfried Hekimi, W. Brent Derry, Siu Sylvia Lee
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pgen.1002530
A Quantitative, High-Throughput Reverse Genetic Screen Reveals Novel Connections between Pre–mRNA Splicing and 5′ and 3′ End Transcript Determinants
Cited by: 31
Author(s): Laura-Oana Albulescu, Nevin Sabet, Mohanram Gudipati, Nicholas Stepankiw, Zane J. Bergman, Tim C. Huffaker, Jeffrey A. Pleiss
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pgen.0030174
Signalling Pathways Involved in Adult Heart Formation Revealed by Gene Expression Profiling in Drosophila
Cited by: 70
Author(s): Bruno Zeitouni, Sébastien Sénatore, Dany Séverac, Cindy Aknin, Michel Sémériva, Laurent Perrin
Software Mentions: 1
Published: about 17 years ago
10.1371/journal.pgen.1003389
Molecular Networks of Human Muscle Adaptation to Exercise and Age
Cited by: 149
Author(s): Bethan E. Phillips, John P. Williams, Thomas Gustafsson, Claude Bouchard, Tuomo Rankinen, Steen Knudsen, Kenneth Smith, James A. Timmons, Philip J. Atherton
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pgen.1000999
Amplification of a Cytochrome P450 Gene Is Associated with Resistance to Neonicotinoid Insecticides in the Aphid Myzus persicae
Cited by: 380
Author(s): Alin M. Puinean, S. P. Foster, L. Oliphant, I. Denholm, L. M. Field, Neil S. Millar, Martin S. Williamson, Chris Bass
Software Mentions: 1
Published: over 14 years ago
10.1371/journal.pgen.1003369
MTL–Independent Phenotypic Switching in Candida tropicalis and a Dual Role for Wor1 in Regulating Switching and Filamentation
Cited by: 40
Author(s): Allison M. Porman, Matthew P. Hirakawa, Stephen K. Jones, Na Wang, Richard J. Bennett
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pgen.0020203
Impact of Nonsense-Mediated mRNA Decay on the Global Expression Profile of Budding Yeast
Cited by: 119
Author(s): Qiaoning Guan, Wei Zheng, Shijie Tang, Xiaosong Liu, Robert A. Zinkel, Kam‐Wah Tsui, Brian S. Yandell, Michael R. Culbertson
Software Mentions: 1
Published: almost 19 years ago
10.1371/journal.pgen.1000450
A Regulated Response to Impaired Respiration Slows Behavioral Rates and Increases Lifespan in Caenorhabditis elegans
Cited by: 144
Author(s): David Cristina, Michael Cary, Adam Lunceford, Catherine F. Clarke, Cynthia Kenyon
Software Mentions: 1
Published: over 15 years ago
10.1371/journal.pgen.1004589
A Gain-of-Function Mutation in Tnni2 Impeded Bone Development through Increasing Hif3a Expression in DA2B Mice
Cited by: 26
Author(s): Xiaoquan Zhu, Fengchao Wang, Yang Zhao, Peng Yang, Jun Chen, Hanzi Sun, Lei Liu, Wenjun Li, Pei Lin, Yafei Guo, Zhaohui Kou, Yu Zhang, Cheng Zhou, Jiang He, Xue Zhang, Jianxin Li, Han Wang, Jian Li, Guanghui Liu, Shaorong Gao, Ze Yang
Software Mentions: 1
Published: about 10 years ago
10.1371/journal.pgen.1009119
Two cis-regulatory SNPs upstream of ABCG2 synergistically cause the blue eggshell phenotype in the duck
Cited by: 8
Author(s): Li Chen, Xiaorong Gu, Xuetao Huang, Rui Liu, Jinxiu Li, Yiqing Hu, Guoqin Li, Tao Zeng, Yong Tian, Xiaoxiang Hu, Lizhi Liu, Ning Li
Software Mentions: 1
Published: about 4 years ago
10.1371/journal.pgen.1003186
Rbfox1 Downregulation and Altered Calpain 3 Splicing by FRG1 in a Mouse Model of Facioscapulohumeral Muscular Dystrophy (FSHD)
Cited by: 32
Author(s): Mariaelena Pistoni, Lily Shiue, Melissa Cline, Sergia Bortolanza, Maria Victoria Neguembor, Alexandros Xynos, Manuel Ares, Davide Gabellini
Software Mentions: 1
Published: almost 12 years ago
10.1371/journal.pgen.1006042
Heat Shock Protein Beta-1 Modifies Anterior to Posterior Purkinje Cell Vulnerability in a Mouse Model of Niemann-Pick Type C Disease
Cited by: 18
Author(s): Chan Chung, Matthew J. Elrick, Zhaohui S. Qin, Shanker Kalyana-Sundaram, Arul M. Chinnaiyan, Vikram G. Shakkottai, Andrew P. Lieberman
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pgen.1007500
Modulation of miR-210 alters phasing of circadian locomotor activity and impairs projections of PDF clock neurons in Drosophila melanogaster
Cited by: 27
Author(s): Paola Cusumano, Alberto Biscontin, Federica Sandrelli, Gabriella Mazzotta, Claudia Tregnago, Cristiano De Pittà, Rodolfo Costa
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pgen.0010028
Differential Expression of Novel Potential Regulators in Hematopoietic Stem Cells
Cited by: 265
Author(s): Erik Forsberg, Susan Prohaska, Sol Katzman, Garrett C. Heffner, Joshua M. Stuart, Irving L. Weissman
Software Mentions: 1
Published: about 19 years ago
10.1371/journal.pgen.1004955
Pooled Sequencing of 531 Genes in Inflammatory Bowel Disease Identifies an Associated Rare Variant in BTNL2 and Implicates Other Immune Related Genes
Cited by: 58
Author(s): Natalie J. Prescott, Benjamin Lehne, Kristina Stone, James C. Lee, Kirstin M. Taylor, Jo Knight, Efterpi Papouli, Muddassar M. Mirza, Michael A. Simpson, Sarah L. Spain, Grace H C Lu, Franca Fraternali, Suzannah Bumpstead, Emma Gray, Ariella Amar, Hannah Bye, Peter Green, Guy Carrault, Bu’Hussain Hayee, Richard Pollok, Jack Satsangi, Miles Parkes, Jeffrey C. Barrett, John C. Mansfield, Jeremy Sanderson, Cathryn M. Lewis, Michael E. Weale, Thomas Schlitt, Christopher G. Mathew
Software Mentions: 1
Published: almost 10 years ago
10.1371/journal.pgen.1000310
Genetic and Computational Identification of a Conserved Bacterial Metabolic Module
Cited by: 28
Author(s): Cara C. Boutte, Balaji Srinivasan, Jason Flannick, Antal F. Novak, Andrew T. Martens, Serafim Batzoglou, Patrick H. Viollier, Sean Crosson
Software Mentions: 1
Published: almost 16 years ago
10.1371/journal.pgen.1003683
Comparative Genomic and Functional Analysis of 100 Lactobacillus rhamnosus Strains and Their Comparison with Strain GG
Cited by: 173
Author(s): François P. Douillard, Angela Ribbera, Ravi Kant, Taija E. Pietilä, Hanna Järvinen, Marcel Messing, Cinzia Lucia Randazzo, Lars Paulín, Pia Laine, Jarmo Ritari, Cinzia Caggia, Tanja Lähteinen, Stan J. J. Brouns, Reetta Satokari, Ingemar von Ossowski, Justus Reunanen, Airi Palva, Willem M. de Vos
Software Mentions: 1
Published: over 11 years ago