cran: SAM | Projects | Ecosyste.ms: Papers

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: over 7 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 11 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: about 7 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: almost 9 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: almost 9 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 10 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: almost 10 years ago

10.7717/peerj.438

Continental variation in wing pigmentation inCalopteryxdamselflies is related to the presence of heterospecifics
Cited by: 12
Author(s): Christopher Hassall
Software Mentions: 1
Published: over 12 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 11 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 12 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: about 5 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: almost 7 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: almost 9 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: about 8 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: about 12 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: over 7 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 8 years ago

10.1002/PHY2.8

Elevated pulmonary arterial pressure and altered expression ofDdah1andArg1in 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 13 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: about 5 years ago

10.1111/pbi.13002

Time-specific and pleiotropic quantitative trait loci coordinately modulate stem growth inPopulus
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 8 years ago

10.1111/pbi.13030

Resequencing of cv 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 8 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: almost 9 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 9 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: about 7 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 7 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 6 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 5 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 5 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 9 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: almost 7 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: over 5 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: over 14 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: over 5 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 5 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 5 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: about 6 years ago

10.3390/plants4030356

Senescence Meets Dedifferentiation
Cited by: 7
Author(s): Yemima Givaty Rapp, Vanessa Ransbotyn, Gideon Grafi
Software Mentions: 1
Published: about 11 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 5 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: over 11 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: almost 18 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: over 15 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 5 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 13 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 12 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: over 20 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 21 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: about 15 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: about 19 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 19 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 13 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: about 6 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 18 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: about 14 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: almost 19 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 11 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 15 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: almost 9 years ago

10.1371/journal.pone.0154638

Correction: Centering the Organizing Center in the Arabidopsis thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization
Cited by: 0
Author(s):
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0079692

Global Transcriptome Analysis of Lactococcus garvieae Strains in Response to Temperature
Cited by: 19
Author(s): Mónica Aguado-Urda, Alicia Gibello, M. Mar Blanco, J. F. Fernández‐Garayzábal, Victoria López-Alonso, Guillermo López-Campos
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0081147

Snf2 Family Gene Distribution in Higher Plant Genomes Reveals DRD1 Expansion and Diversification in the Tomato Genome
Cited by: 10
Author(s): Joachim W. Bargsten, Adam Folta, Ľudmila Mlynárová, Jan-Peter Nap
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0028251

Improving Transmission Efficiency of Large Sequence Alignment/Map (SAM) Files
Cited by: 17
Author(s): Muhammad N. Sakib, Jijun Tang, W. Jim Zheng, Chin Tser Huang
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0013343

A Novel Secretory Poly-Cysteine and Histidine-Tailed Metalloprotein (Ts-PCHTP) from Trichinella spiralis (Nematoda)
Cited by: 12
Author(s): Georgi Radoslavov, Rositsa Jordanova, Denitsa Teofanova, K. Georgieva, Peter Hristov, Marco Salomone‐Stagni, Eva Liebau, Ilia Bankov
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0005637

Molecular Characterization of Lung Dysplasia Induced by c-Raf-1
Cited by: 12
Author(s): Astrid Rohrbeck, Volker Müller, Jürgen Borlak
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0011620

Genomic Binding Profiling of the Fission Yeast Stress-Activated MAPK Sty1 and the bZIP Transcriptional Activator Atf1 in Response to H2O2
Cited by: 57
Author(s): Majid Eshaghi, Jong Hoon Lee, Li Zhu, Suk Yean Poon, Juntao Li, Kwang-Hyun Cho, Zhaoqing Chu, R. Krishna Murthy Karuturi, Jianhua Liu
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0142846

Development and Validation of a Gene-Based Model for Outcome Prediction in Germ Cell Tumors Using a Combined Genomic and Expression Profiling Approach
Cited by: 18
Author(s): James E. Korkola, Sandy Heck, Adam B. Olshen, Darren R. Feldman, Victor E. Reuter, Jane Houldsworth, George J. Bosl, R. S. K. Chaganti
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0200617

Genetic mapping reveals a marker for yellow skin in watermelon (Citrullus lanatus L.)
Cited by: 29
Author(s): Junling Dou, Xingrong Lu, Aslam Ali, Shengjie Zhao, Lei Zhang, Nan He, Wenge Liu
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0013721

Systematical Detection of Significant Genes in Microarray Data by Incorporating Gene Interaction Relationship in Biological Systems
Cited by: 3
Author(s): Junwei Wang, Meiwen Jia, Liping Zhu, Yuan Zeng, Peng Li, Chang Chang, Jian Luo, Mingyao Liu, Tieliu Shi
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0066165

Deep Sequencing the MicroRNA Transcriptome in Colorectal Cancer
Cited by: 133
Author(s): Kristina Schee, Susanne Lorenz, Merete Molton Worren, Clara Cecilie Günther, Matthew T. G. Holden, Eivind Hovig, Øystein Fodstad, Leonardo A. Meza‐Zepeda, Kjersti Flatmark
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0023311

Differences in the Properties and Mirna Expression Profiles between Side Populations from Hepatic Cancer Cells and Normal Liver Cells
Cited by: 23
Author(s): Weihui Liu, Kaishan Tao, Nan You, Zhengcai Liu, Hongtao Zhang, Kefeng Dou
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0167100

Sam2bam: High-Performance Framework for NGS Data Preprocessing Tools
Cited by: 3
Author(s): Takeshi Ogasawara, Yinhe Cheng, Tzy-Hwa Kathy Tzeng
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0034279

Genome-Wide Gene Expression Analysis in Cancer Cells Reveals 3D Growth to Affect ECM and Processes Associated with Cell Adhesion but Not DNA Repair
Cited by: 104
Author(s): Oliver Zschenker, Thomas Streichert, Stephanie Hehlgans, Nils Cordes
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0234650

An analytical study of neocartilage from microtia and otoplasty surgical remnants: A possible application for BMP7 in microtia development and regeneration
Cited by: 3
Author(s): R. Childs, Hitomi Nakao, Noritaka Isogai, Ananth S. Murthy, William J. Landis
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0006288

Layered Functional Network Analysis of Gene Expression in Human Heart Failure
Cited by: 18
Author(s): Wenliang Zhu, Lei Yang, Zhenhong Du
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pone.0076709

Residues in Human Arsenic (+3 Oxidation State) Methyltransferase Forming Potential Hydrogen Bond Network around S-adenosylmethionine
Cited by: 7
Author(s): Xiangli Li, Jing Cao, Shuping Wang, Zhirong Geng, Xiaoli Song, Xin Hu, Zhilin Wang
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0001385

Sex-Related Differences in Gene Expression in Human Skeletal Muscle
Cited by: 158
Author(s): Stephen Welle, Rabi Tawil, Charles A. Thornton
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0087938

Microrna 130b Suppresses Migration and Invasion of Colorectal Cancer Cells through Downregulation of Integrin β1
Cited by: 32
Author(s): Yanyang Zhao, Gang Miao, Yao Li, Tomoya Isaji, Jianguo Gu, Jian Li, Ruomei Qi
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0013655

Transcriptional Profiles of Treponema denticola in Response to Environmental Conditions
Cited by: 15
Author(s): Ian Howard Mchardy, Caroline Keegan, Jee Hyun Sim, Wenyuan Shi, Renate Lux
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0041373

TH17, TH22 and TReg Cells Are Enriched in the Healthy Human Cecum
Cited by: 32
Author(s): Martin Wolff, Jacqueline M. Leung, Michael Davenport, Michael A. Poles, Ilseung Cho, P’ng Loke
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0132433

Small ncRNA Expression-Profiling of Blood from Hemophilia A Patients Identifies miR-1246 as a Potential Regulator of Factor 8 Gene
Cited by: 20
Author(s): Tewarit Sarachana, Neetu Dahiya, Vijaya L. Simhadri, Gouri Shankar Pandey, Surbhi Saini, Christine Guelcher, Michael F. Guerrera, Chava Kimchi-Sarfaty, Zuben E. Sauna, Chintamani D. Atreya
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0192560

Spatial analysis of ecosystem service relationships to improve targeting of payments for hydrological services
Cited by: 22
Author(s): Pierre Mokondoko, Robert H. Manson, Taylor H. Ricketts, Daniel Geissert
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0099593

Decellularized Allogeneic Heart Valves Demonstrate Self-Regeneration Potential after a Long-Term Preclinical Evaluation
Cited by: 69
Author(s): Laura Iop, Antonella Bonetti, Filippo Naso, Stefania Rizzo, Stefano Cagnin, Roberto Bianco, Carlo Dal Lin, Paolo Martini, Helen Poser, Paolo Franci, Gerolamo Lanfranchi, Roberto Busetto, Michel Spina, Cristina Basso, Maurizio Marchini, Alessandro Gandaglia, Fulvia Ortolani, Gino Gerosa
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0017753

Genes Expressed in Specific Areas of the Human Fetal Cerebral Cortex Display Distinct Patterns of Evolution
Cited by: 66
Author(s): Nelle Lambert, Marie-Alexandra Lambot, Angéline Bilheu, Valérie Albert, Yvon Englert, Frédérick Libert, Jean‐Christophe Noël, Christos Sotiriou, Alisha K. Holloway, Katherine S. Pollard, Vincent Detours, Pierre Vanderhaeghen
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0023144

Modulation of Androgen Receptor Signaling in Hormonal Therapy-Resistant Prostate Cancer Cell Lines
Cited by: 46
Author(s): Rute B. Marques, Natasja F. Dits, Sigrun Erkens-Schulze, Wilfred F. J. van IJcken, Wytske M. van Weerden, Guido Jenster
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0050095

Aberrant Neuromagnetic Activation in the Motor Cortex in Children with Acute Migraine: A Magnetoencephalography Study
Cited by: 14
Author(s): Xinyao Guo, Jing Xiang, Yingying Wang, Hope L. O’Brien, Marielle A. Kabbouche, Paul S. Horn, Scott W. Powers, Andrew D. Hershey
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0201918

Identification of induced mutations in hexaploid wheat genome using exome capture assay
Cited by: 43
Author(s): Mubasher Hussain, Muhammad Munwar Iqbal, Bradley J. Till, Mehboob-ur Rahman
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0082385

Age-Related Changes in the Functional Network Underlying Specific and General Autobiographical Memory Retrieval: A Pivotal Role for the Anterior Cingulate Cortex
Cited by: 47
Author(s): Pénélope Martinelli, Marco Sperduti, Anne-Dominique Devauchelle, Sandrine Kalenzaga, Thierry Gallarda, Stéphanie Lion, Marion Delhommeau, Adèle Anssens, Isabelle Amado, J.F. Méder, Marie‐Odile Krebs, Catherine Oppenheim, Pascale Piolino
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0011485

Gene Expression Profiles Characterize Inflammation Stages in the Acute Lung Injury in Mice
Cited by: 22
Author(s): Isabelle Lesur, Julien Textoris, Béatrice Loriod, C. Courbon, Stéphane Garcia, Marc Léone, Catherine Nguyen
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0202286

Hotspot mutations and ColE1 plasmids contribute to the fitness of Salmonella Heidelberg in poultry litter
Cited by: 33
Author(s): Adelumola Oladeinde, Kyle DeMeo Cook, Alex Orlek, Gregory Zock, Kyler Herrington, N. A. Cox, Jodie Plumblee Lawrence, Carolina Hall
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0017091

Phosphodiesterase 4 Inhibition Reduces Innate Immunity and Improves Isoniazid Clearance of Mycobacterium tuberculosis in the Lungs of Infected Mice
Cited by: 65
Author(s): Mi Sun Koo, Claudia Manca, Guang Yang, Paul Edmond O'Brien, Nackmoon Sung, Liana Tsenova, Selvakumar Subbian, Dorothy Fallows, George W. Muller, Sabine Ehrt, Gilla Kaplan
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0003225

Discovery of Porcine microRNAs and Profiling from Skeletal Muscle Tissues during Development
Cited by: 123
Author(s): Tinghua Huang, Mengjin Zhu, Xinyun Li, Zhao Song
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pone.0001218

Proteomic Shifts in Embryonic Stem Cells with Gene Dose Modifications Suggest the Presence of Balancer Proteins in Protein Regulatory Networks
Cited by: 25
Author(s): Lei Mao, Claus Zabel, Markus Herrmann, Tobias Nolden, Florián Mertes, Laetitia Magnol, Caroline Chabert, Daniela Hartl, Yann Hérault, Jean Maurice Delabar, Thomas Manke, Heinz Himmelbauer, Joachim Klose
Software Mentions: 1
Published: almost 19 years ago

10.1371/journal.pone.0242252

Dealing with an aging China—Delaying retirement or the second-child policy?
Cited by: 11
Author(s): Yantao Ling, Zhenzhen Song, Yang Yu, Tangyang Jiang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0103896

Remodeling of the Methylation Landscape in Breast Cancer Metastasis
Cited by: 33
Author(s): Marsha Reyngold, Şevin Turcan, Dilip Giri, Kasthuri Kannan, Logan A. Walsh, Agnès Viale, Marija Drobnjak, Linda T. Vahdat, William Lee, Timothy A. Chan
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0003164

Comparative Analysis of mRNA Targets for Human PUF-Family Proteins Suggests Extensive Interaction with the miRNA Regulatory System
Cited by: 265
Author(s): Alessia Galgano, Michael Forrer, Łukasz Jaśkiewicz, Alexander Kanitz, Mihaela Zavolan, André P. Gerber
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pone.0020103

The Use of Carcasses for the Analysis of Cetacean Population Genetic Structure: A Comparative Study in Two Dolphin Species
Cited by: 24
Author(s): Kerstin Bilgmann, Luciana M. Möller, Robert Harcourt, Catherine M. Kemper, Luciano B. Beheregaray
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0201942

Introduction and validation of the Natural Disasters Picture System (NDPS)
Cited by: 3
Author(s): Gaëtan Merlhiot, Martial Mermillod, Jean‐Luc Le Pennec, Laurie Mondillon
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0123745

Transcriptional Profile of Mycobacterium tuberculosis Replicating in Type II Alveolar Epithelial Cells
Cited by: 54
Author(s): Michelle B. Ryndak, Krishna K. Singh, Zheng-Yu Peng, Suman Laal
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0103994

Fluorosed Mouse Ameloblasts Have Increased SATB1 Retention and Gαq Activity
Cited by: 13
Author(s): Yan Zhang, Ji Yeon Kim, Orapin V. Horst, Yukiko Nakano, Li Zhu, Ralf J. Radlanski, Sunita P. Ho, Pamela K. Den Besten
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0059503

Identifying Resistance Mechanisms against Five Tyrosine Kinase Inhibitors Targeting the ERBB/RAS Pathway in 45 Cancer Cell Lines
Cited by: 21
Author(s): Zsófia Pénzváltó, Bálint Tegze, Attila Marcell Szász, Zsófia Sztupinszki, István Láng, Attila Szendrői, Reinhold Schäfer, Balázs Györffy
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0084854

Microarray Gene Expression Analysis of Tumorigenesis and Regional Lymph Node Metastasis in Laryngeal Squamous Cell Carcinoma
Cited by: 32
Author(s): Meng Lian, Jugao Fang, Demin Han, Hongzhi Ma, Feng Li, Ru Wang, Fan Yang
Software Mentions: 1
Published: over 12 years ago

Projects: cran: SAM

Science Score: 85/100

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Papers Mentioning SAM 4,566