Ecosyste.ms: Papers

10.1186/1472-6807-10-7

Structural investigation of zymogenic and activated forms of human blood coagulation factor VIII: a computational molecular dynamics study
Cited by: 19
Author(s): Divi Venkateswarlu
Software Mentions: 1
Published: almost 15 years ago

10.1186/1472-6807-8-52

SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs
Cited by: 23
Author(s): Arlo Randall, Pierre Baldi
Software Mentions: 1
Published: almost 17 years ago

10.1186/1756-0500-7-869

Next generation sequencing reads comparison with an alignment-free distance
Cited by: 17
Author(s): Emanuel Weitschek, Daniele Santoni, Giulia Fiscon, Maria Cristina De Cola, Paola Bertolazzi, G. Felici
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12870-015-0484-7

NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss
Cited by: 77
Author(s): Tracey A. Ruhlman, Wan Jung Chang, Jeremy J.W. Chen, Yao‐Ting Huang, Ming Tsair Chan, Jin Zhang, De Chih Liao, John C. Blazier, Xiaohua Jin, Ming Che Shih, Robert K. Jansen, Chun-Shin Lin
Software Mentions: 1
Published: over 9 years ago

10.3389/fnhum.2014.00049

The cortical activation pattern by a rehabilitation robotic hand: a functional NIRS study
Cited by: 37
Author(s): Pyung Hun Chang, Seung‐Hee Lee, Geonmo Gu, Seung–Hyun Lee, Sang Hyeon Jin, Sang Seok Yeo, Jeong Hyun Seo, Sung Ho Jang
Software Mentions: 1
Published: almost 11 years ago

10.1186/s40064-016-2642-2

A three phase optimization method for precopy based VM live migration
Cited by: 16
Author(s): Sangeeta Sharma, Meenu Chawla
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2105-15-S16-S7

Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins
Cited by: 41
Author(s): B. Jayaram, Priyanka Dhingra, Avinash Mishra, Rahul Kaushik, Goutam Mukherjee, Ankita Singh, Shashank Shekhar
Software Mentions: 1
Published: almost 10 years ago

10.3389/fimmu.2018.02284

Determining the Quantitative Principles of T Cell Response to Antigenic Disparity in Stem Cell Transplantation
Cited by: 10
Author(s): Ali Raied Salman, Vishal N. Kopardé, Charles A. Hall, Max Jameson-Lee, Catherine Roberts, Myrna G. Serrano, Badar AbdulRazzaq, Jeremy A. Meier, Caleb J. Kennedy, Masoud H. Manjili, Stephen R. Spellman, Dayanjan S. Wijesinghe, Shahrukh K. Hashmi, Greg Buck, Rehan Qayyum, Michael C. Neale, Jason Reed, Amir A. Toor
Software Mentions: 1
Published: about 6 years ago

10.3389/fmicb.2012.00315

Somatic populations of PGT135–137 HIV-1-neutralizing antibodies identified by 454 pyrosequencing and bioinformatic
Cited by: 57
Author(s): Jiang Zhu, Sijy O’Dell, Gilad Ofek, Marie Pancera, Xueling Wu, Baoshan Zhang, Zhenhai Zhang, Nisc Comparative Sequencing Program, James C. Mullikin, Melissa Simek, Dennis R. Burton, Wayne C. Koff, Lawrence Shapiro, John R. Mascola, Peter D. Kwong
Software Mentions: 1
Published: almost 13 years ago

10.3389/fmicb.2016.01476

Comparative Transcriptomic Analysis Reveals Novel Insights into the Adaptive Response of Skeletonema costatum to Changing Ambient Phosphorus
Cited by: 30
Author(s): Shufeng Zhang, Chun-Juan Yuan, Ying Chen, Xiao-Huang Chen, Dongxu Li, Jiu-Ling Liu, Lin Lin, Dazhi Wang
Software Mentions: 1
Published: about 8 years ago

10.3389/fmicb.2016.00484

Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology
Cited by: 78
Author(s): Sarah K Hilton, Eduardo Castro-Nallar, Marcos Pérez‐Losada, Ian Toma, Timothy A. McCaffrey, Eric P. Hoffman, Marc Siegel, Gary L. Simon, W. Evan Johnson, Keith A. Crandall
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2020.574626

Comparative Evolutionary Patterns of Burkholderia cenocepacia and B. multivorans During Chronic Co-infection of a Cystic Fibrosis Patient Lung
Cited by: 4
Author(s): A. Amir Hassan, Sandra C. dos Santos, Vaughn S. Cooper, Isabel Sá‐Correia
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2017.00130

Genome Wide In silico Analysis of the Mismatch Repair Components of Plasmodium falciparum and Their Comparison with Human Host
Cited by: 16
Author(s): Mohammed Tarique, Moaz Ahmad, Manish Chauhan, Renu Tuteja
Software Mentions: 1
Published: almost 8 years ago

10.3389/fmicb.2016.01797

Different Virus-Derived siRNAs Profiles between Leaves and Fruits in Cucumber Green Mottle Mosaic Virus-Infected Lagenaria siceraria Plants
Cited by: 21
Author(s): Junmin Li, Hongying Zheng, Chenhua Zhang, Kelei Han, Shu Wang, Jiejun Peng, Yuwen Lu, Jinping Zhao, Pei Xu, Xiaohua Wu, Guojing Li, Jianping Chen, Fei Yan
Software Mentions: 1
Published: about 8 years ago

10.3389/fnana.2016.00040

Estimating Fiber Orientation Distribution Functions in 3D-Polarized Light Imaging
Cited by: 53
Author(s): Markus Axer, Sven Strohmer, David Gräßel, Oliver Bücker, Melanie Dohmen, Julia Reckfort, Karl Zilles, Katrin Amunts
Software Mentions: 1
Published: over 8 years ago

10.1186/s12911-019-1012-8

Forecasting one-day-forward wellness conditions for community-dwelling elderly with single lead short electrocardiogram signals
Cited by: 9
Author(s): Xiaomao Fan, Yang Zhao, Hailiang Wang, Kwok Leung Tsui
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12859-019-3169-7

Recommendations for performance optimizations when using GATK3.8 and GATK4
Cited by: 20
Author(s): Jacob R Heldenbrand, Saurabh Baheti, Matthew A. Bockol, Travis Drucker, Steven N. Hart, Matthew E. Hudson, Ravishankar K. Iyer, Michael Kalmbach, Katherine Kendig, Eric W. Klee, Nathan R Mattson, Eric D. Wieben, Mathieu Wiepert, Derek E. Wildman, Liudmila Sergeevna Mainzer
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2105-10-178

TOMOBFLOW: feature-preserving noise filtering for electron tomography
Cited by: 28
Author(s): Julio F. Fernández
Software Mentions: 1
Published: over 15 years ago

10.1186/1472-6920-12-104

eMedOffice: A web-based collaborative serious game for teaching optimal design of a medical practice
Cited by: 49
Author(s): Andreas Hannig, Nicole Kuth, Monika Özman, Stephan Jonas, Cord Spreckelsen
Software Mentions: 1
Published: about 12 years ago

10.3389/fninf.2016.00041

Temporal Code-Driven Stimulation: Definition and Application to Electric Fish Signaling
Cited by: 7
Author(s): Ángel Lareo, Caroline Garcia Forlim, Reynaldo D. Pinto, Pablo Varona, Francisco B. Rodríguez
Software Mentions: 1
Published: about 8 years ago

10.1186/1471-2164-11-124

Digital gene expression analysis of two life cycle stages of the human-infective parasite, Trypanosoma brucei gambiense reveals differentially expressed clusters of co-regulated genes
Cited by: 57
Author(s): Nicola Veitch, Paul C. D. Johnson, Urmi Trivedi, Sandra Terry, David Wildridge, Annette MacLeod
Software Mentions: 1
Published: over 14 years ago

10.3389/fnins.2014.00009

Asynchronous visual event-based time-to-contact
Cited by: 32
Author(s): Xavier Clady, Charles De Clercq, Sio-Hoï Ieng, Fouzhan Houseini, Marco Randazzo, Lorenzo Natale, Chiara Bartolozzi, Ryad Benosman
Software Mentions: 1
Published: almost 11 years ago

10.1155/2008/341684

Reordering for Improved Constrained Reconstruction from Undersampled k-Space Data
Cited by: 30
Author(s): Ganesh Adluru, Edward DiBella
Software Mentions: 1
Published: almost 17 years ago

10.3389/fphar.2020.01221

Molecular Modeling Applied to the Discovery of New Lead Compounds for P2 Receptors Based on Natural Sources
Cited by: 10
Author(s): Anael Viana Pinto Alberto, Natiele Carla da Silva Ferreira, Rafael Ferreira Soares, Luiz Anastácio Alves
Software Mentions: 1
Published: about 4 years ago

10.3389/fphar.2020.595335

Heavy Metal Contaminations in Herbal Medicines: Determination, Comprehensive Risk Assessments, and Solutions
Cited by: 81
Author(s): Lu Luo, Bo Wang, Jingwen Jiang, Martin Fitzgerald, Huang Qin, Yu Zheng, Hui Li, Jiqing Zhang, Jianhe Wei, Chenyuyan Yang, Hui Zhang, Lixin Dong, Shilin Chen
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-018-4814-7

Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease
Cited by: 34
Author(s): Guoliang Lyu, Chao Zhang, Te Ling, Rui Li, Le Zong, Yiting Guan, Xiaoke Huang, Lei Sun, Lijun Zhang, Cheng Li, Yu Nie, Wei Tao
Software Mentions: 1
Published: over 6 years ago

10.3389/fpls.2017.01009

Alteration in Auxin Homeostasis and Signaling by Overexpression Of PINOID Kinase Causes Leaf Growth Defects in Arabidopsis thaliana
Cited by: 26
Author(s): Kumud Saini, Marios Nektarios Markakis, Malgorzata Zdanio, Daria Balcerowicz, Tom Beeckman, Lieven De Veylder, Els Prinsen, Gerrit T.S. Beemster, Kris Vissenberg
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-015-2311-9

MycoBASE: expanding the functional annotation coverage of mycobacterial genomes
Cited by: 8
Author(s): Benjamin J. Garcia, Gargi Datta, Rebecca M. Davidson, Michael Strong
Software Mentions: 1
Published: almost 9 years ago

10.1016/j.jtbi.2017.06.007

Identifying circumstances under which high insecticide dose increases or decreases resistance selection
Cited by: 36
Author(s): Joseph Helps, N. D. Paveley, Frank van den Bosch
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2164-9-518

Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats
Cited by: 83
Author(s): Thomas Wicker, Apurva Narechania, François Sabot, Joshua C. Stein, Giang T. H. Vu, Andreas Graner, Doreen Ware, Nils Stein
Software Mentions: 1
Published: about 16 years ago

10.3389/frobt.2019.00027

A Deep Learning Approach to Non-linearity in Wearable Stretch Sensors
Cited by: 20
Author(s): Ben Oldfrey, Richard J. Jackson, Peter Smitham, Mark Miodownik
Software Mentions: 1
Published: over 5 years ago

10.3390/nu11040792

Micronutrients Deficiencies in 374 Severely Malnourished Anorexia Nervosa Inpatients
Cited by: 41
Author(s): Mouna Hanachi, M. Dicembre, Claire Rives‐Lange, Jacques Ropers, P. Bemer, Jean‐Fabien Zazzo, Joël Poupon, Agnès Dauvergne, Jean‐Claude Melchior
Software Mentions: 1
Published: over 5 years ago

10.1155/2013/594528

GOLink: Finding Cooccurring Terms across Gene Ontology Namespaces
Cited by: 4
Author(s): Richard W. Francis
Software Mentions: 1
Published: almost 12 years ago

10.1534/g3.119.400220

Genetic Diversity and Phylogenetic Relationships of Annual and Perennial<i>Glycine</i>Species
Cited by: 5
Author(s): Eun Young Hwang, Wei He, Steven G. Schroeder, E. W. Fickus, Charles V. Quigley, Patrick Elia, Susan Araya, Fangyan Dong, L. C. Costa, Márcio Elias Ferreira, Perry B. Cregan, Qijian Song
Software Mentions: 1
Published: over 5 years ago

10.1093/g3journal/jkaa030

Genomic analysis of dibenzofuran-degrading <i>Pseudomonas veronii</i> strain Pvy reveals its biodegradative versatility
Cited by: 5
Author(s): Eglantina Lopez-Echartea, Jáchym Šuman, Tereza Smrhova, Jakub Rídl, Petr Pajer, Michal Strejcek, Ondřej Uhlík
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-017-3654-1

Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes
Cited by: 81
Author(s): Peng Zhou, Kevin A.T. Silverstein, Thiruvarangan Ramaraj, Joseph Guhlin, Roxanne Denny, Junqi Liu, Andrew Farmer, Kelly P. Steele, Robert M. Stupar, Jason R. Miller, Peter Tiffin, Joann Mudge, Nevin D. Young
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-020-6644-7

Systematic analysis of the basic/helix-loop-helix (bHLH) transcription factor family in pummelo (Citrus grandis) and identification of the key members involved in the response to iron deficiency
Cited by: 19
Author(s): Xiaoyong Zhang, Jie-Ya Qiu, Qiu-Ling Hui, Yuanyuan Xu, Yuan He, Peng LiangZhi, Xing-Zheng Fu
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2164-10-229

A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment
Cited by: 19
Author(s): Shani Tzahor, Dikla Man-Aharonovich, Benjamin C. Kirkup, Tali Yogev, Ilana Berman‐Frank, Martin F. Polz, Oded Béjà, Yael Mandel-Gutfreund
Software Mentions: 1
Published: over 15 years ago

10.1186/s12864-015-2301-y

RDDpred: a condition-specific RNA-editing prediction model from RNA-seq data
Cited by: 27
Author(s): Min-su Kim, Benjamin Hur
Software Mentions: 1
Published: almost 9 years ago

10.3390/antibiotics9110791

Development of Resistance in Escherichia coli ATCC25922 under Exposure of Sub-Inhibitory Concentration of Olaquindox
Cited by: 8
Author(s): Yan Gu, Shuge Wang, Lulu Huang, Wei Sa, Jun Li, Junhong Huang, Menghong Dai, Guyue Cheng
Software Mentions: 1
Published: about 4 years ago

10.1186/1471-2164-9-360

A method for detecting epistasis in genome-wide studies using case-control multi-locus association analysis
Cited by: 70
Author(s): Javier Gayán, Antonio González‐Pérez, Fernando Bermudo, María Eugenia Sáez, José Luis Royo, António Rocha Quintas, José Jorge Galán, Francisco Jesús Morón, Reposo Ramírez-Lorca, Luis Miguel Real, Agustín Ruiz
Software Mentions: 1
Published: over 16 years ago

10.1186/s12864-020-07029-4

PacBio genome sequencing reveals new insights into the genomic organisation of the multi-copy ToxB gene of the wheat fungal pathogen Pyrenophora tritici-repentis
Cited by: 14
Author(s): Paula Moolhuijzen, Pao Theen See, Caroline S. Moffat
Software Mentions: 1
Published: about 4 years ago

10.1186/1471-2164-13-60

Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters
Cited by: 8
Author(s): Zhenyan Miao, Daofeng Li, Zhenhai Zhang, Jiangli Dong, Zhen Su, Tao Wang
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-6-104

A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription
Cited by: 78
Author(s): Tomas Babak, Benjamin J. Blencowe, Timothy R. Hughes
Software Mentions: 1
Published: over 19 years ago

10.1186/1471-2156-7-40

SUP: an extension to SLINK to allow a larger number of marker loci to be simulated in pedigrees conditional on trait values
Cited by: 8
Author(s): Mathieu Lemire
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2156-11-19

An entropy test for single-locus genetic association analysis
Cited by: 26
Author(s): Manuel Ruiz Marín, Mariano Matilla-García, José Antonio García Córdoba, Juan Luis Susillo-González, Alejandro Romo-Astorga, Antonio González‐Pérez, Agustı́n Ruiz, Javier Gayán
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2148-8-214

Phylogenetic analyses suggest multiple changes of substrate specificity within the Glycosyl hydrolase 20 family
Cited by: 47
Author(s): Jari Intra, Giulio Pavesi, David S. Horner
Software Mentions: 1
Published: almost 17 years ago

10.5808/GI.2020.18.1.e5

PAIVS: prediction of avian influenza virus subtype
Cited by: 1
Author(s): Hyeon-Chun Park, Juyoun Shin, Sung Min Cho, Shinseok Kang, Yeun‐Jun Chung, Seung‐Hyun Jung
Software Mentions: 1
Published: over 4 years ago

10.1186/2047-217X-2-9

Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data
Cited by: 70
Author(s): Samuel Lampa, Martin Dahlö, Pall I. Olason, Jonas Hagberg, Ola Spjuth
Software Mentions: 1
Published: over 11 years ago

10.1111/jmi.12474

Automatic thresholding from the gradients of region boundaries
Cited by: 42
Author(s): Gabriel Landini, David A. Randell, Shereen Fouad, Antony Galton
Software Mentions: 1
Published: about 8 years ago

10.1016/j.jsb.2014.11.010

Semi-automated selection of cryo-EM particles in RELION-1.3
Cited by: 342
Author(s): Sjors H.W. Scheres
Software Mentions: 1
Published: almost 10 years ago

10.1120/jacmp.v14i5.4302

Monte Carlo characterization of biocompatible beta-emitting 90Y glass seed incorporated with the radionuclide 153Sm as a SPECT marker for brachytherapy applications
Cited by: 4
Author(s): Asghar Hadadi, Mahdi Sadeghi, Dariush Sardari, Ali Reza Khanchi, Alireza Shirazi
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2148-7-154

Phylogenomic analysis of natural selection pressure in Streptococcus genomes
Cited by: 49
Author(s): Maria Anisimova, Joseph P. Bielawski, Katherine A. Dunn, Ziheng Yang
Software Mentions: 1
Published: almost 18 years ago

10.1186/s13326-017-0131-3

Literature evidence in open targets - a target validation platform
Cited by: 14
Author(s): Şenay Kafkas, Ian Dunham, Johanna McEntyre
Software Mentions: 1
Published: over 7 years ago

10.1007/s13280-017-0961-3

Impact of climate change and seasonal trends on the fate of Arctic oil spills
Cited by: 26
Author(s): Tor Nordam, Dorien Dunnebier, CJ Beegle-Krause, Mark Reed, Dag Slagstad
Software Mentions: 1
Published: about 7 years ago

10.1186/s12862-021-01759-z

Male genital lobe morphology affects the chance to copulate in Drosophila pachea
Cited by: 4
Author(s): Bénédicte M. Lefèvre, Diane Catté, Virginie Courtier‐Orgogozo, Michael Lang
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2407-12-509

Increased frequency of single base substitutions in a population of transcripts expressed in cancer cells
Cited by: 1
Author(s): Laurent Bianchetti, David Kieffer, Rémi Féderkeil, Olivier Poch
Software Mentions: 1
Published: about 12 years ago

10.1186/s12859-017-1883-6

JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals
Cited by: 3
Author(s): Jeb Rosen, Kyle Handy, André Gillan, Rob Smith
Software Mentions: 1
Published: about 7 years ago

10.1098/rsos.180468

A worldwide model for boundaries of urban settlements
Cited by: 11
Author(s): Erneson A. Oliveira, Vasco Furtado, José S. Andrade, Hernán A. Makse
Software Mentions: 1
Published: over 6 years ago

10.1186/1477-7827-7-114

Pathophysiology of cell phone radiation: oxidative stress and carcinogenesis with focus on male reproductive system
Cited by: 155
Author(s): Nisarg Desai, Kavindra Kumar Kesari, Ashok Agarwal
Software Mentions: 1
Published: about 15 years ago

10.1186/1477-7827-8-96

ReCGiP, a database of reproduction candidate genes in pigs based on bibliomics
Cited by: 6
Author(s): Lun Yang, Xiangzhe Zhang, Jian Chen, Qishan Wang, Lishan Wang, Jiang Yue, Yuchun Pan
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-13-S5-S2

PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text
Cited by: 8
Author(s): Yuri Pirola, Raffaella Rizzi, Ernesto Picardi, Graziano Pesole, Gianluca Della Vedova, Paola Bonizzoni
Software Mentions: 1
Published: over 12 years ago

10.1186/1748-7188-8-3

A mixed integer linear programming model to reconstruct phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion
Cited by: 8
Author(s): Daniele Catanzaro, R. Ravi, Russell Schwartz
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2105-6-207

A protein domain interaction interface database: InterPare
Cited by: 50
Author(s): Sungsam Gong, Cb Park Chang-Bum Park, Hs Choi Han-Sol Choi, Js Ko Jun-Su Ko, Is Jang In-Soo Jang, Jungsul Lee, Dan Bolser, Dh Oh Dong-Hoon Oh, Ds Kim Deok-Soo Kim, Jong Bhak
Software Mentions: 1
Published: about 19 years ago

10.1038/sdata.2016.105

A chromosome-level genome assembly of the Asian arowana, Scleropages formosus
Cited by: 13
Author(s): Jia Li, Chao Bian, Yinchang Hu, Xuemei Mu, Xueyan Shen, Vydianathan Ravi, Irina M. Kuznetsova, Yu Sun, Xinxin You, Ying Qiu, Xinhui Zhang, Hui Yu, Yu Huang, Pao Xu, Ruobo Gu, Junmin Xu, László Orbán, Byrappa Venkatesh, Qiong Shi
Software Mentions: 1
Published: almost 8 years ago

10.1038/sdata.2018.168

Residential wearable RSSI and accelerometer measurements with detailed location annotations
Cited by: 26
Author(s): Dallan Byrne, Michał Kozłowski, Raúl Santos-Rodríguez, Robert J. Piechocki, Ian J Craddock
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2105-7-304

Association algorithm to mine the rules that govern enzyme definition and to classify protein sequences
Cited by: 16
Author(s): Shih‐Hau Chiu, Chien-Chi Chen, Gwo‐Fang Yuan, Thy‐Hou Lin
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2105-12-159

RAPSearch: a fast protein similarity search tool for short reads
Cited by: 115
Author(s): Yuzhen Ye, Jeong Hyeon Choi, Haixu Tang
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2105-8-437

Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors
Cited by: 25
Author(s): Xueping Yu, Chia-Chin Lin, Donald J. Zack, Jiang Qian
Software Mentions: 1
Published: about 17 years ago

10.1038/srep14168

Signatures of selection in tilapia revealed by whole genome resequencing
Cited by: 62
Author(s): Jun Xia, Zhiyi Bai, Zining Meng, Yong Zhang, Le Wang, Feng Liu, Jing Wu, Zi Yi Wan, Jiale Li, Haoran Lin, Gen Hua Yue
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2105-11-256

Binary image representation of a ligand binding site: its application to efficient sampling of a conformational ensemble
Cited by: 2
Author(s): Edon Sung, Sang Soo Kim, Wonjae Shin
Software Mentions: 1
Published: over 14 years ago

10.1107/S0909049509035377

A decade of user operation on the macromolecular crystallography MAD beamline ID14-4 at the ESRF
Cited by: 57
Author(s): A.A. McCarthy, Sándor Brockhauser, Didier Nurizzo, Pascal Théveneau, Trevor Mairs, Darren Spruce, Matias Guijarro, M. Lesourd, Raimond B. G. Ravelli, Seán McSweeney
Software Mentions: 1
Published: about 15 years ago

10.1038/srep28162

Shape and size constraints on dust optical properties from the Dome C ice core, Antarctica
Cited by: 54
Author(s): M. A. C. Potenza, Samuel Albani, Barbara Delmonte, S. Villa, Tiziano Sanvito, B. Paroli, A. Pullia, Giovanni Baccolo, N. M. Mahowald, Valter Maggi
Software Mentions: 1
Published: over 8 years ago

10.1038/srep44041

The redox environment triggers conformational changes and aggregation of hIAPP in Type II Diabetes
Cited by: 68
Author(s): Diana C. Rodriguez Camargo, Konstantinos Tripsianes, Katalin Buday, András Frankó, Christoph Göbl, Christoph Hartlmüller, Riddhiman Sarkar, Michaela Aichler, Gabriele Mettenleiter, Michael Schulz, Annett Böddrich, Christian Erck, Henrik Martens, Axel Walch, Tobias Madl, Erich E. Wanker, Marcus Conrad, Martin Hrabé de Angelis, Bernd Reif
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-05109-2

Order and interactions in DNA arrays: Multiscale molecular dynamics simulation
Cited by: 25
Author(s): Julija Zavadlav, Rudolf Podgornik, Matej Praprotnik
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-13392-2

Climate change-induced increases in precipitation are reducing the potential for solar ultraviolet radiation to inactivate pathogens in surface waters
Cited by: 55
Author(s): Craig E. Williamson, S. Madronich, Aparna Lal, Richard G. Zepp, Robyn Lucas, Erin P. Overholt, Kevin C. Rose, S. Geoffrey Schladow, J. Lee-Taylor
Software Mentions: 1
Published: about 7 years ago

10.3390/ijms12129440

Dynamic Structure-Based Pharmacophore Model Development: A New and Effective Addition in the Histone Deacetylase 8 (HDAC8) Inhibitor Discovery
Cited by: 38
Author(s): Sundarapandian Thangapandian, John Strouboulis, Yuno Lee, Songmi Kim, Keun Woo Lee
Software Mentions: 1
Published: almost 13 years ago

10.1038/s41598-017-17026-5

Resting-state functional MRI reveals altered brain connectivity and its correlation with motor dysfunction in a mouse model of Huntington’s disease
Cited by: 21
Author(s): Qiang Li, Gang Li, Dan Wu, Hanbing Lu, Zhipeng Hou, Christopher A. Ross, Yihong Yang, Jiangyang Zhang, Wenzhen Duan
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-017-17362-6

A Pilot Characterization of the Human Chronobiome
Cited by: 68
Author(s): Carsten Skarke, Nicholas F. Lahens, Seth D. Rhoades, Amy Campbell, Kyle Bittinger, Aubrey Bailey, Christian Hoffmann, Randal S. Olson, Lihong Chen, Guangrui Yang, Thomas S. Price, Jason H. Moore, Frederic D. Bushman, Casey S. Greene, Gregory R. Grant, Aalim M. Weljie, Garret A. FitzGerald
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-29690-2

A Personalized Arrhythmia Monitoring Platform
Cited by: 23
Author(s): Sandeep Raj, Kailash Chandra Ray
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-29900-x

A new quinoline-based chemical probe inhibits the autophagy-related cysteine protease ATG4B
Cited by: 31
Author(s): Damien Bosc, Lubomir Vezenkov, Svetlana Bortnik, Jing An, Jing Xu, Courtney Choutka, Adrienne M. Hannigan, Suzana Kovacic, Sandra K. Loo, Peter G. K. Clark, G. Chen, R. N. Guay-Ross, Kevin Yang, Wieslawa H. Dragowska, F. Zhang, Nancy E. Go, Amy Leung, Nicolette S. Honson, Tom Pfeifer, Martin Gleave, Marcel B. Bally, Steven J.M. Jones, Sharon M. Gorski, Robert N. Young
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-32877-2

Genomic assemblies of newly sequenced Trypanosoma cruzi strains reveal new genomic expansion and greater complexity
Cited by: 50
Author(s): Francisco Callejas-Hernández, Alberto Rastrojo, Cristina Poveda, Núria Gironès, Manuel Fresno
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-018-32912-2

Connectivity of larval stages of sedentary marine communities between hard substrates and offshore structures in the North Sea
Cited by: 26
Author(s): Johan van der Molen, L. García-García, Paul Whomersley, Alexander Callaway, Paulette Posen, Kieran Hyder
Software Mentions: 1
Published: about 6 years ago

10.3390/ijms21186876

The Biocontrol Root-Oomycete, Pythium Oligandrum, Triggers Grapevine Resistance and Shifts in the Transcriptome of the Trunk Pathogenic Fungus, Phaeomoniella Chlamydospora
Cited by: 15
Author(s): Amira Yacoub, Noël Magnin, Jonathan Gerbore, Rana Haidar, Émilie Bruez, Stéphane Compant, Rémy Guyoneaud, Patrice Rey
Software Mentions: 1
Published: about 4 years ago

10.1186/s12859-020-3417-x

Gamevar.f90: a software package for calculating individual gametic diversity
Cited by: 2
Author(s): Daniel Jordan de Abreu Santos, John B. Cole, George E. Liu, P.M. VanRaden, Li Ma
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-019-39477-8

Alignment-free similarity analysis for protein sequences based on fuzzy integral
Cited by: 8
Author(s): Ajay Kumar Saw, Binod Chandra Tripathy, Soumyadeep Nandi
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-40452-6

Alignment-free method for DNA sequence clustering using Fuzzy integral similarity
Cited by: 14
Author(s): Ajay Kumar Saw, Garima Raj, Manashi Das, Narayan Chandra Talukdar, Binod Chandra Tripathy, Soumyadeep Nandi
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2105-11-406

MS4 - Multi-Scale Selector of Sequence Signatures: An alignment-free method for classification of biological sequences
Cited by: 8
Author(s): Eduardo Corel, Florian Pitschi, Ivan Laprevotte, Gilles Grasseau, Gilles Didier, Claudine Devauchelle
Software Mentions: 1
Published: over 14 years ago

10.1186/1748-7188-1-13

A combinatorial optimization approach for diverse motif finding applications
Cited by: 28
Author(s): Elena Zaslavsky, Mona Singh
Software Mentions: 1
Published: over 18 years ago

10.1038/s41598-019-52991-z

Reliable variant calling during runtime of Illumina sequencing
Cited by: 10
Author(s): Tobias P. Loka, Simon H. Tausch, Bernhard Y. Renard
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2105-9-93

Supervised Lowess normalization of comparative genome hybridization data – application to lactococcal strain comparisons
Cited by: 22
Author(s): Sacha A. F. T. van Hijum, Richard J. S. Baerends, Aldert Zomer, Harma Karsens, Victoria Martín-Requena, Oswaldo Trelles, Jan Kok, Oscar P. Kuipers
Software Mentions: 1
Published: almost 17 years ago

10.1038/s41598-020-70028-8

Automated and rapid self-report of nociception in transgenic mice
Cited by: 5
Author(s): Christopher J. Black, Anusha Allawala, Kiernan Bloye, Kevin N Vanent, Muhammad Muzzammil Edhi, Carl Y. Saab, David A. Borton
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-71557-y

The effect on clinical outcomes when targeting spinal manipulation at stiffness or pain sensitivity: a randomized trial
Cited by: 17
Author(s): Casper Glissmann Nim, Gregory N. Kawchuk, Berit Schiøttz‐Christensen, Søren O’Neill
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-020-78118-3

De-novo transcriptome analysis unveils differentially expressed genes regulating drought and salt stress response in Panicum sumatrense
Cited by: 18
Author(s): Rasmita Rani Das, Seema Pradhan, Ajay Parida
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-020-80126-2

Drivers use active gaze to monitor waypoints during automated driving
Cited by: 7
Author(s): Callum Mole, Jami Pekkanen, William E. A. Sheppard, Gustav Markkula, Richard M. Wilkie
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-021-81275-8

Population difference gratings created on vibrational transitions by nonoverlapping subcycle THz pulses
Cited by: 13
Author(s): Р. М. Архипов, А. В. Пахомов, М. В. Архипов, Ihar Babushkin, Ayhan Demircan, Uwe Morgner, N. N. Rosanov
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2105-8-448

PedGenie: meta genetic association testing in mixed family and case-control designs
Cited by: 21
Author(s): Karen Curtin, Jathine Wong, Kristina Allen‐Brady, Nicola J. Camp
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2105-6-139

PentaPlot: A software tool for the illustration of genome mosaicism
Cited by: 6
Author(s): Lutz Hamel, Olga Zhaxybayeva, J. Peter Gogarten
Software Mentions: 1
Published: over 19 years ago

10.1186/1471-2105-13-S3-S12

Genome-scale NCRNA homology search using a Hamming distance-based filtration strategy
Cited by: 4
Author(s): Yanni Sun, Osama Aljawad, Jikai Lei, Alex Liu
Software Mentions: 1
Published: over 12 years ago

10.1038/s41598-021-99123-0

The Drake Passage opening from an experimental fluid dynamics point of view
Cited by: 2
Author(s): Miklós Vincze, Tamás Bozóki, Mátyás Herein, Ion Dan Borcia, Uwe Harlander, Attila Horicsányi, Anita Nyerges, Costanza Rodda, András Pál, József Pálfy
Software Mentions: 1
Published: about 3 years ago