Ecosyste.ms: Papers

10.1186/1471-2105-12-S2-S5

Automatic classification of sentences to support Evidence Based Medicine
Cited by: 149
Author(s): Su Nam Kim, David Martínez, Lawrence Cavedon, Lars Yencken
Software Mentions: 2
Published: over 13 years ago

10.1186/s12859-018-2141-2

A site specific model and analysis of the neutral somatic mutation rate in whole-genome cancer data
Cited by: 9
Author(s): Johanna Bertl, Qianyun Guo, Malene Juul, Søren Besenbacher, Morten Muhlig Nielsen, Henrik Hornshøj, Jakob Skou Pedersen, Asger Hobolth
Software Mentions: 2
Published: over 6 years ago

10.1186/s12859-015-0626-9

BitMapper: an efficient all-mapper based on bit-vector computing
Cited by: 31
Author(s): Haoyu Cheng, Huaipan Jiang, Jiaoyun Yang, Yun Xu, Yi Shang
Software Mentions: 2
Published: over 9 years ago

10.1186/s12859-014-0438-3

Fast inexact mapping using advanced tree exploration on backward search methods
Cited by: 2
Author(s): José Miguel Salavert, Andrés E. Tomás, Joaquín Tárraga, Ignacio Medina, Joaquín Dopazo, Ignácio Blanquer
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12918-018-0587-5

Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa
Cited by: 35
Author(s): Xin Fang, Jonathan M. Monk, Nathan Mih, Bin Du, Anand V. Sastry, Erol Kavvas, Yara Seif, Larry Smarr, Bernhard Ø. Palsson
Software Mentions: 2
Published: over 6 years ago

10.3390/microorganisms8020197

Computational Modeling of the Human Microbiome
Cited by: 21
Author(s): Shomeek Chowdhury, Stephen S. Fong
Software Mentions: 2
Published: almost 5 years ago

10.3390/s20236777

Continual Learning Strategy in One-Stage Object Detection Framework Based on Experience Replay for Autonomous Driving Vehicle
Cited by: 14
Author(s): Jeng-Lun Shieh, Qazi Mazhar ul Haq, Muhamad Amirul Haq, Said Karam, Peter Chondro, De-Qin Gao, Shanq-Jang Ruan
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12915-018-0581-9

Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences
Cited by: 38
Author(s): Cesare de Filippo, Matthias Meyer, Kay Prüfer
Software Mentions: 2
Published: about 6 years ago

10.1007/s11214-020-00788-2

Multi-model Meteorological and Aeolian Predictions for Mars 2020 and the Jezero Crater Region
Cited by: 32
Author(s): C. E. Newman, Manuel de la Torre Juárez, Jorge Pla‐García, R. J. Wilson, S. R. Lewis, L. Neary, M. A. Kahre, F. Forget, Aymeric Spiga, M. I. Richardson, F. Daerden, Tanguy Bertrand, Daniel Viúdez‐Moreiras, R. Sullivan, A. Sánchez‐Lavega, Baptiste Chide, J. A. Rodriguez-Manfredi
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0148031

Integration and Validation of the Genome-Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism
Cited by: 52
Author(s): Màrius Tomàs-Gamisans, Pau Ferrer, Joan Albiol
Software Mentions: 2
Published: almost 9 years ago

10.3390/microorganisms8030437

Genome-Scale Metabolic Model Reconstruction and in Silico Investigations of Methane Metabolism in Methylosinus trichosporium OB3b
Cited by: 18
Author(s): Sanzhar Naizabekov, Eun Yeol Lee
Software Mentions: 2
Published: over 4 years ago

10.1186/s12896-021-00702-w

Genome-scale insights into the metabolic versatility of Limosilactobacillus reuteri
Cited by: 6
Author(s): Hao Luo, Peishun Li, Hao Wang, Stefan Roos, Boyang Ji, Jens Nielsen
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2105-15-100

Adaptable probabilistic mapping of short reads using position specific scoring matrices
Cited by: 43
Author(s): Peter Kerpedjiev, Jes Frellsen, Stinus Lindgreen, Anders Krogh
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0199434

Coexpression network and phenotypic analysis identify metabolic pathways associated with the effect of warming on grain yield components in wheat
Cited by: 17
Author(s): Christine Girousse, Jane Roche, Claire Guérin, Jacques Le Gouis, Sandrine Balzegue, Saïd Mouzeyar, Mohamed Fouad Bouzidi
Software Mentions: 2
Published: over 6 years ago

10.1186/1752-0509-8-41

Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction
Cited by: 82
Author(s): Ibrahim E. Elsemman, Fredrik Karlsson, Saeed Shoaie, Intawat Nookaew, Taysir Hassan A. Soliman, Jens Nielsen
Software Mentions: 2
Published: over 10 years ago

10.1186/1752-0509-6-55

Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network
Cited by: 131
Author(s): Benjamin D. Heavner, Kieran Smallbone, Brandon Barker, Pedro Mendes, Larry P. Walker
Software Mentions: 2
Published: over 12 years ago

10.18632/oncotarget.24228

Discovery and validation of a glioblastoma co-expressed gene module
Cited by: 8
Author(s): Leland J. Dunwoodie, William L. Poehlman, Stephen P. Ficklin, Frank Alexander Feltus
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12939-019-1000-8

Scenarios for population health inequalities in 2030 in Europe: the EURO-HEALTHY project experience
Cited by: 9
Author(s): Antônio de Pádua Alvarenga, Carlos A. Bana e Costa, Carme Borrell, Pedro Lopes Ferreira, Ângela Freitas, Liliana Freitas, Mónica Duarte Oliveira, T. Rodrigues, Paula Santana, Maria Cristina Santos, A. Vieira
Software Mentions: 2
Published: over 5 years ago

10.3390/metabo11090606

Next-Generation Genome-Scale Metabolic Modeling through Integration of Regulatory Mechanisms
Cited by: 15
Author(s): Carolina H Chung, Dawei Lin, Alec Eames, Sriram Chandrasekaran
Software Mentions: 2
Published: about 3 years ago

10.1186/1476-072X-13-25

Methods to measure potential spatial access to delivery care in low- and middle-income countries: a case study in rural Ghana
Cited by: 74
Author(s): Robin Nesbitt, Sabine Gabrysch, Alexandra Laub, Seyi Soremekun, Alexander Manu, Betty Kirkwood, Seeba Amenga‐Etego, Kenneth Wiru, Bernhard Höfle, Chris Grundy
Software Mentions: 2
Published: almost 11 years ago

10.2196/20713

Blockchain Applications in Health Care and Public Health: Increased Transparency
Cited by: 13
Author(s): Pedro Elkind Velmovitsky, Frederico M. Bublitz, Laura Xavier Fadrique, Plinio Pelegrini Morita
Software Mentions: 2
Published: over 3 years ago

10.3390/ijerph17103569

Epigenome-Wide Association Study Reveals Duration of Breastfeeding Is Associated with Epigenetic Differences in Children
Cited by: 12
Author(s): William B. Sherwood, Dilini M. Kothalawala, Latha Kadalayil, Susan Ewart, Hongmei Zhang, Wilfried Karmaus, Syed Hasan Arshad, John W. Holloway, Faisal I. Rezwan
Software Mentions: 2
Published: over 4 years ago

10.1093/bioinformatics/btw336

Zerone: a ChIP-seq discretizer for multiple replicates with built-in quality control
Cited by: 12
Author(s): Pol Cuscó, Guillaume J. Filion
Software Mentions: 2
Published: over 8 years ago

10.1093/bioinformatics/bty648

Scaling read aligners to hundreds of threads on general-purpose processors
Cited by: 381
Author(s): Ben Langmead, Christopher Wilks, Valentin Antonescu, Rone Charles
Software Mentions: 2
Published: over 6 years ago

10.3390/metabo9050081

The Fate of Glutamine in Human Metabolism. The Interplay with Glucose in Proliferating Cells
Cited by: 20
Author(s): Jean‐Pierre Mazat, Stéphane Ransac
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-018-5376-4

GOPHER: Generator Of Probes for capture Hi-C Experiments at high Resolution
Cited by: 9
Author(s): Peter J. Hansen, Salaheddine Ali, Hannah Blau, Daniel Daniš, Jochen Hecht, Uwe Kornak, Darío G. Lupiáñez, Stefan Mundlos, Robin Steinhaus, Peter N. Robinson
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0138030

msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding
Cited by: 37
Author(s): Anil Raj, Heejung Shim, Yoav Gilad, Jonathan K. Pritchard, Matthew Stephens
Software Mentions: 2
Published: about 9 years ago

10.1002/cam4.2764

Identification of chemoresistance‐related mRNAs based on gemcitabine‐resistant pancreatic cancer cell lines
Cited by: 14
Author(s): Jiarong Zhou, Linshi Zhang, Huilin Zheng, Weifeng Ge, Yu Huang, Yu Yan, Xin Zhou, Wei Zhu, Yahui Kong, Yuan Ding, Weilin Wang
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0183081

Whole exome sequencing as a diagnostic tool for patients with ciliopathy-like phenotypes
Cited by: 8
Author(s): Sheila Castro-Sánchez, María Álvarez-Satta, M.A. Tohamy, Sergi Beltrán, Sophia Derdak, Diana Valverde
Software Mentions: 2
Published: over 7 years ago

10.1186/s13072-017-0165-x

Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning
Cited by: 17
Author(s): Gabriel Gutiérrez, Gonzalo Millán-Zambrano, Daniel A. Medina, Antonio Jordán-Pla, Jose E. Pérez-Ortı́n, Xenia Peñate, Sebastián Chávez
Software Mentions: 2
Published: almost 7 years ago

10.1093/bib/bbt081

A bioinformatician's guide to the forefront of suffix array construction algorithms
Cited by: 30
Author(s): Anish Man Singh Shrestha, Martin C. Frith, Paul Horton
Software Mentions: 2
Published: almost 11 years ago

10.1093/database/bat059

Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance
Cited by: 85
Author(s): Benjamin D. Heavner, Kieran Smallbone, Nathan D. Price, Larry P. Walker
Software Mentions: 2
Published: almost 12 years ago

10.3390/ijms19082191

Mesotheliomas in Genetically Engineered Mice Unravel Mechanism of Mesothelial Carcinogenesis
Cited by: 10
Author(s): Didier Jean, Marie‐Claude Jaurand
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0179411

Differential chromatin profiles partially determine transcription factor binding
Cited by: 4
Author(s): Rujian Chen, David K. Gifford
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pcbi.1002335

Protein Design Using Continuous Rotamers
Cited by: 87
Author(s): Pablo Gainza, Kyle E. Roberts, Bruce Randall Donald
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12859-021-04097-5

A flexible ChIP-sequencing simulation toolkit
Cited by: 4
Author(s): An Zheng, Michael Lamkin, Yutong Qiu, Kevin Ren, Alon Goren, Melissa Gymrek
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-019-2849-7

Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets
Cited by: 76
Author(s): Tobias Neumann, Veronika A. Herzog, Matthias Muhar, Arndt von Haeseler, Johannes Zuber, Stefan L. Ameres, Philipp Rescheneder
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1009447

A heterochromatin inducing protein differentially recognizes self versus foreign genomes
Cited by: 7
Author(s): Eric Burton, Ibukun A. Akinyemi, Tiffany R. Frey, Huanzhou Xu, Xiaofan Li, Lai Jing Su, Jizu Zhi, Michael T. McIntosh, Sumita Bhaduri‐McIntosh
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms22115914

Inferring Single-Cell 3D Chromosomal Structures Based on the Lennard-Jones Potential
Cited by: 1
Author(s): mengsheng zha, Nan Wang, Chaoyang Zhang, Zheng Wang
Software Mentions: 2
Published: over 3 years ago

10.1186/s13073-014-0067-5

VISPA: a computational pipeline for the identification and analysis of genomic vector integration sites
Cited by: 21
Author(s): Andrea Calabria, Simone Leo, Fabrizio Benedicenti, Daniela Cesana, Giulio Spinozzi, Massimilano Orsini, Stefania Merella, Elia Stupka, Gianluigi Zanetti, Eugenio Montini
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pgen.1008931

Impact of insertion sequences on convergent evolution of Shigella species
Cited by: 37
Author(s): Jane Hawkey, Jonathan M. Monk, Helen Billman‐Jacobe, Jaehyung Kim, Kathryn E. Holt
Software Mentions: 2
Published: over 4 years ago

10.1186/s13059-014-0553-5

Evaluation of de novo transcriptome assemblies from RNA-Seq data
Cited by: 230
Author(s): Bo Li, Nathanael Fillmore, Yongsheng Bai, M. J. Collins, James A. Thomson, Ron Stewart, Colin N. Dewey
Software Mentions: 2
Published: almost 10 years ago

10.1155/2014/675158

Defining Loci in Restriction-Based Reduced Representation Genomic Data from Nonmodel Species: Sources of Bias and Diagnostics for Optimal Clustering
Cited by: 84
Author(s): Daniel C. Ilut, Marie L. Nydam, Matthew P. Hare
Software Mentions: 2
Published: almost 11 years ago

10.3390/cells10020397

DVDeconv: An Open-Source MATLAB Toolbox for Depth-Variant Asymmetric Deconvolution of Fluorescence Micrographs
Cited by: 2
Author(s): Boyoung Kim
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12859-016-0957-1

Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection
Cited by: 4
Author(s): Qi Zhang, Xin Zeng, Samuel G. Younkin, Trupti Kawli, M Snyder, Sündüz Keleş
Software Mentions: 2
Published: over 8 years ago

10.1186/s12284-016-0130-5

Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions
Cited by: 30
Author(s): Juan Luis Reig-Valiente, Juan Viruel, Ester Sales, Luis Marqués, Javier Terol, Marta Gut, Sophia Derdak, Manuel Talón, Concha Domingo
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2164-15-633

Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?
Cited by: 4
Author(s): Verónica Lloréns‐Rico, Luís Serrano, María Lluch‐Senar
Software Mentions: 2
Published: over 10 years ago

10.7717/peerj.7015

Metabolic traits specific for lipid-overproducing strain of <i>Mucor circinelloides</i> WJ11 identified by genome-scale modeling approach
Cited by: 3
Author(s): Nattapat Isarankura Na Ayudhya, Kobkul Laoteng, Yuanda Song, Asawin Meechai, Wanwipa Vongsangnak
Software Mentions: 2
Published: over 5 years ago

10.1186/s12859-018-2094-5

Fast and efficient short read mapping based on a succinct hash index
Cited by: 16
Author(s): Haowen Zhang, Yuandong Chan, Kaichao Fan, Bertil Schmidt, Weiguo Liu
Software Mentions: 2
Published: over 6 years ago

10.1186/1472-6947-12-128

A study of diverse clinical decision support rule authoring environments and requirements for integration
Cited by: 18
Author(s): Li Zhou, Neelima Karipineni, Janet Lewis, Saverio M. Maviglia, Amanda Fairbanks, Tonya Hongsermeier, Blackford Middleton, Roberto A. Rocha
Software Mentions: 2
Published: about 12 years ago

10.1128/mSystems.01351-20

Genome-Scale Metabolic Model of <i>Caldicellulosiruptor bescii</i> Reveals Optimal Metabolic Engineering Strategies for Bio-based Chemical Production
Cited by: 3
Author(s): Ke Zhang, Weishu Zhao, Dmitry A. Rodionov, Gabriel M. Rubinstein, Diep N. Nguyen, Tania N. N. Tanwee, James R. Crosby, Ryan G. Bing, Robert M. Kelly, Michael W. W. Adams, Ying Zhang
Software Mentions: 1
Published: over 3 years ago

10.1002/2017JB014394

Apparent Splitting of <i>S</i> Waves Propagating Through an Isotropic Lowermost Mantle
Cited by: 17
Author(s): Laura Parisi, Ana M. G. Ferreira, Jeroen Ritsema
Software Mentions: 1
Published: over 6 years ago

10.7554/eLife.25157

Evolution of reduced co-activator dependence led to target expansion of a starvation response pathway
Cited by: 17
Author(s): Bin He, Xu Zhou, Erin K. O’Shea
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.23907

Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate
Cited by: 60
Author(s): Chungang Feng, Mats E. Pettersson, Sangeet Lamichhaney, Carl-Johan Rubin, Nima Rafati, Michèle Casini, Arild Folkvord, Leif Andersson
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.02028

The translational landscape of the splicing factor SRSF1 and its role in mitosis
Cited by: 90
Author(s): Magdalena M. Maslon, Sara R. Heras, Nicolás Bellora, Eduardo Eyras, Javier F. Cáceres
Software Mentions: 1
Published: over 10 years ago

10.3390/ijms21072308

Added Value of Clinical Sequencing: WGS-Based Profiling of Pharmacogenes
Cited by: 25
Author(s): Sylvan M. Caspar, Timo Schneider, Janine Meienberg, Gábor Mátyás
Software Mentions: 1
Published: over 4 years ago

10.2196/jmir.9268

Prediction of Incident Hypertension Within the Next Year: Prospective Study Using Statewide Electronic Health Records and Machine Learning
Cited by: 134
Author(s): Chengyin Ye, Tianyun Fu, Shiying Hao, Yan Zhang, Oliver Wang, Bo Jin, Minjie Xia, Modi Liu, Xin Zhou, Qian Wu, Guo Yang, Chunqing Zhu, Yuming Li, Devore S Culver, Shaun T Alfreds, Frank Stearns, Karl G. Sylvester, Eric Widen, Doff B. McElhinney, Xuefeng B. Ling
Software Mentions: 1
Published: almost 7 years ago

10.2196/jmir.7638

Psychometric Properties of Patient-Facing eHealth Evaluation Measures: Systematic Review and Analysis
Cited by: 28
Author(s): Bonnie J. Wakefield, Carolyn Turvey, Kim M. Nazi, John E. Holman, Timothy P. Hogan, Stephanie L. Shimada, Diana Kennedy
Software Mentions: 1
Published: about 7 years ago

10.18632/oncotarget.20445

The efficacy and safety of different pharmacological interventions for patients with advanced biliary tract cancer: A network meta-analysis
Cited by: 2
Author(s): Xin-Fang Sun, Zhikuan He, Jinping Sun, Quan-Xing Ge, Erdong Shen
Software Mentions: 1
Published: about 7 years ago

10.18632/oncotarget.22795

A multicenter prospective phase II study of first-line modified FOLFIRINOX for unresectable advanced pancreatic cancer
Cited by: 36
Author(s): Kensaku Yoshida, Takuji Iwashita, Shiro Uemura, Akinori Maruta, Mitsuru Okuno, Nobuhiro Ando, Koichi Iwata, Jyunji Kawaguchi, Tsuyoshi Mukai, Masahito Shimizu
Software Mentions: 1
Published: almost 7 years ago

10.18632/oncotarget.25862

Deep analysis of acquired resistance to FGFR1 inhibitor identifies MET and AKT activation and an expansion of <i>AKT1</i> mutant cells
Cited by: 7
Author(s): Pol Giménez-Xavier, Eva Pros, Ana Aza, Sebastian Morán, Raúl Tonda, Anna Esteve‐Codina, Marc Dabad, Montse Sanchez-Cespedes
Software Mentions: 1
Published: over 6 years ago

10.1098/rsob.180098

Reproducibility of academic preclinical translational research: lessons from the development of Hedgehog pathway inhibitors to treat cancer
Cited by: 24
Author(s): Tom Curran
Software Mentions: 1
Published: over 6 years ago

10.1155/2021/6610500

Ngaa-bi-nya-nhumi-nya (to Test First): Piloting the Feasibility of Using the Growth and Empowerment Measure with Aboriginal Pregnant Women Who Smoke
Cited by: 1
Author(s): Michelle Bovill, Yael Bar‐Zeev, Billie Bonevski, Jennifer Reath, Christopher Oldmeadow, Alix Hall, Gillian Sandra Gould
Software Mentions: 1
Published: almost 4 years ago

10.1186/1750-1172-9-57

Phenotype and frequency of STUB1 mutations: next-generation screenings in Caucasian ataxia and spastic paraplegia cohorts
Cited by: 51
Author(s): Matthis Synofzik, Rebecca Schüle, Martin Schulze, Janina Gburek‐Augustat, Roland Schweizer, Anja Schirmacher, Ingeborg Krägeloh‐Mann, Michael Gonzalez, Peter Young, Stephan Züchner, Lüdger Schöls, Péter Bauer
Software Mentions: 1
Published: almost 11 years ago

10.1186/1750-1172-9-59

Assessment of a targeted resequencing assay as a support tool in the diagnosis of lysosomal storage disorders
Cited by: 39
Author(s): Ana Fernández–Marmiesse, Marcos Morey, Merçè Pineda, Jesús Eirís-Puñal, María L. Couce, Manuel Castro-Gago, José M. Fraga, Lúcia Lacerda, Sofía Gouveia, María S. Pérez-Poyato, Judith Armstrong, Daisy Castiñeiras, José A. Cocho
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12967-014-0277-z

Future perspectives in melanoma research: meeting report from the "Melanoma Bridge", Napoli, December 5th-8th 2013
Cited by: 13
Author(s): Paolo A. Ascierto, Antonio Grimaldi, Ana C. Anderson, Carlo Bifulco, Alistair J. Cochran, Claus Garbe, Alexander M.M. Eggermont, Mark B. Faries, Soldano Ferrone, Jeffrey E. Gershenwald, Thomas F. Gajewski, Ruth Halaban, F. Stephen Hodi, Richard Kefford, John M. Kirkwood, James Larkin, Sancy A. Leachman, Michele Maio, Richard Marais, Giuseppe Masucci, Ignacio Melero, Giuseppe Palmieri, Igor Puzanov, Antoni Ribas, Yvonne M. Saenger, Bastian Schilling, Barbara Seliger, David F. Stroncek, Ryan J. Sullivan, Alessandro Testori, Ena Wang, Gennaro Ciliberto, Nicola Mozzillo, Francesco M. Marincola, Magdalena Thurin
Software Mentions: 1
Published: about 10 years ago

10.3390/nu9101052

Mediterranean Diet and Multi-Ingredient-Based Interventions for the Management of Non-Alcoholic Fatty Liver Disease
Cited by: 67
Author(s): Manuel Suárez, Noemí Boqué, Josep Maria del Bas, Jordi Mayneris‐Perxachs, Lluı́s Arola, Antoni Caimari
Software Mentions: 1
Published: about 7 years ago

10.3389/fcell.2021.701175

Interactions and Feedbacks in E-Cadherin Transcriptional Regulation
Cited by: 9
Author(s): Miguel Ramírez Moreno, Przemyslaw Stempor, Natalia A. Bulgakova
Software Mentions: 1
Published: over 3 years ago

10.1002/advs.202100199

Synthetic Formatotrophs for One‐Carbon Biorefinery
Cited by: 12
Author(s): Bang Junho, Jung Ho Ahn, Jong An Lee, Chang Hun Hwang, Gi Bae Kim, Jinwon Lee, Sang Yup Lee
Software Mentions: 1
Published: over 3 years ago

10.1002/advs.202003327

Nanocomposite Hydrogel with Tantalum Microparticles for Rapid Endovascular Hemostasis
Cited by: 22
Author(s): Hassan Albadawi, İzzet Altun, Jingjie Hu, Zefu Zhang, Anshuman Panda, Hanjun Kim, Ali Khademhosseini, Rahmi Öklü
Software Mentions: 1
Published: almost 4 years ago

10.1155/2012/419348

Preclinical Remodeling of Human Prostate Cancer through the PTEN/AKT Pathway
Cited by: 14
Author(s): Marco A. De Velasco, Hirotsugu Uemura
Software Mentions: 1
Published: almost 13 years ago

10.1007/s11869-021-01039-1

Isolating the impact of COVID-19 lockdown measures on urban air quality in Canada
Cited by: 14
Author(s): Rabab Mashayekhi, Radenko Pavlovic, Jacinthe Racine, Michael D. Moran, Patrick M. Manseau, A. Duhamel, Ali Katal, Jessica Miville, David Niemi, Si Jun Peng, Mourad Sassi, Debora Griffin, Chris A. McLinden
Software Mentions: 1
Published: over 3 years ago

10.1007/s13280-016-0860-z

Foreword: Synthesis of the Greenland Ecosystem Monitoring program
Cited by: 14
Author(s): Torben R. Christensen, Elmer Topp-Jørgensen, Mikael K. Sejr, Niels Martin Schmidt
Software Mentions: 1
Published: almost 8 years ago

10.1007/s13280-016-0871-9

Postscript: The future of the Greenland Ecosystem Monitoring programme
Cited by: 1
Author(s): Torben R. Christensen, Elmer Topp-Jørgensen, Mikael K. Sejr, Niels Martin Schmidt
Software Mentions: 1
Published: almost 8 years ago

10.1007/s13280-016-0876-4

Towards quantifying the glacial runoff signal in the freshwater input to Tyrolerfjord–Young Sound, NE Greenland
Cited by: 16
Author(s): Michele Citterio, Mikael K. Sejr, Peter L. Langen, Ruth Mottram, Jakob Abermann, Signe Hillerup Larsen, Kirstine Skov, Magnus Lund
Software Mentions: 1
Published: almost 8 years ago

10.3390/ani1010007

An International Comparison of Female and Male Students’ Attitudes to the Use of Animals
Cited by: 87
Author(s): Clive J. C. Phillips, Serdar İzmirli, Javid Aldavood, Marta Elena Alonso, B I Choe, Alison Hanlon, Anastasija Handziska, Gudrun Illmann, Linda J. Keeling, Mark Kennedy, Gwi Lee, Vonne Lund, Cecilie Marie Mejdell, Veselinas Radanov Pelagic, Therese Rehn
Software Mentions: 1
Published: almost 14 years ago

10.5194/acp-21-951-2021

Aircraft-based inversions quantify the importance of wetlands and livestock for Upper Midwest methane emissions
Cited by: 10
Author(s): Xueying Yu, Dylan B. Millet, Kelley C. Wells, D. K. Henze, Hansen Cao, Timothy J. Griffis, E. A. Kort, Genevieve Plant, M. J. Deventer, Randall K. Kolka, Daniel T. Roman, Kenneth J. Davis, Ankur R. Desai, Bianca C. Baier, Kathryn McKain, Alan C. Czarnetzki, A. Anthony Bloom
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12859-017-1471-9

A computational method for estimating the PCR duplication rate in DNA and RNA-seq experiments
Cited by: 21
Author(s): Vikas Bansal
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2105-13-S5-S4

Multi-dimensional characterization of electrostatic surface potential computation on graphics processors
Cited by: 3
Author(s): Mayank Daga, Wu-chun Feng
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2105-7-168

GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes
Cited by: 42
Author(s): Kazuharu Arakawa, Yasuaki Yamada, Kosaku Shinoda, Yoichi Nakayama, Masaru Tomita
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2105-15-42

Improving read mapping using additional prefix grams
Cited by: 18
Author(s): Jongik Kim, Chen Li, Xiaohui Xie
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12859-015-0533-0

A Long Fragment Aligner called ALFALFA
Cited by: 11
Author(s): Michaël Vyverman, Bernard De Baets, Veerle Fack, Peter Dawyndt
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2105-12-8

Flexible taxonomic assignment of ambiguous sequencing reads
Cited by: 24
Author(s): José C. Clemente, Jesper Jansson, Gabriel Valiente
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12859-019-2827-0

Pairwise alignment of nucleotide sequences using maximal exact matches
Cited by: 4
Author(s): Arash Bayat, Bruno Gaëta, Aleksandar Ignjatović, Sri Parameswaran
Software Mentions: 1
Published: over 5 years ago

10.1186/s12872-018-0912-3

Coronary calcium score improves the estimation for pretest probability of obstructive coronary artery disease and avoids unnecessary testing in individuals at low extreme of traditional risk factor burden: validation and comparison of CONFIRM score and genders extended model
Cited by: 9
Author(s): Minghui Wang, Yujie Liu, Xiujun Zhou, Jia Zhou, Hong Zhang, Ying Zhang
Software Mentions: 1
Published: about 6 years ago

10.1186/s12873-019-0286-6

Towards developing a consensus assessment framework for global emergency medicine fellowships
Cited by: 5
Author(s): Haiko Kurt Jahn, James Kwan, Gerard O’Reilly, Heike Geduld, Katherine Douglass, Andrea G. Tenner, Lee Wallis, Janis P. Tupesis, Hani Mowafi
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-230X-13-134

Improvement of long-term outcomes in pancreatic cancer and its associated factors within the gemcitabine era: a collaborative retrospective multicenter clinical review of 1,082 patients
Cited by: 30
Author(s): Taira Kuroda, Teru Kumagi, Tomoyuki Yokota, Hirotaka Seike, Mari Nishiyama, Yusuke Imai, Nobu Inada, Naozumi Shibata, Satoshi Imamine, Shinichi Okada, Masaru Koizumi, Hirofumi Yamanishi, Nobuaki Azemoto, Jiro Miyaike, Yoshinori Tanaka, Haruka Tatsukawa, Hiroki Utsunomiya, Yoshinori Ohno, Teruki Miyake, Masashi Hirooka, Shinya Furukawa, Masanori Abe, Yoshiou Ikeda, Bunzo Matsuura, Yoichi Hiasa, Morikazu Onji
Software Mentions: 1
Published: about 11 years ago

10.1186/s12864-015-1548-7

Genomic characterization of mutant laboratory mouse strains by exome sequencing and annotation lift-over
Cited by: 0
Author(s): Sophia Derdak, Sibylle Sabrautzki, Martin Hrabé de Angelis, Marta Gut, Ivo Gut, Sergi Beltrán
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-14-536

Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome
Cited by: 132
Author(s): Kraig R. Stevenson, Joseph D. Coolon, Patricia J. Wittkopp
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-14-363

The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild
Cited by: 45
Author(s): Javier Prado-Martinez, Irene Hernando-Herraez, Belén Lorente-Galdós, Marc Dabad, Óscar Ramírez, Carlos Baeza-Delgado, Carlos Morcillo-Suárez, Can Alkan, Fereydoun Hormozdiari, Emanuele Raineri, Jordi Estellé, Marcos Fernández-Callejo, Mònica Vallès, Lars Ritscher, Torsten Schöneberg, Elisa de la Calle‐Mustienes, Sònia Casillas, Raquel Rubio-Acero, Marta Melé, Johannes Engelken, Mario Cáceres, José Luis Gómez-Skármeta, Marta Gut, Jaume Bertranpetit, Teresa Abelló, Evan E. Eichler, Ismael Mingarro, Carles Lalueza-Fox, Arcadi Navarro, Tomàs Marquès‐Bonet
Software Mentions: 1
Published: over 11 years ago

10.1186/s12864-019-5642-0

A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds
Cited by: 146
Author(s): Andreas Wållberg, Ignas Bunikis, Olga Vinnere Pettersson, Mai Britt Mosbech, Anna K. Childers, Jay D. Evans, Alexander S. Mikheyev, Hugh M. Robertson, Gene E. Robinson, Matthew T. Webster
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-016-2972-z

Identification of protein-damaging mutations in 10 swine taste receptors and 191 appetite-reward genes
Cited by: 5
Author(s): Alex Clop, A. Sharaf, Anna Castelló, Sebastián E. Ramos-Onsins, Susanna Cirera, A. Mercadé, Sophia Derdak, Sergi Beltrán, Abe Huisman, Merete Fredholm, Pieter Van As, Armand Sánchez
Software Mentions: 1
Published: about 8 years ago

10.1186/s12913-018-2834-2

Development of a 5As-based technology-assisted weight management intervention for veterans in primary care
Cited by: 9
Author(s): Katrina F. Mateo, Natalie B. Berner, Natalie L. Ricci, Pich Seekaew, Sandeep Sikerwar, Craig Tenner, Joanna Dognin, Scott E. Sherman, Adina Kalet, Melanie Jay
Software Mentions: 1
Published: almost 7 years ago

10.1186/1472-6963-12-67

Integrating a health-related-quality-of-life module within electronic health records: a comparative case study assessing value added
Cited by: 5
Author(s): Christopher M. Shea, Jacqueline R. Halladay, David Reed, Timothy P. Daaleman
Software Mentions: 1
Published: over 12 years ago

10.1186/1472-6920-12-124

Profiling strugglers in a graduate-entry medicine course at Nottingham: a retrospective case study
Cited by: 16
Author(s): Paul Garrud, J. K. Yates
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12909-020-02405-w

Factors influencing specialty choice and the effect of recall bias on findings from Irish medical graduates: a cross-sectional, longitudinal study
Cited by: 6
Author(s): Frances Cronin, Nick Clarke, Louise Hendrick, Ronàn Conroy, Ruairı́ Brugha
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12909-021-02634-7

Listening to student voice-understanding student and faculty experience at two UK graduate entry programmes
Cited by: 0
Author(s): M. Abdulhadi Alagha, Linda Jones
Software Mentions: 1
Published: over 3 years ago

10.1186/1472-6947-8-41

Non-compliance with a postmastectomy radiotherapy guideline: Decision tree and cause analysis
Cited by: 8
Author(s): Amir Reza Razavi, Hans Gill, Hans Åhlfeldt, Nosrat Shahsavar
Software Mentions: 1
Published: about 16 years ago

10.1186/s12911-016-0253-z

Leveraging workflow control patterns in the domain of clinical practice guidelines
Cited by: 14
Author(s): Katharina Kaiser, Mar Marcos
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2288-11-92

The Global Evidence Mapping Initiative: Scoping research in broad topic areas
Cited by: 198
Author(s): Peter Bragge, Ornella Clavisi, Tari Turner, Emma Tavender, Alex Collie, Russell L. Gruen
Software Mentions: 1
Published: over 13 years ago