cran: ABACUS | Projects | Ecosyste.ms: Papers

10.26508/lsa.202000658

Predicting gene regulatory networks from cell atlases
Cited by: 7
Author(s): Andreas Fønss Møller, Kedar Nath Natarajan
Software Mentions: 9
Published: about 4 years ago

Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling
Cited by: 0
Author(s): Rosario M. Piro, Stefan Wiesberg, Gunnar Schramm, Nico Rebel, Marcus Oswald, Roland Eils, Gerhard Reinelt, Rainer König
Software Mentions: 5
Published: over 10 years ago

10.1007/s10858-018-0220-3

NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments
Cited by: 28
Author(s): Eldon L. Ulrich, Kumaran Baskaran, Hesam Dashti, Yannis Ioannidis, Miron Livny, Pedro Romero, Dimitri Maziuk, Jonathan R. Wedell, Hongyang Yao, Hamid R. Eghbalnia, Jeffrey C. Hoch, John L. Markley
Software Mentions: 4
Published: almost 6 years ago

10.7554/eLife.01739

FRET-based reporters for the direct visualization of abscisic acid concentration changes and distribution in Arabidopsis
Cited by: 198
Author(s): Rainer Waadt, Katsundo Hitomi, Noriyuki Nishimura, Chiharu Hitomi, Stephen Adams, Elizabeth D. Getzoff, Julian I. Schroeder
Software Mentions: 2
Published: over 10 years ago

10.7717/peerj.806

Population structure of<i>Neisseria gonorrhoeae</i>based on whole genome data and its relationship with antibiotic resistance
Cited by: 67
Author(s): Matthew Ezewudo, Sandeep J. Joseph, Santiago Castillo-Ramírez, Deborah Dean, Carlos del Rı́o, Xavier Didelot, Jo-Anne R. Dillon, Richard F. Selden, William M. Shafer, Rosemary S. Turingan, Magnus Unemo, Timothy D. Read
Software Mentions: 2
Published: over 9 years ago

10.1186/1759-4499-2-1

Towards Robot Scientists for autonomous scientific discovery
Cited by: 97
Author(s): Andrew C. Sparkes, Wayne Aubrey, Emma Byrne, Amanda Clare, M. N. A. Khan, Maria Liakata, Magdalena Markham, Jem J. Rowland, Larisa Soldatova, Kenneth Edward Whelan, Michael J. Young, Ross D. King
Software Mentions: 2
Published: almost 15 years ago

10.1186/gb-2008-9-4-r63

Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays
Cited by: 36
Author(s): Shin Lin, Benilton Carvalho, David J. Cutler, Dan E. Arking, Aravinda Chakravarti, Rafael A. Irizarry
Software Mentions: 2
Published: almost 17 years ago

10.1186/s12889-017-4224-9

A cross-sectional survey assessing factors associated with reading cancer screening information: previous screening behaviour, demographics and decision-making style
Cited by: 18
Author(s): Alex Ghanouni, Cristina Renzi, Jo Waller
Software Mentions: 1
Published: over 7 years ago

10.1186/s12889-020-09243-x

Community knowledge and practices regarding antibiotic use in rural Mozambique: where is the starting point for prevention of antibiotic resistance?
Cited by: 28
Author(s): Olga Cambaco, Yara Alonso, John Kinsman, Betuel Sigaúque, Heiman Wertheim, Nga Do, Margaret Gyapong, Johannes John-Langba, Esperança Sevene, Khátia Munguambe
Software Mentions: 1
Published: over 4 years ago

10.3390/medicina57080769

Neoadjuvant Immunotherapy for Muscle-Invasive Bladder Cancer
Cited by: 18
Author(s): A. Peyrottes, I. Ouzaïd, Gianluigi Califano, Jean-François Hermieu, Évanguelos Xylinas
Software Mentions: 1
Published: over 3 years ago

10.1186/1476-4598-5-73

Mitochondrial DNA mutations in preneoplastic lesions of the gastrointestinal tract: A biomarker for the early detection of cancer
Cited by: 58
Author(s): Guoping Sui, Shaoyu Zhou, Jean Wang, Marcia Irene Canto, Edward E. Lee, James R. Eshleman, Elizabeth A. Montgomery, David Sidransky, Joseph A. Califano, Anirban Maitra
Software Mentions: 1
Published: almost 18 years ago

10.1038/msb.2013.26

The functional interactome landscape of the human histone deacetylase family
Cited by: 241
Author(s): Preeti Joshi, Todd M. Greco, Amanda J. Guise, Yang Luo, Fang Yu, Alexey I. Nesvizhskii, Ileana M. Cristea
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12985-018-1094-4

Treatment of hepatitis C virus genotype 4 in the DAA era
Cited by: 16
Author(s): Antonio Di Biagio, Lucia Taramasso, Giovanni Cenderello
Software Mentions: 1
Published: almost 6 years ago

10.12688/wellcomeopenres.11985.1

Community-level antibiotic access and use (ABACUS) in low- and middle-income countries: Finding targets for social interventions to improve appropriate antimicrobial use – an observational multi-centre study
Cited by: 18
Author(s): Heiman Wertheim, Nguyễn Thị Kim Chúc, Sureeporn Punpuing, Wasif Ali Khan, Margaret Gyapong, Kwaku Poku Asante, Khátia Munguambe, F. Xavier Gómez‐Olivé, Proochista Ariana, Johannes John-Langba, Betuel Sigaúque, Trần Khánh Toàn, Stephen Tollman, Amelieke J. H. Cremers, Nga T. T., Behzad Nadjm, H. Rogier van Doorn, John Kinsman, Osman Sankoh
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0000917

Persistent Infection and Promiscuous Recombination of Multiple Genotypes of an RNA Virus within a Single Host Generate Extensive Diversity
Cited by: 49
Author(s): Ziming Weng, Roger A. Barthelson, Siddarame Gowda, Mark E. Hilf, William O. Dawson, David W. Galbraith, Xiong Zhou
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pone.0027894

Mutation Screening of Multiple Genes in Spanish Patients with Autosomal Recessive Retinitis Pigmentosa by Targeted Resequencing
Cited by: 38
Author(s): María González del Pozo, Salud Borrego, Isabel Barragán, Juan Ignacio Pieras, Javier Santoyo, Nerea Matamala, Belén Naranjo, Joaquı́n Dopazo, Guillermo Antiñolo
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0077020

Solution NMR Structure and Histone Binding of the PHD Domain of Human MLL5
Cited by: 25
Author(s): Alexander Lemak, Adelinda Yee, Hong Wu, Damian Yap, Hong Zeng, L. Dombrovski, Scott Houliston, Samuel Aparicio, C.H. Arrowsmith
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0015243

Reconstructed Ancestral Sequences Improve Pathogen Identification Using Resequencing DNA Microarrays
Cited by: 5
Author(s): Nicolás Berthet, Alexis Delétoile, Virginie Passet, Giulia C. Kennedy, Jean-Claude Manuguerra, Stewart T. Cole, Sylvain Brisse
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0109301

Resequencing Microarray Technology for Genotyping Human Papillomavirus in Cervical Smears
Cited by: 3
Author(s): Nicolás Berthet, Michaël Falguières, Claudia Filippone, Chloé Bertolus, Christine Bôle‐Feysot, Sylvain Brisse, Antoine Gessain, Isabelle Heard, Michel Favre
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0104694

Mitochondriome and Cholangiocellular Carcinoma
Cited by: 12
Author(s): Wesam Bahitham, Xiaoping Liao, Fred Y. Peng, Fiona Bamforth, Alicia Chan, Andrew L. Mason, Bradley R. Stone, Paul Stothard, Consolato Sergi
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0008493

Mitochondrial Mutations in Adenoid Cystic Carcinoma of the Salivary Glands
Cited by: 21
Author(s): Suhail K. Mithani, Chunbo Shao, Marietta Tan, Ian Smith, Joseph A. Califano, Adel K. El‐Naggar, Patrick K. Ha
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0119553

Development of a High-Throughput Resequencing Array for the Detection of Pathogenic Mutations in Osteogenesis Imperfecta
Cited by: 9
Author(s): Yao Wang, Yazhou Cui, Xiaoyan Zhou, Jinxiang Han
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0009476

Array-Based FMR1 Sequencing and Deletion Analysis in Patients with a Fragile X Syndrome–Like Phenotype
Cited by: 26
Author(s): Stephen C. Collins, Brad Coffee, Paul J. Benke, Elizabeth Berry‐Kravis, Fiona J. Gilbert, Ben A. Oostra, Dicky Halley, Michael E. Zwick, David J. Cutler, Stephen T. Warren
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0002513

Genotyping of Bacillus cereus Strains by Microarray-Based Resequencing
Cited by: 20
Author(s): Michael E. Zwick, Maureen Kiley, Andrew C. Stewart, Alfred Mateczun, Timothy D. Read
Software Mentions: 1
Published: over 16 years ago

10.1186/s12940-016-0133-0

The reduction of birth weight by fine particulate matter and its modification by maternal and neighbourhood-level factors: a multilevel analysis in British Columbia, Canada
Cited by: 29
Author(s): Anders C. Erickson, Aleck Ostry, Hing Man Chan, Laura Arbour
Software Mentions: 1
Published: over 8 years ago

10.1093/ecam/nep048

Looking for a Person-Centered Medicine: Non Conventional Medicine in the Conventional European and Italian Setting
Cited by: 18
Author(s): Paolo Roberti di Sarsina, Ilaria Iseppato
Software Mentions: 1
Published: almost 14 years ago

10.3389/fcvm.2016.00017

Multivariate Methods for Genetic Variants Selection and Risk Prediction in Cardiovascular Diseases
Cited by: 11
Author(s): Alberto Malovini, Riccardo Bellazzi, Carlo Napolitano, Guia Guffanti
Software Mentions: 1
Published: over 8 years ago

10.3389/fchem.2020.589910

Parallel Implementation of Large-Scale Linear Scaling Density Functional Theory Calculations With Numerical Atomic Orbitals in HONPAS
Cited by: 2
Author(s): Zhaolong Luo, Xinming Qin, Lingyun Wan, Wei Hu, Jinlong Yang
Software Mentions: 1
Published: almost 4 years ago

10.3389/fpubh.2020.617000

Editorial: Antimicrobial Stewardship in Low- and Middle-Income Countries
Cited by: 5
Author(s): Inge C. Gyssens, Heiman Wertheim
Software Mentions: 1
Published: almost 4 years ago

10.1186/gb-2004-6-1-r10

Cited by: 61
Author(s): Michael E. Zwick, Farrell D McAfee, David J. Cutler, Timothy D. Read, Jacques Ravel, Gregory R. Bowman, Darrell R. Galloway, Alfred Mateczun
Software Mentions: 1
Published: almost 21 years ago

10.1080/16549716.2020.1824383

Rural community perceptions of antibiotic access and understanding of antimicrobial resistance: qualitative evidence from the Health and Demographic Surveillance System site in Matlab, Bangladesh
Cited by: 19
Author(s): Moyukh Chowdhury, Jennifer Stewart Williams, Heiman Wertheim, Wasif Ali Khan, Abdul Matin, John Kinsman
Software Mentions: 1
Published: almost 5 years ago

10.1093/jacamr/dlaa048

Community-level consumption of antibiotics according to the AWaRe (Access, Watch, Reserve) classification in rural Vietnam
Cited by: 26
Author(s): Nam Vinh Nguyen, Nga Thi Thuy, Chuc Thi Kim Nguyen, Toan Khanh Tran, Phuc Dang Ho, Hanh H. Nguyen, Vu Thi Lan Huong, Heiman Wertheim, H. Rogier van Doorn, Sonia Lewycka
Software Mentions: 1
Published: about 4 years ago

10.1093/jac/dkt384

Genomic identification of a novel co-trimoxazole resistance genotype and its prevalence amongst Streptococcus pneumoniae in Malawi
Cited by: 20
Author(s): Jennifer Cornick, Simon R. Harris, Christopher M. Parry, Michael J. Moore, Chikondi Jassi, Arox W Kamng’ona, Benard W. Kulohoma, Robert S. Heyderman, Stephen D. Bentley, Dean Everett
Software Mentions: 1
Published: about 11 years ago

10.1074/jbc.M117.799700

Conformational dynamics of the TTD–PHD histone reader module of the UHRF1 epigenetic regulator reveals multiple histone-binding states, allosteric regulation, and druggability
Cited by: 35
Author(s): R. Scott Houliston, Alexander Lemak, Aman Iqbal, Danton Ivanochko, Shili Duan, Lilia Kaustov, Michelle S. Ong, Fan Li, Guillermo Senisterra, Peter J. Brown, Yun‐Xing Wang, C.H. Arrowsmith
Software Mentions: 1
Published: almost 7 years ago

10.1007/s10858-015-9953-4

The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013
Cited by: 25
Author(s): Antonio Rosato, Wim Vranken, Rasmus H. Fogh, Timothy J. Ragan, Roberto Tejero, Kari Pederson, Hsiau‐Wei Lee, James H. Prestegard, Adelinda Yee, Bin Wu, Alexander Lemak, Scott Houliston, C.H. Arrowsmith, Michael A. Kennedy, Thomas Acton, Rong Xiao, Gaohua Liu, Gaetano T. Montelione, Geerten W. Vuister
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.ppat.1000477

Analysis of Pools of Targeted Salmonella Deletion Mutants Identifies Novel Genes Affecting Fitness during Competitive Infection in Mice
Cited by: 171
Author(s): Carlos A. Santiviago, Mark Reynolds, Steffen Porwollik, Sang‐Ho Choi, Fred Long, Helene Andrews‐Polymenis, Michael McClelland
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.ppat.1004029

New Insights into How Yersinia pestis Adapts to Its Mammalian Host during Bubonic Plague
Cited by: 43
Author(s): Elizabeth Pradel, Nadine Lemaître, Maud Merchez, Isabelle Ricard, Anne Reboul, Amélie Dewitte, Florent Sebbane
Software Mentions: 1
Published: over 10 years ago

10.1016/j.pmedr.2019.101002

Perceived life expectancy and colorectal cancer screening intentions and behaviour: A population-based UK study
Cited by: 2
Author(s): Rachael H Dodd, Lindsay C. Kobayashi, Christian von Wagner
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-018-24760-x

Computational Protein Design with Deep Learning Neural Networks
Cited by: 107
Author(s): Jingxue Wang, Huali Cao, John Z. H. Zhang, Yifei Qi
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-34872-z

Genome Features and Biochemical Characteristics of a Robust, Fast Growing and Naturally Transformable Cyanobacterium Synechococcus elongatus PCC 11801 Isolated from India
Cited by: 79
Author(s): Damini Jaiswal, Annesha Sengupta, Sujata Vijay Sohoni, Shinjinee Sengupta, Ambarish G. Phadnavis, Himadri B. Pakrasi, Pramod P. Wangikar
Software Mentions: 1
Published: about 6 years ago

10.3390/s150818360

From Laser Scanning to Finite Element Analysis of Complex Buildings by Using a Semi-Automatic Procedure
Cited by: 125
Author(s): Giovanni Castellazzi, Antonio Maria D’Altri, Gabriele Bitelli, Ilenia Selvaggi, Alessandro Lambertini
Software Mentions: 1
Published: over 9 years ago

10.2196/24156

Perceptions and Acceptability of a Smartphone App Intervention (ChildSafe) in Malaysia: Qualitative Exploratory Study
Cited by: 3
Author(s): Teresa Sui Mien Yong, Komathi Perialathan, Masitah Ahmad, Nurashma Juatan, Nur Liana Ab Majid, Mohammad Zabri Johari
Software Mentions: 1
Published: over 3 years ago

10.3390/ijerph15020387

Advances in Residential Design Related to the Influence of Geomagnetism
Cited by: 2
Author(s): Francisco Glaria, I. Arnedo, Ana Sánchez-Ostiz Gutiérrez
Software Mentions: 1
Published: over 6 years ago

10.2196/11130

The App Behavior Change Scale: Creation of a Scale to Assess the Potential of Apps to Promote Behavior Change
Cited by: 68
Author(s): Fiona H. McKay, Sarah Slykerman, Matthew Dunn
Software Mentions: 1
Published: almost 6 years ago

10.2196/11926

Using Health and Well-Being Apps for Behavior Change: A Systematic Search and Rating of Apps
Cited by: 128
Author(s): Fiona H. McKay, Annemarie Wright, Jane Shill, Hugh Stephens, Mary Uccellini
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.02763

Plant biologists FRET over stress
Cited by: 5
Author(s): Won‐Gyu Choi, Simon Gilroy
Software Mentions: 1
Published: over 10 years ago

10.7554/eLife.01741

Abscisic acid dynamics in roots detected with genetically encoded FRET sensors
Cited by: 190
Author(s): Alexander M. Jones, Jonas Å. H. Danielson, Shruti N ManojKumar, Viviane Lanquar, Guido Großmann, Wolf B. Frommer
Software Mentions: 1
Published: over 10 years ago

10.3390/ijms22052768

Rational Design of Adenylate Kinase Thermostability through Coevolution and Sequence Divergence Analysis
Cited by: 3
Author(s): Jian Chang, Chengxin Zhang, Huaqiang Cheng, Yan‐Wen Tan
Software Mentions: 1
Published: over 3 years ago

10.3390/ijms22062800

Improving Anti-PD-1/PD-L1 Therapy for Localized Bladder Cancer
Cited by: 13
Author(s): Florus C. de Jong, Vera C Rutten, Tahlita C.M. Zuiverloon, Dan Theodorescu
Software Mentions: 1
Published: over 3 years ago

10.18632/oncotarget.23040

A comparative global phosphoproteomics analysis of obinutuzumab (GA101) versus rituximab (RTX) against RTX sensitive and resistant Burkitt lymphoma (BL) demonstrates differential phosphorylation of signaling pathway proteins after treatment
Cited by: 15
Author(s): Aradhana Awasthi, Delphine C.M. Rolland, Janet Ayello, Carmella van de Ven, Venkatesha Basrur, Kevin Conlon, Damian Fermin, Matthew J. Barth, Christian Klein, Kojo S.J. Elenitoba-Johnson, Megan S. Lim, Mitchell S. Cairo
Software Mentions: 1
Published: almost 7 years ago

10.4269/ajtmh.18-0171

Rural South African Community Perceptions of Antibiotic Access and Use: Qualitative Evidence from a Health and Demographic Surveillance System Site
Cited by: 18
Author(s): Jocelyn Anstey Watkins, Fezile Wagner, Francesc Xavier Gómez‐Olivé, Heiman Wertheim, Osman Sankoh, John Kinsman
Software Mentions: 1
Published: over 5 years ago

10.1186/s40545-020-00212-8

What influences antibiotic sales in rural Bangladesh? A drug dispensers’ perspective
Cited by: 15
Author(s): Abdul Matin, Wasif Ali Khan, Mohammad Mahbubul Karim, Sabeena Ahmed, Johannes John-Langba, Osman Sankoh, Margaret Gyapong, John Kinsman, Heiman Wertheim
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2105-10-440

ReseqChip: Automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA sequence assembly
Cited by: 6
Author(s): Marian Thieme, Claudio Lottaz, Harald Niederstätter, Walther Parson, Rainer Spang, Peter J. Oefner
Software Mentions: 1
Published: almost 15 years ago

10.1186/1741-7007-4-28

A molecular scheme for improved characterization of human embryonic stem cell lines
Cited by: 51
Author(s): Richard Josephson, Gregory Sykes, Ying Liu, Carol Ording, Wei Xu, Xianmin Zeng, Soojung Shin, Jeanne F. Loring, Anirban Maitra, Mahendra S. Rao, Jonathan M. Auerbach
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2199-9-77

Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR
Cited by: 73
Author(s): Nicolás Berthet, Anita Reinhardt, India Leclercq, Sven van Ooyen, Christophe Batéjat, Philip Dickinson, Rayna Stamboliyska, Iain G. Old, Katherine A. Kong, Laurent Dacheux, Hervé Bourhy, Giulia C. Kennedy, Christian Korfhage, Stewart T. Cole, Jean-Claude Manuguerra
Software Mentions: 1
Published: almost 17 years ago

10.1186/s12889-016-3273-9

Air pollution, neighbourhood and maternal-level factors modify the effect of smoking on birth weight: a multilevel analysis in British Columbia, Canada
Cited by: 11
Author(s): Anders C. Erickson, Aleck Ostry, Hing Man Chan, Laura Arbour
Software Mentions: 1
Published: over 8 years ago

10.1186/s12889-019-7300-5

What is in the drug packet?: access and use of non-prescribed poly-pharmaceutical packs (Yaa Chud) in the community in Thailand
Cited by: 11
Author(s): Malee Sunpuwan, Sureeporn Punpuing, Wipaporn Jaruruengpaisan, John Kinsman, Heiman Wertheim
Software Mentions: 1
Published: over 5 years ago

10.1186/s12889-019-7812-z

“I can make more from selling medicine when breaking the rules” – understanding the antibiotic supply network in a rural community in Viet Nam
Cited by: 18
Author(s): Hong Hanh Nguyen, Dang Phuc Ho, Thi Lan Huong Vu, Khanh Toan Tran, Thanh Do Tran, Thi Kim Chuc Nguyen, H. Rogier van Doorn, Behzad Nadjm, John Kinsman, Heiman Wertheim
Software Mentions: 1
Published: almost 5 years ago

Projects: cran: ABACUS

Papers Mentioning ABACUS 58