bioconductor: SMAP | Projects | Ecosyste.ms: Papers

10.1186/s13148-019-0795-x

DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis
Cited by: 50
Author(s): Ieva Rauluševičiūtė, Finn Drabløs, Morten Rye
Software Mentions: 10
Published: almost 5 years ago

10.1186/s13072-016-0075-3

Profiling genome-wide DNA methylation
Cited by: 245
Author(s): Wai-Shin Yong, Fei‐Man Hsu, Pao‐Yang Chen
Software Mentions: 4
Published: over 8 years ago

10.1038/s41419-021-03920-4

TNF-α induces endothelial–mesenchymal transition promoting stromal development of pancreatic adenocarcinoma
Cited by: 22
Author(s): Marjorie Adjuto-Saccone, Philippe Soubeyran, Julie Garcia, Stéphane Audebert, Luc Camoin, Marion Rubis, Julie Roques, Bernard Binétruy, Juan Iovanna, Roselyne Tournaire
Software Mentions: 3
Published: over 3 years ago

10.1186/1752-0509-7-102

Antibacterial mechanisms identified through structural systems pharmacology
Cited by: 23
Author(s): Roger L. Chang, Lei Xie, Philip E. Bourne, Bernhard Ø. Palsson
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0065894

Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key
Cited by: 121
Author(s): V. Joachim Haupt, Simone Daminelli, Michael Schroeder
Software Mentions: 3
Published: over 11 years ago

10.1038/s41598-020-69343-x

River flow prediction in data scarce regions: soil moisture integrated satellite rainfall products outperform rain gauge observations in West Africa
Cited by: 34
Author(s): Luca Brocca, Christian Massari, Thierry Pellarin, Paolo Filippucci, Luca Ciabatta, Stefania Camici, Yann H. Kerr, Diego Fernàndez–Prieto
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pcbi.1006483

A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs)
Cited by: 41
Author(s): Christiane Ehrt, Tobias Brinkjost, Oliver Koch
Software Mentions: 3
Published: about 6 years ago

10.3390/land9100398

Challenging a Global Land Surface Model in a Local Socio-Environmental System
Cited by: 1
Author(s): Kyla M. Dahlin, Donald Akanga, Danica Lombardozzi, David E. Reed, Gabriela Shirkey, Cheyenne Lei, Michael Abraha, Jiquan Chen
Software Mentions: 3
Published: about 4 years ago

10.1038/s41597-020-00748-z

A continental-scale soil evaporation dataset derived from Soil Moisture Active Passive satellite drying rates
Cited by: 5
Author(s): Ronnie Abolafia‐Rosenzweig, Andrew M. Badger, E. E. Small, Ben Livneh
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-019-38639-y

Examining Interactions Between and Among Predictors of Net Ecosystem Exchange: A Machine Learning Approach in a Semi-arid Landscape
Cited by: 18
Author(s): Qingtao Zhou, Aaron W. Fellows, G. N. Flerchinger, Alejandro N. Flores
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-021-88405-2

Future rice farming threatened by drought in the Lower Mekong Basin
Cited by: 22
Author(s): Hyunwoo Kang, Venkataramana Sridhar, Mohammed Mainuddin, Le Duc Trung
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1000938

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model
Cited by: 184
Author(s): Roger L. Chang, Li Xie, Lei Xie, Philip E. Bourne, Bernhard Ø. Palsson
Software Mentions: 2
Published: about 14 years ago

10.3390/s19040802

Potential of Sentinel-1 Surface Soil Moisture Product for Detecting Heavy Rainfall in the South of France
Cited by: 15
Author(s): Hassan Bazzi, Nicolas Baghdadi, Mohammad El Hajj, Mehrez Zribi
Software Mentions: 2
Published: almost 6 years ago

10.3390/s21103457

Novel Weight-Based Approach for Soil Moisture Content Estimation via Synthetic Aperture Radar, Multispectral and Thermal Infrared Data Fusion
Cited by: 5
Author(s): Oualid Yahia, Raffaella Guida, Pasquale Iervolino
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-016-0941-9

Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology
Cited by: 43
Author(s): Zheng Zhao, Che L. Martin, Raymond Fan, Philip E. Bourne, Lei Xie
Software Mentions: 2
Published: almost 9 years ago

10.1186/s13742-015-0070-9

SMAP: a streamlined methylation analysis pipeline for bisulfite sequencing
Cited by: 11
Author(s): Shengjie Gao, Dan Zou, Likai Mao, Quan Zhou, Wenlong Jia, Yi Huang, Shancen Zhao, Gang Chen, Song Wu, Dongdong Li, Fei Xia, Huafeng Chen, Maoshan Chen, Torben F. Ørntoft, Lars Bolund, Karina D. Sørensen
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2105-11-555

The LabelHash algorithm for substructure matching
Cited by: 30
Author(s): Mark Moll, Drew Bryant, Lydia E. Kavraki
Software Mentions: 2
Published: about 14 years ago

10.1093/gigascience/gix123

BS-virus-finder: virus integration calling using bisulfite sequencing data
Cited by: 5
Author(s): Shengjie Gao, Xuesong Hu, Fengping Xu, Changduo Gao, Kai Xiong, Xiao Zhao, Haixiao Chen, Shancen Zhao, Mengyao Wang, Deliang Fu, Xiaohui Zhao, Jie Bai, Likai Mao, Bo Li, Song Wu, Jian Wang, Shengbin Li, Huangming Yang, Lars Bolund, Christian N. S. Pedersen
Software Mentions: 2
Published: almost 7 years ago

10.1111/geb.12887

Towards connecting biodiversity and geodiversity across scales with satellite remote sensing
Cited by: 74
Author(s): Phoebe L. Zarnetske, Quentin D. Read, Sydne Record, Keith D. Gaddis, Stéphanie Pau, Martina L. Hobi, Sparkle L. Malone, Jennifer K. Costanza, Kyla M. Dahlin, Andrew M. Latimer, Adam M. Wilson, John M. Grady, Scott V. Ollinger, Andrew O. Finley
Software Mentions: 2
Published: over 5 years ago

10.3390/insects12030233

Application of Remote Sensing Data for Locust Research and Management—A Review
Cited by: 28
Author(s): Igor Klein, Natascha Oppelt, Claudia Kuenzer
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1000387

Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors
Cited by: 239
Author(s): Li Xie, Jerry Li, Lei Xie, Philip E. Bourne
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0179936

Insights into the binding mode of MEK type-III inhibitors. A step towards discovering and designing allosteric kinase inhibitors across the human kinome
Cited by: 34
Author(s): Zheng Zhao, Lei Xie, Philip E. Bourne
Software Mentions: 2
Published: over 7 years ago

10.3390/rs10081265

Leveraging the Google Earth Engine for Drought Assessment Using Global Soil Moisture Data
Cited by: 90
Author(s): Nazmus Sazib, I. E. Mladenova, J. D. Bolten
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pcbi.1006718

DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network
Cited by: 77
Author(s): Limeng Pu, Rajiv Gandhi Govindaraj, Jeffrey Mitchell Lemoine, Hsiao Chun Wu, Michał Bryliński
Software Mentions: 2
Published: almost 6 years ago

10.3390/rs9111179

Data Assimilation to Extract Soil Moisture Information from SMAP Observations
Cited by: 25
Author(s): Jana Kolassa, Rolf H. Reichle, Qing Liu, Michael H. Cosh, David D. Bosch, Todd G. Caldwell, Andreas Colliander, Chandra D. Holifield Collins, Thomas J. Jackson, Stanley Livingston, Mahta Moghaddam, Patrick J. Starks
Software Mentions: 1
Published: about 7 years ago

10.1038/s41597-021-00925-8

A long term global daily soil moisture dataset derived from AMSR-E and AMSR2 (2002–2019)
Cited by: 37
Author(s): Panpan Yao, Hui Lu, Jiancheng Shi, Tianjie Zhao, Kun Yang, Michael H. Cosh, Daniel J. Short Gianotti, Dara Entekhabi
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-018-23684-w

Morphometric analysis of spread platelets identifies integrin αIIbβ3-specific contractile phenotype
Cited by: 24
Author(s): Sebastian Lickert, Simona Sorrentino, Jan‐Dirk Studt, Ohad Medalia, Viola Vogel, Ingmar Schoen
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-27127-4

A New Paradigm in Earth Environmental Monitoring with the CYGNSS Small Satellite Constellation
Cited by: 171
Author(s): Christopher S. Ruf, Clara Chew, Timothy J. Lang, Mary Morris, Kyle Nave, A. J. Ridley, Rajeswari Balasubramaniam
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-27673-x

CYGNSS data map flood inundation during the 2017 Atlantic hurricane season
Cited by: 103
Author(s): Clara Chew, J. T. Reager, E. E. Small
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-019-46152-5

Cloud-driven modulations of Greenland ice sheet surface melt
Cited by: 14
Author(s): Michio Niwano, Akihiro Hashimoto, Teruo Aoki
Software Mentions: 1
Published: over 5 years ago

10.3390/s16081308

Estimation of Soil Moisture from Optical and Thermal Remote Sensing: A Review
Cited by: 165
Author(s): Dianjun Zhang, Guoqing Zhou
Software Mentions: 1
Published: over 8 years ago

10.3390/s19051247

Spatial Evaluation of Soil Moisture (SM), Land Surface Temperature (LST), and LST-Derived SM Indexes Dynamics during SMAPVEX12
Cited by: 11
Author(s): Hao Sun, Baichi Zhou, Hongxing Liu
Software Mentions: 1
Published: over 5 years ago

10.3390/tropicalmed4010015

Use of Geospatial Surveillance and Response Systems for Vector-Borne Diseases in the Elimination Phase
Cited by: 27
Author(s): John B. Malone, Robert Bergquist, Moara S Martins, Jeffrey C. Luvall
Software Mentions: 1
Published: almost 6 years ago

10.18632/oncotarget.11905

New HSP27 inhibitors efficiently suppress drug resistance development in cancer cells
Cited by: 44
Author(s): Jörg C. Heinrich, Sainitin Donakonda, V. Joachim Haupt, Petra Lennig, Yixin Zhang, Michael Schroeder
Software Mentions: 1
Published: about 8 years ago

10.3389/frai.2021.636234

Assessment of a Spatiotemporal Deep Learning Approach for Soil Moisture Prediction and Filling the Gaps in Between Soil Moisture Observations
Cited by: 19
Author(s): Mohamed ElSaadani, Emad Habib, Ahmed M. Abdelhameed, Magdy Bayoumi
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-14-S3-S9

Multiscale modeling of the causal functional roles of nsSNPs in a genome-wide association study: application to hypoxia
Cited by: 6
Author(s): Li Xie, Clara Ng, Thahmina Ali, Raoul Valencia, Barbara L Ferreira, Vincent Xue, Maliha Tanweer, Dan Zhou, Gabriel G. Haddad, Philip E. Bourne, Lei Xie
Software Mentions: 1
Published: over 11 years ago

10.1186/s12874-018-0485-y

Using bundle embeddings to predict daily cortisol levels in human subjects
Cited by: 0
Author(s): Roelof B. Toonen, Klaas J. Wardenaar, Elisabeth H. Bos, Sonja L. van Ockenburg, Peter de Jonge
Software Mentions: 1
Published: over 6 years ago

10.1186/s12882-017-0737-9

Bowel perforation by a peritoneal dialysis catheter: report of two cases
Cited by: 12
Author(s): Maki Fujiwara, Takeshi Soda, Takuya Okada, Hiroshi Kanamaru, Takahiro Inoue, Osamu Ogawa
Software Mentions: 1
Published: about 7 years ago

10.1155/2018/5486403

A Novel Method for Drug Screen to Regulate G Protein-Coupled Receptors in the Metabolic Network of Alzheimer’s Disease
Cited by: 1
Author(s): Li Yang, Wei Zheng, Qiqige Wuyun, Shujuan Cao, Jishou Ruan, Yanping Zhang
Software Mentions: 1
Published: almost 7 years ago

10.1155/2013/170356

Cloud Computing for Protein-Ligand Binding Site Comparison
Cited by: 19
Author(s): Che Lun Hung, Guan Hua
Software Mentions: 1
Published: almost 12 years ago

10.1002/lno.11763

Moving ecological and biogeochemical transitions across the North Pacific
Cited by: 10
Author(s): Christopher L. Follett, Stephanie Dutkiewicz, Gaël Forget, B. B. Cael, Michael J. Follows
Software Mentions: 1
Published: over 3 years ago

10.1029/2019WR026561

Surface Depression and Wetland Water Storage Improves Major River Basin Hydrologic Predictions
Cited by: 39
Author(s): Adnan Rajib, Heather E. Golden, Charles R. Lane, Qiusheng Wu
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pcbi.1006619

Rational discovery of dual-indication multi-target PDE/Kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology
Cited by: 32
Author(s): Hansaim Lim, Di He, Yue Qiu, Patrycja Krawczuk, Xiaoru Sun, Lei Xie
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pcbi.1000976

The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications
Cited by: 91
Author(s): Sarah L. Kinnings, Li Xie, Kingston H. Fung, Richard M. Jackson, Lei Xie, PhilipE Bourne
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pcbi.1000648

A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology
Cited by: 67
Author(s): Jacob D. Durrant, Rommie E. Amaro, Lei Xie, Michael D. Urbaniak, Michael A. J. Ferguson, Antti M. Haapalainen, Zhijun Chen, Anne Marie Di Guilmi, Frank Wunder, Philip E. Bourne, J. Andrew McCammon
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pcbi.1002037

Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir
Cited by: 154
Author(s): Li Xie, Thomas Evangelidis, Lei Xie, Philip E. Bourne
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0081427

Structural Analysis of microRNA-Target Interaction by Sequential Seed Mutagenesis and Stem-Loop 3' RACE
Cited by: 6
Author(s): Marc Bohmer, Jutta Sharbati, Jennifer zur Bruegge, Ralf Einspanier, Soroush Sharbati
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0100829

Pros and Cons of the Tuberculosis Drugome Approach – An Empirical Analysis
Cited by: 14
Author(s): Feng‐Chi Chen, Yu-Chieh Liao, Jie-Mao Huang, Chih-Long Lin, Yih-Yuan Chen, Horng-Yunn Dou, Chao A. Hsiung
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0080278

Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome
Cited by: 95
Author(s): Daniel Garijo, Sarah L. Kinnings, Li Xie, Lei Xie, Yinliang Zhang, Philip E. Bourne, Yolanda Gil
Software Mentions: 1
Published: almost 11 years ago

10.1016/j.cell.2018.06.032

Systematic Nanoscale Analysis of Endocytosis Links Efficient Vesicle Formation to Patterned Actin Nucleation
Cited by: 174
Author(s): Markus Mund, Jan van der Beek, Joran Deschamps, Serge Dmitrieff, Philipp Hoess, Jooske L. Monster, Andrea Picco, François Nédélec, Marko Kaksonen, Jonas Ries
Software Mentions: 1
Published: over 6 years ago

10.1021/acsnano.1c03677

Site-Specifically-Labeled Antibodies for Super-Resolution Microscopy Reveal <i>In Situ</i> Linkage Errors
Cited by: 31
Author(s): Susanna M. Früh, Ulf Matti, Philipp R. Spycher, Marina Rubini, Sebastian Lickert, Thomas Schlichthaerle, Ralf Jungmann, Viola Vogel, Jonas Ries, Ingmar Schoen
Software Mentions: 1
Published: over 3 years ago

10.3389/fdata.2020.597720

Monitoring Crop Status in the Continental United States Using the SMAP Level-4 Carbon Product
Cited by: 3
Author(s): Patrick Wurster, Marco P. Maneta, John S. Kimball, K. Arthur Endsley, Santiago Beguerı́a
Software Mentions: 1
Published: almost 4 years ago

10.3389/fdata.2020.00010

Agricultural Drought Monitoring via the Assimilation of SMAP Soil Moisture Retrievals Into a Global Soil Water Balance Model
Cited by: 31
Author(s): I. E. Mladenova, J. D. Bolten, Wade T. Crow, Nazmus Sazib, Curt Reynolds
Software Mentions: 1
Published: over 4 years ago

Projects: bioconductor: SMAP

Papers Mentioning SMAP 58