10.3390/jpm11080785

Inference of an Integrative, Executable Network for Rheumatoid Arthritis Combining Data-Driven Machine Learning Approaches and a State-of-the-Art Mechanistic Disease Map
Cited by: 10
Author(s): Quentin Miagoux, Vidisha Singh, Dereck de Mézquita, Valérie Chaudru, Mohamed Elati, Élisabeth Petit-Teixeira, Anna Niarakis
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0251458

Statistical privacy-preserving message broadcast for peer-to-peer networks
Cited by: 1
Author(s): David Mödinger, Jan-Hendrik Lorenz, Franz J. Hauck
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.27014

Regulation of life span by the gut microbiota in the short-lived African turquoise killifish
Cited by: 262
Author(s): Patrick M. Smith, David Willemsen, Miriam Popkes, Franziska Metge, Edson Gandiwa, Martin Reichard, Dario Riccardo Valenzano
Software Mentions: 5
Published: almost 9 years ago

10.1186/s40168-021-01001-4

The bacterial communities of Alaskan mosses and their contributions to N2-fixation
Cited by: 26
Author(s): Hannah Holland‐Moritz, Julia Stuart, Lily R. Lewis, Samantha N. Miller, Michelle C. Mack, José Miguel Ponciano, Stuart F. McDaniel, Noah Fierer
Software Mentions: 5
Published: over 5 years ago

10.1186/s40168-018-0496-2

Signatures of ecological processes in microbial community time series
Cited by: 64
Author(s): Karoline Faust, Franziska Bauchinger, Béatrice Laroche, Sophie de Buyl, Leo Lahti, Alex D. Washburne, Didier Gonze, Stefanie Widder
Software Mentions: 5
Published: about 8 years ago

10.3389/fonc.2021.633950

Identification of a Novel Glycolysis-Related Gene Signature Correlates With the Prognosis and Therapeutic Responses in Patients With Clear Cell Renal Cell Carcinoma
Cited by: 13
Author(s): Zhengtong Lv, Qi Lin, Xiheng Hu, Miao Mo, Huichuan Jiang, Yuan Li
Software Mentions: 5
Published: over 5 years ago

10.3389/fnins.2019.00211

Brain Connectivity and Information-Flow Breakdown Revealed by a Minimum Spanning Tree-Based Analysis of MRI Data in Behavioral Variant Frontotemporal Dementia
Cited by: 26
Author(s): Valentina Saba, Enrico Premi, Viviana Cristillo, Stefano Gazzina, Fernando Palluzzi, Orazio Zanetti, Roberto Gasparotti, Alessandro Padovani, Barbara Borroni, Mario Grassi
Software Mentions: 5
Published: over 7 years ago

10.3390/ijerph18073370

The Academic Landscapes of Manufacturing Enterprise Performance and Environmental Sustainability: A Study of Commonalities and Differences
Cited by: 7
Author(s): Cristian Mejía, Yuya Kajikawa
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.49424

Single-cell transcriptomes and whole-brain projections of serotonin neurons in the mouse dorsal and median raphe nuclei
Cited by: 164
Author(s): Jing Ren, Alina Isakova, Drew Friedmann, Jiawei Zeng, Sophie M. Grutzner, Albert Pun, Grace Zhao, Sai Saroja Kolluru, Ruiyu Wang, Rui Lin, Pengcheng Li, Anan Li, Jennifer L. Raymond, Qi Luo, Minmin Luo, Stephen R. Quake, Liqun Luo
Software Mentions: 5
Published: almost 7 years ago

10.1016/j.devcel.2020.11.013

Diverse Routes toward Early Somites in the Mouse Embryo
Cited by: 40
Author(s): Carolina Guibentif, J. B. Griffiths, Iván Imaz-Rosshandler, Shila Ghazanfar, Jennifer Nichols, Valerie Wilson, Berthold Göttgens, John C. Marioni
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-021-04112-9

NoRCE: non-coding RNA sets cis enrichment tool
Cited by: 4
Author(s): Gülden Olgun, Afshan Nabi, Öznur Taştan
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0225651

A Bayesian gene network reveals insight into the JAK-STAT pathway in systemic lupus erythematosus
Cited by: 8
Author(s): Yupeng Li, Richard E. Higgs, Robert W. Hoffman, Ernst R. Dow, Xiong Liu, Michelle Petri, Daniel J. Wallace, Thomas Dörner, Brian J. Eastwood, Bradley B. Miller, Yushi Liu
Software Mentions: 5
Published: over 6 years ago

10.1186/s12866-020-01938-w

A comprehensive analysis of the microbiota composition and gene expression in colorectal cancer
Cited by: 15
Author(s): Qian Zhang, Huan Zhao, Dedong Wu, D Y Cao, Wei Ma
Software Mentions: 5
Published: almost 6 years ago

10.3389/fmicb.2020.603692

Shift and Metabolic Potentials of Microbial Eukaryotic Communities Across the Full Depths of the Mariana Trench
Cited by: 3
Author(s): Xiaoyu Zhu, Jiwen Liu, Chun-Xu Xue, Jiwei Tian, Xiao‐Hua Zhang
Software Mentions: 5
Published: over 5 years ago

10.1007/s43926-021-00016-5

Social media analytics of the Internet of Things
Cited by: 4
Author(s): Jim Scheibmeir, Yashwant K. Malaiya
Software Mentions: 5
Published: about 5 years ago

10.3389/fonc.2021.686044

A Novel Prognostic Model Based on Ferroptosis-Related Gene Signature for Bladder Cancer
Cited by: 27
Author(s): Libo Yang, Chunyan Li, Yang Qin, Guoying Zhang, Bin Zhao, Ziyuan Wang, Yang H. Huang, Yong Yang
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41396-018-0321-8

Genomic and transcriptomic insights into the ecology and metabolism of benthic archaeal cosmopolitan, Thermoprofundales (MBG-D archaea)
Cited by: 80
Author(s): Zhichao Zhou, Yang Liu, Karen G. Lloyd, Jie Pan, Yuchun Yang, Ji‐Dong Gu, Meng Li
Software Mentions: 5
Published: over 7 years ago

10.3390/ijerph18041505

The Role of Societal Aspects in the Formation of Official COVID-19 Reports: A Data-Driven Analysis
Cited by: 5
Author(s): Marcell T. Kurbucz, Attila Imre Katona, Zoltán Lantos, Zsolt Tibor Kosztyán
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0234489

Application of network analysis and cluster analysis for better prevention and control of swine diseases in Argentina
Cited by: 11
Author(s): Jerome N. Baron, María Natalia Aznar, M. Monterubbianesi, Beatriz Martínez‐López
Software Mentions: 5
Published: about 6 years ago

10.1038/s42003-020-0914-4

Birds have peramorphic skulls, too: anatomical network analyses reveal oppositional heterochronies in avian skull evolution
Cited by: 29
Author(s): Olivia Plateau, Christian Foth
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0244377

A methodology and theoretical taxonomy for centrality measures: What are the best centrality indicators for student networks?
Cited by: 7
Author(s): Kristel Vignery, Wim Laurier
Software Mentions: 5
Published: over 5 years ago

10.1101/2020.09.16.20196154

SARS-CoV-2 antibody signatures robustly predict diverse antiviral functions relevant for convalescent plasma therapy
Cited by: 20
Author(s): Harini Natarajan, Andrew R. Crowley, Savannah E. Butler, Shiwei Xu, Joshua A. Weiner, Evan M. Bloch, Kirsten Littlefield, Wendy Wieland-Alter, Ruth I. Connor, Peter F. Wright, Sarah E. Benner, Tania S. Bonny, Oliver Laeyendecker, David J. Sullivan, Shmuel Shoham, Thomas C. Quinn, H. Benjamin Larman, Arturo Casadevall, Andrew Pekosz, Andrew D. Redd, Aaron A.R. Tobian, Margaret E. Ackerman
Software Mentions: 5
Published: almost 6 years ago

10.1128/mSystems.00477-21

Comprehensive Cultivation of the Swine Gut Microbiome Reveals High Bacterial Diversity and Guides Bacterial Isolation in Pigs
Cited by: 11
Author(s): Xiaofan Wang, Samantha Howe, Xiaoyuan Wei, Feilong Deng, Tsung‐Ting Tsai, Jianmin Chai, Yingping Xiao, Hua Yang, C. V. Maxwell, Ying Li, Jiangchao Zhao
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0117909

Potential Parasite Transmission in Multi-Host Networks Based on Parasite Sharing
Cited by: 59
Author(s): Shai Pilosof, Sergé Morand, Boris R. Krasnov, Charles L. Nunn
Software Mentions: 5
Published: over 11 years ago

10.1128/mSphere.00982-20

Decreased Ecological Resistance of the Gut Microbiota in Response to Clindamycin Challenge in Mice Colonized with the Fungus Candida albicans
Cited by: 2
Author(s): Laura Markey, Antonia Pugliese, Theresa Tian, Farrah Roy, Kyongbum Lee, Carol A. Kumamoto
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.37816

Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity
Cited by: 65
Author(s): Xue Song Zhang, Jackie Li, Kimberly A. Krautkramer, Michelle Badri, Thomas Battaglia, Timothy C. Borbet, Hyunwook Koh, Sandy Ng, Rachel A Sibley, Yuanyuan Li, Wimal Pathmasiri, Jindal Sk, Robin R. Shields-Cutler, Ben Hillmann, Gabriel A. Al‐Ghalith, Victoria Ruiz, Alexandra E. Livanos, Angélique B. van’t Wout, Nabeetha A. Nagalingam, Arlin B. Rogers, Susan Sumner, Dan Knights, John M. Denu, Huilin Li, Kelly V. Ruggles, Richard Bonneau, R. Anthony Williamson, Marcus Rauch, Martin J. Blaser
Software Mentions: 5
Published: about 8 years ago

10.1099/mgen.0.000240

Genomic analysis of bacteria in the Acute Oak Decline pathobiome
Cited by: 29
Author(s): James Doonan, Sandra Denman, Justin A. Pachebat, James E. McDonald
Software Mentions: 5
Published: over 7 years ago

10.1186/s12976-019-0103-7

Gene regulatory networks on transfer entropy (GRNTE): a novel approach to reconstruct gene regulatory interactions applied to a case study for the plant pathogen Phytophthora infestans
Cited by: 19
Author(s): Juan Castro, Iván Valdés, Laura González-García, Giovanna Danies, Silvia Cañas, Flávia Vischi Winck, Carlos Eduardo Ñústez, Silvia Restrepo, Diego Mauricio Riaño‐Pachón
Software Mentions: 5
Published: over 7 years ago

10.1264/jsme2.ME20153

Inoculation of <i>Mimosa Pudica</i> with <i>Paraburkholderia phymatum</i> Results in Changes to the Rhizoplane Microbial Community Structure
Cited by: 5
Author(s): Shashini U. Welmillage, Qian Zhang, Virinchipuram S. Sreevidya, Michael J. Sadowsky, Prasad Gyaneshwar
Software Mentions: 5
Published: over 5 years ago

10.1002/sam.11495

A framework for stability‐based module detection in correlation graphs
Cited by: 3
Author(s): Mingmei Tian, Rachael Hageman Blair, Lina Mu, Matthew Bonner, Richard W. Browne, Han Yu
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0184015

Population genetics, community of parasites, and resistance to rodenticides in an urban brown rat (Rattus norvegicus) population
Cited by: 38
Author(s): Amélie Desvars-Larrive, Michel Pascal, Patrick Gasqui, Jean-François Cosson, Etienne Benoît, Virginie Lattard, Laurent Crespin, Olivier Lorvelec, Benoît Pisanu, Alexandre Teynié, Muriel Vayssier‐Taussat, Sarah Bonnet, Philippe Marianneau, Sandra Lacôte, Pascale Bourhy, Philippe Berny, Nicole Pavio, Sophie Le Poder, Emmanuelle Gilot‐Fromont, Elsa Jourdain, Abdessalem Hammed, Isabelle Fourel, Farid Chikh, Gwenaël Vourc’H
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pone.0225001

Mammary microbiome of lactating organic dairy cows varies by time, tissue site, and infection status
Cited by: 38
Author(s): Tucker Andrews, Deborah A. Neher, Thomas R. Weicht, John W. Barlow
Software Mentions: 5
Published: over 6 years ago

10.1007/s00248-020-01657-9

Identifying Potential Hosts of Short-Branch Microsporidia
Cited by: 3
Author(s): Annemie Doliwa, Micah Dunthorn, Erika Rassoshanska, Frédéric Mahe, David Bass, Camila Duarte Ritter
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-98075-9

Distinguishing feature of gut microbiota in Tibetan highland coronary artery disease patients and its link with diet
Cited by: 14
Author(s): Yu-Lan Ma, Lulu Zhu, Zhuo Ma, Zhong-Shan Gao, Yumiao Wei, Youlu Shen, Lin Liu, Xingli Liu, Ming Ren
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0129074

Making Large-Scale Networks from fMRI Data
Cited by: 16
Author(s): Verena D. Schmittmann, Sara Jahfari, Denny Borsboom, Alexander Olof Savi, Lourens J. Waldorp
Software Mentions: 5
Published: almost 11 years ago

10.3389/fmicb.2018.01128

Sediment Depth-Dependent Spatial Variations of Bacterial Communities in Mud Deposits of the Eastern China Marginal Seas
Cited by: 23
Author(s): Yanlu Qiao, Jiwen Liu, Meixun Zhao, Xiaohua Zhang
Software Mentions: 5
Published: about 8 years ago

10.1038/s41598-021-95486-6

Genetic diversity and population structure of Alternaria species from tomato and potato in North Carolina and Wisconsin
Cited by: 10
Author(s): Tika B. Adhikari, Norman Muzhinji, Dennis Halterman, Frank J. Louws
Software Mentions: 5
Published: almost 5 years ago

10.1128/mBio.01870-17

Gene Co-occurrence Networks Reflect Bacteriophage Ecology and Evolution
Cited by: 40
Author(s): Jason W. Shapiro, Catherine Putonti
Software Mentions: 5
Published: about 8 years ago

10.1007/s11306-015-0927-z

GC–MS metabolic profiling of Cabernet Sauvignon and Merlot cultivars during grapevine berry development and network analysis reveals a stage- and cultivar-dependent connectivity of primary metabolites
Cited by: 51
Author(s): Álvaro Cuadros-Inostroza, Simón Ruíz-Lara, Enrique González, Änne Eckardt, Lothar Willmitzer, Hugo Peña‐Cortés
Software Mentions: 5
Published: over 10 years ago

10.1038/s41598-021-91399-6

Bacillus amyloliquefaciens FH-1 significantly affects cucumber seedlings and the rhizosphere bacterial community but not soil
Cited by: 15
Author(s): Jingjing Wang, Sheng Xu, Rong Yang, Wei Zhao, Dan Zhu, Xiaoxia Zhang, Zhiyong Huang
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0044514

Bipartite Graphs as Models of Population Structures in Evolutionary Multiplayer Games
Cited by: 28
Author(s): Jorge Peña, Yannick Rochat
Software Mentions: 5
Published: almost 14 years ago

10.3389/fmicb.2016.01637

Response of Core Microbial Consortia to Chronic Hydrocarbon Contaminations in Coastal Sediment Habitats
Cited by: 60
Author(s): Mathilde Jeanbille, Jérôme Gury, Robert Duran, Jacek Tronczyński, Hélène Agogué, Olfa Ben Saïd, Jean-François Ghiglione, Jean‐Christophe Auguet
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pone.0183144

Environmental disturbance increases social connectivity in a passerine bird
Cited by: 22
Author(s): Samantha M. Lantz, Jordan Karubian
Software Mentions: 5
Published: almost 9 years ago

10.3389/fmicb.2017.01516

Long-term Fertilization Structures Bacterial and Archaeal Communities along Soil Depth Gradient in a Paddy Soil
Cited by: 68
Author(s): Yunfu Gu, Yingyan Wang, Liangang Shen, Quanju Xiang, Xiumei Yu, Ke Zhao, Likou Zou, Qiang Chen, Shuangshuang Tu, Xiaoping Zhang
Software Mentions: 5
Published: almost 9 years ago

10.1097/MD.0000000000016477

Comparative effectiveness of different forms of traditional Chinese medicine for treatment of post-stroke depression
Cited by: 4
Author(s): Huiling Chen, Meidan Zhao, Xiuming Li, Yanhong Zhang, Hui Yu, Ergang Xiao, Weizhen Gao, Hongwu Wang
Software Mentions: 5
Published: about 7 years ago

10.1038/s41598-021-86544-0

An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk
Cited by: 5
Author(s): Gabriel Jiménez-Domínguez, Patrice Ravel, Stéphan Jalaguier, Vincent Cavaillès, Jacques Colinge
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2019.03138

Rare Species Shift the Structure of Bacterial Communities Across Sphagnum Compartments in a Subalpine Peatland
Cited by: 13
Author(s): Wen Tian, Xiang Xiao, Liyuan Ma, Stephanie Evers, Ruicheng Wang, Xuan Qiu, Hongmei Wang
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0148459

Assessment of Overlap of Phylogenetic Transmission Clusters and Communities in Simple Sexual Contact Networks: Applications to HIV-1
Cited by: 28
Author(s): Luc Villandré, David A. Stephens, Aurélie Labbe, Huldrych F. Günthard, Roger D. Kouyos, Tanja Stadler
Software Mentions: 5
Published: over 10 years ago

10.1038/s41598-021-81447-6

Acetyl-CoA flux from the cytosol to the ER regulates engagement and quality of the secretory pathway
Cited by: 16
Author(s): Inca A. Dieterich, Yusi Cui, Megan M. Braun, Alexis J. Lawton, Nicklaus H. Robinson, Jennifer L. Peotter, Qing Yu, Jason C. Casler, Benjamin S. Glick, Anjon Audhya, John M. Denu, Lingjun Li, Luigi Puglielli
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2020.00571

Composition, Predicted Functions and Co-occurrence Networks of Rhizobacterial Communities Impacting Flowering Desert Events in the Atacama Desert, Chile
Cited by: 17
Author(s): Marcia Astorga-Eló, Qian Zhang, Giovanni Larama, Alexandra Stoll, Michael J. Sadowsky, Milko A. Jorquera
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0057190

The Poultry-Associated Microbiome: Network Analysis and Farm-to-Fork Characterizations
Cited by: 103
Author(s): Brian B. Oakley, Cesar A. Morales, J. Eric Line, M. E. Berrang, Richard J. Meinersmann, Glenn E. Tillman, Mark G. Wise, Gregory R. Siragusa, Kelli L. Hiett, Bruce S. Seal
Software Mentions: 5
Published: over 13 years ago

10.1038/s41598-021-85061-4

Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility
Cited by: 12
Author(s): Jerry C. Wang, Gokul Ramaswami, Daniel H. Geschwind
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2021.647861

Nutrient Exposure Alters Microbial Composition, Structure, and Mercury Methylating Activity in Periphyton in a Contaminated Watershed
Cited by: 4
Author(s): Alyssa A. Carrell, Grace E. Schwartz, Melissa Cregger, Caitlin M. Gionfriddo, Dwayne A. Elias, Regina L. Wilpiszeski, Dawn M. Klingeman, Ann M. Wymore, Katherine A. Muller, Scott C. Brooks
Software Mentions: 5
Published: over 5 years ago

10.3389/fphar.2020.599760

Modulation of the Gut Microbiota and Liver Transcriptome by Red Yeast Rice and Monascus Pigment Fermented by Purple Monascus SHM1105 in Rats Fed with a High-Fat Diet
Cited by: 10
Author(s): Hua Yang, Ronghua Pan, Jing Wang, Lizhong Zheng, Zhenjing Li, Qingbin Guo, Changlu Wang
Software Mentions: 5
Published: over 5 years ago

10.1007/s00262-020-02833-z

Early changes in the circulating T cells are associated with clinical outcomes after PD-L1 blockade by durvalumab in advanced NSCLC patients
Cited by: 14
Author(s): Elliot Naidus, Jérôme Bouquet, David Y. Oh, Timothy J. Looney, Hai Yang, Lawrence Fong, Nathan Standifer, Li Zhang
Software Mentions: 4
Published: over 5 years ago

10.3390/brainsci11010094

Assessing the Relationship between Verbal and Nonverbal Cognitive Abilities Using Resting-State EEG Functional Connectivity
Cited by: 1
Author(s): Inna Feklicheva, Ilya Zakharov, Nadezda Chipeeva, Ekaterina Maslennikova, Svetlana Korobova, Timofey Adamovich, Victoria Ismatullina, Sergey Malykh
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0202063

Cross-species alcohol dependence-associated gene networks: Co-analysis of mouse brain gene expression and human genome-wide association data
Cited by: 11
Author(s): Kristin M. Mignogna, Silviu‐Alin Bacanu, Brien P. Riley, Aaron R. Wolen, Michael F. Miles
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0057780

Functional and Structural Neural Network Characterization of Serotonin Transporter Knockout Rats
Cited by: 15
Author(s): Kajo van der Marel, Judith R. Homberg, Willem M. Otte, Rick M. Dijkhuizen
Software Mentions: 4
Published: over 13 years ago

10.3389/fmicb.2020.618287

Niche Differentiation of Comammox Nitrospira in the Mudflat and Reclaimed Agricultural Soils Along the North Branch of Yangtze River Estuary
Cited by: 22
Author(s): Xinxin Wang, Lu Lu, Xue Zhou, Xiufeng Tang, Lu Kuang, Junhui Chen, Jun Shan, Huijie Lü, Hua Qin, Jonathan M. Adams, Baozhan Wang
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0070551

The Discrimination Power of Structural SuperIndices
Cited by: 3
Author(s): Matthias Dehmer, Abbe Mowshowitz
Software Mentions: 4
Published: about 13 years ago

10.1038/s41598-020-61288-5

Forecasting risk gene discovery in autism with machine learning and genome-scale data
Cited by: 21
Author(s): Leo Brueggeman, Tanner Koomar, Jacob J. Michaelson
Software Mentions: 4
Published: over 6 years ago

10.3389/fmed.2021.685124

Network Analysis of Outpatients to Identify Predictive Symptoms and Combinations of Symptoms Associated With Positive/Negative SARS-CoV-2 Nasopharyngeal Swabs
Cited by: 4
Author(s): Hervé Spechbach, Frédérique Jacquerioz, Virginie Prendki, Laurent Kaiser, Mikaëla Smit, Alexandra Calmy, François Chappuis, Idris Guessous, Julien Salamun, Stéphanie Baggio
Software Mentions: 4
Published: about 5 years ago

10.3389/fimmu.2020.00852

Lnc-ITSN1-2, Derived From RNA Sequencing, Correlates With Increased Disease Risk, Activity and Promotes CD4+ T Cell Activation, Proliferation and Th1/Th17 Cell Differentiation by Serving as a ceRNA for IL-23R via Sponging miR-125a in Inflammatory Bowel Disease
Cited by: 36
Author(s): Jiayan Nie, Qiu Zhao
Software Mentions: 4
Published: about 6 years ago

10.1186/1471-2164-14-728

Quantitative trait loci-dependent analysis of a gene co-expression network associated with Fusarium head blight resistance in bread wheat (Triticum aestivumL.)
Cited by: 80
Author(s): Karl G. Kugler, Gerald Siegwart, Thomas Nußbaumer, Christian Ametz, Manuel Spannagl, Barbara Steiner, Marc Lemmens, Klaus Mayer, Hermann Buerstmayr, Wolfgang Schweiger
Software Mentions: 4
Published: almost 13 years ago

10.3389/fmicb.2017.02559

Patterns and Drivers of Vertical Distribution of the Ciliate Community from the Surface to the Abyssopelagic Zone in the Western Pacific Ocean
Cited by: 32
Author(s): Feng Zhao, Sabine Filker, Kuidong Xu, Pingping Huang, Shan Zheng
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-019-53966-w

Alteration of the aggregation and spatial organization of the vector of Chagas disease, Triatoma infestans, by the parasite Trypanosoma cruzi
Cited by: 8
Author(s): Stéphanie Depickère, Gonzalo Marcelo Ramírez-Ávila, Jean‐Louis Deneubourg
Software Mentions: 4
Published: over 6 years ago

10.3389/fnhum.2015.00440

Genetic network properties of the human cortex based on regional thickness and surface area measures
Cited by: 12
Author(s): Anna R. Docherty, Chelsea Sawyers, Matthew S. Panizzon, Michael C. Neale, Lisa T. Eyler, Christine Fennema-Notestine, Carol E. Franz, Chi‐Hua Chen, Linda K. McEvoy, Brad Verhulst, Ming T. Tsuang, William S. Kremen
Software Mentions: 4
Published: almost 11 years ago

10.3389/fnhum.2020.00255

Aerobic Exercise Induces Functional and Structural Reorganization of CNS Networks in Multiple Sclerosis: A Randomized Controlled Trial
Cited by: 9
Author(s): Jan‐Patrick Stellmann, Adil Maarouf, Schulz Kh, Lisa Baquet, Jana Pöttgen, Stefan Patra, Iris Katharina Penner, Susanne Gellißen, Gesche Ketels, Pierre Besson, Jean Philippe Ranjeva, Maxime Guye, Guido Nolte, Andreas K. Engel, Bertrand Audoin, Christoph Heesen, Stefan M. Gold
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pcbi.1002603

An Integrated Regulatory Network Reveals Pervasive Cross-Regulation among Transcription and Splicing Factors
Cited by: 15
Author(s): Idit Kosti, Predrag Radivojac, Yael Mandel-Gutfreund
Software Mentions: 4
Published: about 14 years ago

10.3390/biom10060850

Can We Assume the Gene Expression Profile as a Proxy for Signaling Network Activity?
Cited by: 8
Author(s): Mehran Piran, Reza Karbalaei, Mehrdad Piran, Jehad Aldahdooh, Mehdi Mirzaie, Naser Ansari-Pour, Jing Tang, Mohieddin Jafari
Software Mentions: 4
Published: about 6 years ago

10.1155/2015/167249

mmnet: An R Package for Metagenomics Systems Biology Analysis
Cited by: 10
Author(s): Yang Cao, Xiaofei Zheng, Fēi Li, Xiaochen Bo
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pcbi.1003808

SANTA: Quantifying the Functional Content of Molecular Networks
Cited by: 56
Author(s): Alex J. Cornish, Florian Markowetz
Software Mentions: 4
Published: almost 12 years ago

10.1186/2043-9113-1-34

Profiling the human response to physical exercise: a computational strategy for the identification and kinetic analysis of metabolic biomarkers
Cited by: 36
Author(s): Michael Netzer, Klaus M. Weinberger, Michael Handler, Michael Seger, Xuekun Fang, Karl G. Kugler, Armin Graber, Christian Baumgartner
Software Mentions: 4
Published: over 15 years ago

10.1186/s12859-017-1762-1

Variable selection for disease progression models: methods for oncogenetic trees and application to cancer and HIV
Cited by: 3
Author(s): Katrin Hainke, Sebastian Szugat, Roland Fried, Jörg Rahnenführer
Software Mentions: 4
Published: almost 9 years ago

10.3390/jcm8101663

Revealing Associations between Diagnosis Patterns and Acupoint Prescriptions Using Medical Data Extracted from Case Reports
Cited by: 13
Author(s): Cheol Han Kim, Da Eun Yoon, Ye-Seul Lee, Won Jai Jung, Joo Hee Kim, Younbyoung Chae
Software Mentions: 4
Published: almost 7 years ago

10.3389/fgene.2018.00412

Network, Transcriptomic and Genomic Features Differentiate Genes Relevant for Drug Response
Cited by: 14
Author(s): Janet Piñero, Abel González-Pérez, Emre Güney, Joaquim Aguirre‐Plans, Ferrán Sanz, Baldo Oliva, Laura I. Furlong
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pcbi.1008018

Visual perception of liquids: Insights from deep neural networks
Cited by: 11
Author(s): Jan Jaap R. van Assen, Shin’ya Nishida, Roland W. Fleming
Software Mentions: 4
Published: almost 6 years ago

10.1074/jbc.RA119.011010

Synergistic mutations in soluble guanylyl cyclase (sGC) reveal a key role for interfacial regions in the sGC activation mechanism
Cited by: 8
Author(s): Kenneth C Childers, Xin‐Qiu Yao, Sam Giannakoulias, Joshua Amason, Donald Hamelberg, Elsa D. Garcin
Software Mentions: 4
Published: over 6 years ago

10.1242/bio.049809

Single cell force profiling of human myofibroblasts reveals a biophysical spectrum of cell states
Cited by: 6
Author(s): T. B. Layton, Lynn M. Williams, Huw Colin‐York, Fiona E. McCann, Marisa Cabrita, Marc Feldmann, Cameron Brown, Weilin Xie, Marco Fritzsche, Dominic Furniss, Jagdeep Nanchahal
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2164-16-S5-S2

Integrative network-based approach identifies key genetic elements in breast invasive carcinoma
Cited by: 27
Author(s): Mohamed Hamed, Christian Spaniol, Alexander Zapp, Volkhard Helms
Software Mentions: 4
Published: about 11 years ago

10.6026/97320630013025

Elucidation of the sequential transcriptional activity in Escherichia coli using time-series RNA-seq data
Cited by: 1
Author(s): Pui Shan Wong, Kosuke Tashiro, Satoru Kuhara, Sachiyo Aburatani
Software Mentions: 4
Published: over 9 years ago

10.1016/j.heliyon.2021.e07748

Massive surge of mRNA expression of clonal B-cell receptor in patients with COVID-19
Cited by: 4
Author(s): Yohei Funakoshi, Goh Ohji, Kimikazu Yakushijin, Kei Ebisawa, Yu Arakawa, Jun Saegusa, Hidenari Matsumoto, Tatsuya Imanishi, Eriko Fukuda, Takaji Matsutani, Yasuko Mori, Kentaro Iwata, Hironobu Minami
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pcbi.1002223

Transcriptomic Coordination in the Human Metabolic Network Reveals Links between n-3 Fat Intake, Adipose Tissue Gene Expression and Metabolic Health
Cited by: 35
Author(s): Melissa J. Morine, Audrey C. Tierney, Ben van Ommen, Hannelore Daniel, Sinéad Toomey, Ingrid M.F. Gjelstad, Isobel Claire Gormley, Pablo Pérez-Martı́nez, Christian A. Drevon, José López‐Miranda, Helen M. Roche
Software Mentions: 4
Published: over 14 years ago

10.3389/fgene.2019.00070

Global Genetics Research in Prostate Cancer: A Text Mining and Computational Network Theory Approach
Cited by: 5
Author(s): Md. Facihul Azam, Aliyu Musa, Matthias Dehmer, Olli Yli‐Harja, Frank Emmert‐Streib
Software Mentions: 4
Published: over 7 years ago

10.3758/s13428-018-1186-5

spreadr: An R package to simulate spreading activation in a network
Cited by: 24
Author(s): Cynthia S. Q. Siew
Software Mentions: 4
Published: over 7 years ago

10.3389/fgene.2015.00208

Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality
Cited by: 585
Author(s): Zhian N. Kamvar, Jonah C. Brooks, Niklaus J. Grünwald
Software Mentions: 4
Published: about 11 years ago

10.1186/s12864-020-07148-y

Analysing the meta-interaction between pathways by gene set topological impact analysis
Cited by: 2
Author(s): Yan Shu, Xu Chi, Xiao Chang, Mengliang Tian
Software Mentions: 4
Published: almost 6 years ago

10.1016/j.gpb.2016.04.004

Comparative Gene Expression Analysis of Mouse and Human Cardiac Maturation
Cited by: 38
Author(s): Hideki Uosaki, Y-h. Taguchi
Software Mentions: 4
Published: almost 10 years ago

10.1016/j.gpb.2018.08.002

PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System
Cited by: 19
Author(s): Huan Qi, Zhenhong Jiang, Kang Zhang, Shiping Yang, Fei He, Ziding Zhang
Software Mentions: 4
Published: almost 8 years ago

10.3390/ani10010144

Characterization of Anaerobic Rumen Fungal Community Composition in Yak, Tibetan Sheep and Small Tail Han Sheep Grazing on the Qinghai-Tibetan Plateau
Cited by: 16
Author(s): Wei Guo, Weiwei Wang, Sisi Bi, Ruijun Long, Farman Ullah, Muhammad Shafiq, Mi Zhou, Ying Zhang
Software Mentions: 4
Published: over 6 years ago

10.1098/rstb.2016.0095

Uncertain links in host–parasite networks: lessons for parasite transmission in a multi-host system
Cited by: 28
Author(s): Josephine G. Walker, Michaela Plein, Eric R. Morgan, Peter A. Vesk
Software Mentions: 4
Published: over 9 years ago

10.3390/ph14060553

Equine Mesenchymal Stem/Stromal Cells Freeze-Dried Secretome (Lyosecretome) for the Treatment of Musculoskeletal Diseases: Production Process Validation and Batch Release Test for Clinical Use
Cited by: 8
Author(s): Michela Mocchi, Stefano Grolli, Silvia Dotti, Dario Di Silvestre, Riccardo Villa, Priscilla Berni, Virna Conti, Giulia Passignani, Francesca Brambilla, Maurizio Del Bue, Laura Catenacci, Milena Sorrenti, Lorena Segale, Elia Bari, Pierluigi Mauri, Maria Luisa Torre, Sara Perteghella
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-017-4242-0

Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria
Cited by: 16
Author(s): Franck Cerutti, Ludovic Mallet, Anaïs Painset, Claire Hoede, Annick Moisan, Christophe Bécavin, Manuel Duval, Olivier Dussurget, Pascale Cossart, Christine Gaspin, Hélène Chiapello
Software Mentions: 4
Published: over 8 years ago

10.7717/peerj.10057

Brain hothubs and dark functional networks: correlation analysis between amplitude and connectivity for Broca’s aphasia
Cited by: 1
Author(s): Feng Lin, Sheue-yann Cheng, Dongqing Qi, Yu-Er Jiang, Qian-Qian Lyu, Lijuan Zhong, Zhongli Jiang
Software Mentions: 4
Published: almost 6 years ago

10.3389/fgene.2021.629475

Luminal A Breast Cancer Co-expression Network: Structural and Functional Alterations
Cited by: 11
Author(s): Diana García-Cortés, Enrique Hernández‐Lemus, Jesús Espinal-Enríquez
Software Mentions: 4
Published: over 5 years ago

10.1186/s12917-018-1406-3

Dynamic network measures reveal the impact of cattle markets and alpine summering on the risk of epidemic outbreaks in the Swiss cattle population
Cited by: 21
Author(s): Beatriz Vidondo, Bernhard Voelkl
Software Mentions: 4
Published: over 8 years ago

10.3389/fcimb.2018.00187

Staphylococcus aureus CC30 Lineage and Absence of sed,j,r-Harboring Plasmid Predict Embolism in Infective Endocarditis
Cited by: 3
Author(s): Jean-Philippe Rasigade, Amélie Leclère, François Alla, Adrien Tessier, Michèle Bes, Catherine Lechiche, Véronique Vernet-Garnier, Cédric Laouénan, François Vandenesch, Catherine Leport
Software Mentions: 4
Published: about 8 years ago

10.1186/s13012-016-0499-y

Forging a link between mentoring and collaboration: a new training model for implementation science
Cited by: 35
Author(s): Douglas A. Luke, Ana A. Baumann, Bobbi J. Carothers, John Landsverk, Enola K. Proctor
Software Mentions: 4
Published: almost 10 years ago

10.7717/peerj.10594

Identification of hub genes and biological pathways in hepatocellular carcinoma by integrated bioinformatics analysis
Cited by: 6
Author(s): Qian Zhao, Yan Zhang, Shichun Shao, Yeqing Sun, Zhengkui Lin
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.9395

Doing nothing and what it looks like: inactivity in fattening cattle
Cited by: 8
Author(s): Sara Hintze, Freija Maulbetsch, Lucy Asher, Christoph Winckler
Software Mentions: 4
Published: about 6 years ago