Ecosyste.ms: Papers

10.3390/insects12070639

Estimation of the Recent Expansion Rate of Ruspolia nitidula (Orthoptera) on a Regional and Landscape Scale
Cited by: 3
Author(s): Oto Kaláb, Petr Pyszko, Petr Kočárek
Software Mentions: 9
Published: about 3 years ago

10.1186/s40168-016-0154-5

Recovering complete and draft population genomes from metagenome datasets
Cited by: 195
Author(s): Naseer Sangwan, Fangfang Xia, Jack A. Gilbert
Software Mentions: 7
Published: over 8 years ago

10.1038/s41598-018-23494-0

Methylation-to-Expression Feature Models of Breast Cancer Accurately Predict Overall Survival, Distant-Recurrence Free Survival, and Pathologic Complete Response in Multiple Cohorts
Cited by: 6
Author(s): Jeffrey Thompson, Brock C. Christensen, Carmen J. Marsit
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pcbi.1004568

Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways
Cited by: 43
Author(s): Sean L. Seyler, Avishek Kumar, M. F. Thorpe, Oliver Beckstein
Software Mentions: 5
Published: almost 9 years ago

10.1007/s10928-020-09730-z

Population pharmacokinetic modeling of intramuscular and oral dexamethasone and betamethasone in Indian women
Cited by: 8
Author(s): Wojciech Krzyzanski, Mark A. Milad, Alan H. Jobe, Thomas Peppard, Robert R. Bies, William J. Jusko
Software Mentions: 4
Published: over 3 years ago

10.1186/1752-0509-3-93

Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle
Cited by: 11
Author(s): Pierre R. Bushel, Nicholas A. Heard, Roee Gutman, Liwen Liu, Shyamal D. Peddada, Saumyadipta Pyne
Software Mentions: 4
Published: about 15 years ago

10.1186/1471-2148-8-201

Complex population genetic and demographic history of the Salangid, Neosalanx taihuensis, based on cytochrome b sequences
Cited by: 33
Author(s): Liang Zhao, Jie Zhang, Zhijin Liu, Stephan M. Funk, Fuwen Wei, Muqi Xu, Ming Li
Software Mentions: 4
Published: about 16 years ago

10.1186/1475-2859-10-18

Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli
Cited by: 157
Author(s): Jeremy J. Minty, Ann A Lesnefsky, Fengming Lin, Yu Chen, Ted A. Zaroff, Artur Veloso, Bin Xie, Catie A McConnell, Rebecca J Ward, Donald R. Schwartz, Jean-Marie Rouillard, Yuan Gao, Erdogan Gülari, Xiaoxia Lin
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.pone.0204426

Elucidation and analyses of the regulatory networks of upland and lowland ecotypes of switchgrass in response to drought and salt stresses
Cited by: 7
Author(s): Chunman Zuo, Yuhong Tang, Fang Hao, Yiming Liu, Xunzhong Zhang, Bingyu Zhao, Ying Xu
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pcbi.1003323

Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response
Cited by: 26
Author(s): Ashwini Patil, Yutaro Kumagai, Kuo-ching Liang, Yutaka Suzuki, Kenta Nakai
Software Mentions: 3
Published: almost 11 years ago

10.3390/e22111235

An Evaluation of Entropy Measures for Microphone Identification
Cited by: 8
Author(s): Gianmarco Baldini, Irene Amerini
Software Mentions: 2
Published: almost 4 years ago

10.3389/fpsyg.2021.558930

The Importance of Well-Being on Resiliency of Filipino Adults During the COVID-19 Enhanced Community Quarantine: A Necessary Condition Analysis
Cited by: 13
Author(s): Desiderio S. Camitan, Lalaine N. Bajin
Software Mentions: 2
Published: over 3 years ago

10.1007/s11095-021-02994-1

Which Analysis Approach Is Adequate to Leverage Clinical Microdialysis Data? A Quantitative Comparison to Investigate Exposure and Response Exemplified by Levofloxacin
Cited by: 7
Author(s): David Busse, André Schaeftlein, Alexander Solms, Luis Ilia, Robin Michelet, Markus Zeitlinger, Wilhelm Huisinga, Charlotte Kloft
Software Mentions: 2
Published: over 3 years ago

10.1007/s00497-015-0261-7

A decade of pollen transcriptomics
Cited by: 113
Author(s): Nicholas Rutley, David Twell
Software Mentions: 2
Published: over 9 years ago

10.3389/fvets.2020.00586

Pharmacokinetics of Intravenous, Intramuscular, Oral, and Transdermal Administration of Flunixin Meglumine in Pre-wean Piglets
Cited by: 8
Author(s): Heather Kittrell, Jonathan P. Mochel, Justin T. Brown, Anna Marie K Forseth, Kristen Hayman, Suzanne M. Rajewski, Johann F. Coetzee, Benjamin Schneider, Brette Ratliffe, Kristin Skoland, Locke A. Karriker
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-019-56097-4

Impact of iterative reconstruction with resolution recovery in myocardial perfusion SPECT: phantom and clinical studies
Cited by: 3
Author(s): Koichi Okuda, Kénichi Nakajima, Hiroto Yoneyama, Takayuki Shibutani, Masahisa Onoguchi, Shinro Matsuo, Mitsumasa Hashimoto, Seigo Kinuya
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0031984

Dynamic Network of Transcription and Pathway Crosstalk to Reveal Molecular Mechanism of MGd-Treated Human Lung Cancer Cells
Cited by: 10
Author(s): Li‐Hua Shao, Lishan Wang, Zengxin Wei, Yüting Xiong, Yan Wang, Kefu Tang, Yang Li, Guo-yin Feng, Qinghe Xing, Lin He
Software Mentions: 2
Published: over 12 years ago

10.1155/2014/891761

Dynamic Regulatory Network Reconstruction for Alzheimer’s Disease Based on Matrix Decomposition Techniques
Cited by: 10
Author(s): Wei Kong, Xiaoyang Mou, Xiefei Zhi, Xing Zhang, Yang Yang
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1004122

Coherent Functional Modules Improve Transcription Factor Target Identification, Cooperativity Prediction, and Disease Association
Cited by: 31
Author(s): Konrad J. Karczewski, M Snyder, Russ B. Altman, Nicholas P. Tatonetti
Software Mentions: 2
Published: over 10 years ago

10.1186/s12864-021-07461-0

Analysis of temporal gene regulation of Listeria monocytogenes revealed distinct regulatory response modes after exposure to high pressure processing
Cited by: 4
Author(s): Bahareh Nikparvar, Margarita Andreevskaya, Ilhan Cem Duru, Florentina Ionela Bucur, Leontina Grigore‐Gurgu, Daniela Borda, Anca Ioana Nicolau, Christian U. Riedel, Petri Auvinen, Nadav Bar
Software Mentions: 2
Published: over 3 years ago

10.1186/1752-0509-7-126

Network component analysis provides quantitative insights on an Arabidopsis transcription factor-gene regulatory network
Cited by: 14
Author(s): Ashok Misra, Ganesh Sriram
Software Mentions: 1
Published: over 11 years ago

10.1186/1752-0509-4-16

Inferring genetic interactions via a nonlinear model and an optimization algorithm
Cited by: 22
Author(s): Chung-Ming Chen, Chih Lee, Chi‐Cheng Chuang, Chia-Chang Wang, Grace S. Shieh
Software Mentions: 1
Published: over 14 years ago

10.1186/1752-0509-3-110

Inferring a transcriptional regulatory network of the cytokinesis-related genes by network component analysis
Cited by: 9
Author(s): Shun Fu Chen, Yue Li Juang, Wei Kang Chou, Jin Mei Lai, Chi Ying F. Huang, Cheng Yen Kao, Feng Sheng Wang
Software Mentions: 1
Published: almost 15 years ago

10.1186/1752-0509-8-S2-S2

Use of prior knowledge for the analysis of high-throughput transcriptomics and metabolomics data
Cited by: 19
Author(s): Polina Reshetova, Age K. Smilde, Antoine H. C. van Kampen, Johan A. Westerhuis
Software Mentions: 1
Published: over 10 years ago

10.1186/1752-0509-5-S3-S8

A transcriptional dynamic network during Arabidopsis thaliana pollen development
Cited by: 15
Author(s): Jigang Wang, Xiaojie Qiu, Yuhua Li, Youping Deng, Tieliu Shi
Software Mentions: 1
Published: almost 13 years ago

10.1093/bioinformatics/btx508

Efficient inference for sparse latent variable models of transcriptional regulation
Cited by: 3
Author(s): Zhenwen Dai, Mudassar Iqbal, Neil D. Lawrence, Magnus Rattray
Software Mentions: 1
Published: about 7 years ago

10.1186/1475-2875-13-281

Pharmacokinetic evaluation of intravenous artesunate in adults with uncomplicated falciparum malaria in Kenya: a phase II study
Cited by: 13
Author(s): Qigui Li, Shon Remich, Scott R. Miller, Bernhards Ogutu, Walter Otieno, Víctor Meléndez, Paktiya Teja‐Isavadharm, Peter J. Weina, Mark Hickman, Bryan Smith, Mark E. Polhemus
Software Mentions: 1
Published: about 10 years ago

10.1186/1475-2875-11-293

Population pharmacokinetics of Artemether and dihydroartemisinin in pregnant women with uncomplicated Plasmodium falciparum malaria in Uganda
Cited by: 41
Author(s): Joel Tärning, Frank Kloprogge, Patrice Piola, Mehul Dhorda, Sulaiman Muwanga, Eleanor Turyakira, Nitra Nuengchamnong, François Nosten, Nicholas P. J. Day, Nicholas J. White, Philippe J. Guérin, Niklas Lindegårdh
Software Mentions: 1
Published: about 12 years ago

10.3390/metabo2040844

Analysis and Design of Stimulus Response Curves of E. coli
Cited by: 0
Author(s): Andreas Kremling, Anna Goehler, Knut Jahreis, Matthias Nees, Benedikt Auerbach, Wolfgang Schmidt‐Heck, Öznur Kökpınar, Robert Geffers, Ursula Rinas, Katja Bettenbrock
Software Mentions: 1
Published: almost 12 years ago

10.3390/microarrays4040596

An Overview of NCA-Based Algorithms for Transcriptional Regulatory Network Inference
Cited by: 5
Author(s): Xu Wang, Mustafa Alshawaqfeh, Xuan Hong Dang, Bilal Wajid, Amina Noor, Marwa Qaraqe, Erchin Serpedin
Software Mentions: 1
Published: almost 9 years ago

10.15252/msb.20156236

An experimentally supported model of the <i>Bacillus subtilis</i> global transcriptional regulatory network
Cited by: 177
Author(s): Mario L. Arrieta-Ortiz, Christoph Hafemeister, Ashley R. Bate, Timothy R. Chu, Alex Greenfield, Bentley Shuster, Samantha N. Barry, Matthew Gallitto, Brian Liu, Thadeous J. Kacmarczyk, Francis J. Santoriello, Jie Chen, Christopher D. A. Rodrigues, Tsutomu Sato, David Z. Rudner, Adam Driks, Richard Bonneau, Patrick Eichenberger
Software Mentions: 1
Published: almost 9 years ago

10.7717/peerj.5247

Performance comparison of machine learning techniques in sleep scoring based on wavelet features and neighboring component analysis
Cited by: 15
Author(s): Behrouz Alizadeh Savareh, Azadeh Bashiri, Ali Behmanesh, Gholam Hossein Meftahi, Boshra Hatef
Software Mentions: 1
Published: about 6 years ago

10.3390/pharmaceutics13040535

Matrix Effects of the Hydroethanolic Extract of Calyces of Physalis peruviana L. on Rutin Pharmacokinetics in Wistar Rats Using Population Modeling
Cited by: 3
Author(s): Gina Paola Domínguez Moré, María Isabel Cardona, Paula Michelle Sepúlveda, Sandra Milena Echeverry, Cláudia Maria Oliveira Simões, Diana Marcela Aragón
Software Mentions: 1
Published: over 3 years ago

10.3390/pharmaceutics12111040

Effects of Carbamazepine and Phenytoin on Pharmacokinetics and Pharmacodynamics of Rivaroxaban
Cited by: 3
Author(s): Lien Thi Ngo, Sung-Yoon Yang, Quyen Thi Tran, Sang Kyum Kim, Hwi-yeol Yun, Jung-Woo Chae
Software Mentions: 1
Published: almost 4 years ago

10.1007/s11095-018-2373-x

Anti-GD2 Immunoliposomes for Targeted Delivery of the Survivin Inhibitor Sepantronium Bromide (YM155) to Neuroblastoma Tumor Cells
Cited by: 21
Author(s): Shima Gholizadeh, M. Emmy M. Dolman, Rebecca Wieriks, Rolf W. Sparidans, Wim E. Hennink, Robbert J. Kok
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pcbi.1000311

Using Network Component Analysis to Dissect Regulatory Networks Mediated by Transcription Factors in Yeast
Cited by: 29
Author(s): Chun Yuan, Simon J. Galbraith, James C. Liao, Eleazar Eskin
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0180337

Differences of immune disorders between Alzheimer’s disease and breast cancer based on transcriptional regulation
Cited by: 10
Author(s): Wei Kong, Xiaoyang Mou, Jin Deng, Benteng Di, Ruxing Zhong, Shuaiqun Wang, Yang Yang, Weiming Zeng
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0031053

Determining PTEN Functional Status by Network Component Deduced Transcription Factor Activities
Cited by: 10
Author(s): Linh M. Tran, Chun Ju Chang, Seema B. Plaisier, Shumin Wu, Julie Dang, Paul S. Mischel, James C. Liao, Thomas G. Graeber, Hong Wu
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0252657

Muscle network topology analysis for the classification of chronic neck pain based on EMG biomarkers extracted during walking
Cited by: 7
Author(s): David Jiménez-Grande, S. Farokh Atashzar, Eduardo Martinez‐Valdes, Deborah Falla
Software Mentions: 1
Published: about 3 years ago

10.1208/s12248-015-9829-2

Pharmacokinetic Interactions for Drugs with a Long Half-Life—Evidence for the Need of Model-Based Analysis
Cited by: 22
Author(s): Elin M Svensson, Chayan Acharya, Björn Clauson, Kelly E. Dooley, Mats O. Karlsson
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0123262

Automatic Detection of Diseased Tomato Plants Using Thermal and Stereo Visible Light Images
Cited by: 122
Author(s): Shan E. Ahmed Raza, Gillian Prince, John P. Clarkson, Nasir M. Rajpoot
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0035762

Learning Transcriptional Regulatory Relationships Using Sparse Graphical Models
Cited by: 4
Author(s): Xiang Zhang, Wei Cheng, Jennifer Listgarten, Carl Kadie, Shangyu Huang, Wei Wang, David Heckerman
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0037694

Genus Paracoccidioides: Species Recognition and Biogeographic Aspects
Cited by: 123
Author(s): Raquel Cordeiro Theodoro, Marcus de Melo Teixeira, Maria Sueli Soares Felipe, Karina dos Santos Paduan, Paulo Eduardo Martins Ribolla, Gioconda San-Blas, Eduardo Bagagli
Software Mentions: 1
Published: over 12 years ago

10.1080/10717544.2016.1253798

Successful delivery of docetaxel to rat brain using experimentally developed nanoliposome: a treatment strategy for brain tumor
Cited by: 45
Author(s): Tapan Kumar Shaw, Debabrata Mandal, Goutam Dey, Mahesh Pal, Paramita Paul, Samrat Chakraborty, Kazi Asraf Ali, Biswajit Mukherjee, Amitabha Bandyopadhyay, Mahitosh Mandal
Software Mentions: 1
Published: over 7 years ago

10.1080/10717544.2016.1230904

Research on the comparison of the demethylvancomycin’s diffusion–deposition characteristics in the ocular solid tissues of sustained subtenon drug delivery with subconjunctival injection
Cited by: 2
Author(s): Yiqin Duan, Yezhen Yang, Xian-Ju Huang, Ding Lin
Software Mentions: 1
Published: over 7 years ago

10.1080/10717544.2018.1435749

Lipid-based nanocarrier efficiently delivers highly water soluble drug across the blood–brain barrier into brain
Cited by: 19
Author(s): Lopamudra Dutta, Biswajit Mukherjee, Tapash Chakraborty, Malay K. Das, Laboni Mondal, Sanchari Bhattacharya, Raghuvir H. Gaonkar, Mita Chatterjee Debnath
Software Mentions: 1
Published: over 6 years ago

10.1002/ece3.1268

Phylogeography and palaeodistribution modelling of<i>Nassauvia</i>subgenus<i>Strongyloma</i>(Asteraceae): exploring phylogeographical scenarios in the Patagonian steppe
Cited by: 16
Author(s): Marcela Viviana Nicola, Silvana M. Sede, Raúl Pozner, Leigh A. Johnson
Software Mentions: 1
Published: almost 10 years ago

10.3389/fnhum.2017.00251

The Impact of Monaural Beat Stimulation on Anxiety and Cognition
Cited by: 17
Author(s): Leila Chaieb, Caroline Wilpert, Christian Hoppe, Nikolai Axmacher, Juergen Fell
Software Mentions: 1
Published: over 7 years ago

10.3389/fphar.2019.00712

In Vivo Metabolism of Ibuprofen in Growing Conventional Pigs: A Pharmacokinetic Approach
Cited by: 7
Author(s): Joske Millecam, Siegrid De Baere, Mathias Devreese
Software Mentions: 1
Published: about 5 years ago

10.3389/fpls.2013.00532

Genome scale transcriptional response diversity among ten ecotypes of Arabidopsis thaliana during heat stress
Cited by: 35
Author(s): Pankaj Barah, Naresh Doni Jayavelu, John Mundy, Atle M. Bones
Software Mentions: 1
Published: over 11 years ago

10.3389/fpsyg.2017.00254

Relationship between Divergent Thinking and Intelligence: An Empirical Study of the Threshold Hypothesis with Chinese Children
Cited by: 34
Author(s): Baoguo Shi, Lijing Wang, Jiahui Yang, Mengpin Zhang, Li Xu
Software Mentions: 1
Published: over 7 years ago

10.3389/fpsyg.2017.02192

Necessity as a Function of Skewness
Cited by: 8
Author(s): Kimmo Sorjonen, Jenny Wikström Alex, Bo Melin
Software Mentions: 1
Published: over 6 years ago

10.3389/fpsyg.2019.00283

Predicting the Significance of Necessity
Cited by: 6
Author(s): Kimmo Sorjonen, Bo Melin
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-58290-2

Machine Learning and Network Analyses Reveal Disease Subtypes of Pancreatic Cancer and their Molecular Characteristics
Cited by: 52
Author(s): Musalula Sinkala, Nicola Mulder, Darren P. Martin
Software Mentions: 1
Published: over 4 years ago

10.3390/s110303163

Delaunay Triangulation as a New Coverage Measurement Method in Wireless Sensor Network
Cited by: 33
Author(s): Hassan Chizari, Majid Hosseini, Timothy Poston, Shukor Abd Razak, Abdul Hanan Abdullah
Software Mentions: 1
Published: over 13 years ago

10.3390/s20164639

Graph Eigen Decomposition-Based Feature-Selection Method for Epileptic Seizure Detection Using Electroencephalography
Cited by: 14
Author(s): Md. Khademul Islam Molla, Kazi Mahmudul Hassan, Md. Rabiul Islam, Tomomi Tanaka
Software Mentions: 1
Published: about 4 years ago

10.3390/s20236742

Wind Turbine Gearbox Condition Monitoring Based on Class of Support Vector Regression Models and Residual Analysis
Cited by: 23
Author(s): Harsh S. Dhiman, Dipankar Deb, J. Douglas Carroll, Vlad Mureşan, Mihaela-Ligia Ungureşan
Software Mentions: 1
Published: almost 4 years ago

10.3390/s21113650

EEG-Based Prediction of the Recovery of Carotid Blood Flow during Cardiopulmonary Resuscitation in a Swine Model
Cited by: 1
Author(s): Heejin Kim, Ki Hong Kim, Ki Jeong Hong, Yun Hyi Ku, Sang Do Shin, Hee Chan Kim
Software Mentions: 1
Published: over 3 years ago

10.1186/1742-4682-2-23

Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach
Cited by: 102
Author(s): Anne‐Laure Boulesteix, Korbinian Strimmer
Software Mentions: 1
Published: about 19 years ago

10.1186/s12959-018-0185-1

Pharmacokinetics of rivaroxaban in children using physiologically based and population pharmacokinetic modelling: an EINSTEIN-Jr phase I study
Cited by: 37
Author(s): Stefan Willmann, Kirstin Thelen, Dagmar Kubitza, Anthonie W. A. Lensing, Matthias Frede, Katrin Coboeken, Jan Stampfuss, Rolf Burghaus, Wolfgang Mück, Jörg Lippert
Software Mentions: 1
Published: almost 6 years ago

10.1007/s10928-017-9562-9

gPKPDSim: a SimBiology®-based GUI application for PKPD modeling in drug development
Cited by: 18
Author(s): Iraj Hosseini, Anita Gajjala, Daniela Bumbaca Yadav, Siddharth Sukumaran, Saroja Ramanujan, Ricardo Paxson, Kapil Gadkar
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0029145

Novel Positive-Sense, Single-Stranded RNA (+ssRNA) Virus with Di-Cistronic Genome from Intestinal Content of Freshwater Carp (Cyprinus carpio)
Cited by: 52
Author(s): Ákos Boros, Péter Pankovics, Peter Simmonds, Gábor Reuter
Software Mentions: 1
Published: almost 13 years ago

10.1186/1748-7188-2-2

Transcriptional regulatory network discovery via multiple method integration: application to e. coli K12
Cited by: 11
Author(s): Jin-Hua Sun, Kağan Tuncay, Alaa Abi Haidar, Lisa Ensman, Frank Stanley, Michael Trelinski, P. Ortoleva
Software Mentions: 1
Published: over 17 years ago

10.1186/s13075-015-0651-0

The preclinical pharmacology of the high affinity anti-IL-6R Nanobody® ALX-0061 supports its clinical development in rheumatoid arthritis
Cited by: 127
Author(s): Maarten Van Roy, Cedric Ververken, Els Beirnaert, Sven Hoefman, Joost A. Kolkman, Michel Vierboom, Elia Breedveld, Bert ‘t Hart, Sofie Poelmans, Lieselot Bontinck, Alex Hemeryck, S. Jacobs, Judith Baumeister, Hans Ulrichts
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2105-11-308

Computational modeling with forward and reverse engineering links signaling network and genomic regulatory responses: NF-κB signaling-induced gene expression responses in inflammation
Cited by: 26
Author(s): Shih Chi Peng, David Shan Hill Wong, Kai Che Tung, Yan Yu Chen, Chun Cheih Chao, Chien Hua Peng, Yung-Jen Chuang, Chuan Yi Tang
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-12-233

Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities
Cited by: 53
Author(s): Yu‐Fan Fu, Laura R. Jarboe, Julie A. Dickerson
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2105-8-10

Bioinformatics analysis of the early inflammatory response in a rat thermal injury model
Cited by: 30
Author(s): Eric Yang, Timothy J. Maguire, Martin L. Yarmush, François Berthiaume, Ioannis P. Androulakis
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2105-12-82

Motif-guided sparse decomposition of gene expression data for regulatory module identification
Cited by: 15
Author(s): Ting Gong, Jianhua Xuan, Li Chen, Rebecca B. Riggins, Huai Li, Eric P. Hoffman, Robert Clarke, Yue Joseph Wang
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2105-8-188

Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data
Cited by: 35
Author(s): Wei Wu, Wen-Hsiung Li, Bor Sen Chen
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2105-11-511

Trimming of mammalian transcriptional networks using network component analysis
Cited by: 13
Author(s): Linh M. Tran, Daniel R. Hyduke, James C. Liao
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12859-015-0768-9

Iterative sub-network component analysis enables reconstruction of large scale genetic networks
Cited by: 11
Author(s): Naresh Doni Jayavelu, Lasse Svenkerud Aasgaard, Nadav Bar
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2105-8-20

Transcriptional regulatory network refinement and quantification through kinetic modeling, gene expression microarray data and information theory
Cited by: 25
Author(s): Abdallah Sayyed-Ahmad, Kağan Tuncay, P. Ortoleva
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2105-9-S1-S21

Motif-directed network component analysis for regulatory network inference
Cited by: 23
Author(s): Chen Wang, Jianhua Xuan, Li Chen, Po Zhao, Yue Joseph Wang, Robert Clarke, Eric P. Hoffman
Software Mentions: 1
Published: over 16 years ago

10.1186/1472-6785-7-7

The importance of comparative phylogeography in diagnosing introduced species: a lesson from the seal salamander, Desmognathus monticola
Cited by: 18
Author(s): Ronald M. Bonett, Kenneth H. Kozak, David R. Vieites, Alison Bare, Jessica A. Wooten, Stanley E. Trauth
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2148-8-21

Phylogeography and Demographic History of Chinese Black-Spotted Frog Populations (Pelophylax nigromaculata): Evidence for Independent Refugia Expansion and Secondary Contact
Cited by: 97
Author(s): Hua Zhang, Jie Yan, Guoqiang Zhang, Kaiya Zhou
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2148-8-161

Evolutionary history of the endangered fish Zoogoneticus quitzeoensis (Bean, 1898) (Cyprinodontiformes: Goodeidae) using a sequential approach to phylogeography based on mitochondrial and nuclear DNA data
Cited by: 41
Author(s): Omar Domínguez‐Domínguez, Fernando Alda, Gerardo Pérez‐Ponce de León, José Luis García-Garitagoitia, Ignacio Doadrio
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-6-90

Inferring yeast cell cycle regulators and interactions using transcription factor activities
Cited by: 67
Author(s): Young Lyeol Yang, Jason K. Suen, Mark P. Brynildsen, Simon J. Galbraith, James C. Liao
Software Mentions: 1
Published: over 19 years ago

10.1186/s12864-015-2260-3

Reconstruction of temporal activity of microRNAs from gene expression data in breast cancer cell line
Cited by: 5
Author(s): Naresh Doni Jayavelu, Nadav Bar
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-021-07524-2

Deep learning assisted multi-omics integration for survival and drug-response prediction in breast cancer
Cited by: 32
Author(s): Vidhi Malik, Yogesh Kalakoti, Durai Sundar
Software Mentions: 1
Published: over 3 years ago

10.1186/1752-0509-3-78

A dynamic network of transcription in LPS-treated human subjects
Cited by: 37
Author(s): Junhee Seok, Wenzhong Xiao, Lyle L. Moldawer, Ronald W. Davis, Markus W. Covert
Software Mentions: 1
Published: about 15 years ago

10.1186/1752-0509-7-S5-S4

mAPC-GibbsOS: an integrated approach for robust identification of gene regulatory networks
Cited by: 7
Author(s): Xu Shi, Jin Gu, Xi Chen, Ayesha N. Shajahan, Leena Hilakivi‐Clarke, Robert Clarke, Jianhua Xuan
Software Mentions: 1
Published: almost 11 years ago