Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: analysis

https://packages.ecosyste.ms/registries/pypi.org/packages/analysis

Source code analysis of Python programs
8 versions
Latest release: over 18 years ago
348 downloads last month

Papers Mentioning analysis 2,036

10.3390/metabo10080316
Metabolite Profiles of the Relationship between Body Mass Index (BMI) Milestones and Metabolic Risk during Early Adolescence
Cited by: 3
Author(s): Wei Perng, Mohammad L. Rahman, Izzuddin M. Aris, Gregory A. Michelotti, Joanne E. Sordillo, Jorge E. Chavarro, Emily Oken, Marie‐France Hivert
Software Mentions: 2
Published: over 4 years ago
10.3390/metabo10020059
TGF-ß1 Induces Changes in the Energy Metabolism of White Adipose Tissue-Derived Human Adult Mesenchymal Stem/Stromal Cells In Vitro
Cited by: 2
Author(s): Olga Hahn, Lena-Christin Ingwersen, Abdel-Rahman Soliman, Mohamed Hamed, Georg Fuellen, Markus Wolfien, Julia Scheel, Olaf Wolkenhauer, Dirk Koczan, Günter Kamp, Kirsten Peters
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12934-018-1052-2
Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains
Cited by: 51
Author(s): Ilaria Massaiu, Lorenzo Pasotti, Nikolaus Sonnenschein, Erlinda Rama, Matteo Cavaletti, Paolo Magni, Cinzia Calvio, Markus J. Herrgård
Software Mentions: 2
Published: almost 6 years ago
10.1186/s12934-017-0824-4
Metabolic engineering of Synechococcus elongatus PCC 7942 for improvement of 1,3-propanediol and glycerol production based on in silico simulation of metabolic flux distribution
Cited by: 29
Author(s): Yasutaka Hirokawa, Shingo Matsuo, Hiroyuki Hamada, Fumio Mizutani, Taizo Hanai
Software Mentions: 2
Published: almost 7 years ago
10.1186/s12934-015-0355-9
Genetic and nutrient modulation of acetyl-CoA levels in Synechocystis for n-butanol production
Cited by: 89
Author(s): Josefine Anfelt, Danuta Kaczmarzyk, Kiyan Shabestary, Björn Renberg, Johan Rockberg, Jens Nielsen, Mathias Uhlén, Elton P. Hudson
Software Mentions: 2
Published: about 9 years ago
10.1186/s12934-019-1229-3
A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory
Cited by: 18
Author(s): Thordis Kristjansdottir, Elleke Fenna Bosma, Filipe Branco dos Santos, Emre Özdemir, Markus J. Herrgård, Lucas França, Bruno Sommer Ferreira, Alex Toftgaard Nielsen, Steinn Guðmundsson
Software Mentions: 2
Published: about 5 years ago
10.1186/s40168-020-00923-9
The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for complex human diseases
Cited by: 64
Author(s): Fengzhe Xu, Yuanqing Fu, Tao Sun, Zengliang Jiang, Zelei Miao, Menglei Shuai, Wanglong Gou, Chu-wen Ling, Jian Yang, Jun Wang, Yuming Chen, Ju‐Sheng Zheng
Software Mentions: 2
Published: about 4 years ago
10.3390/microorganisms9020240
Shedding Light on the African Enigma: In Vitro Testing of Homo sapiens-Helicobacter pylori Coevolution
Cited by: 9
Author(s): Bruno Cavadas, Marina Concli Leite, Nicole Pedro, Ana C. Magalhães, Joana Melo, Marcelo Correia, Valdemar Máximo, Rui Camacho, Nuno A. Fonseca, Céu Figueiredo, Luı́sa Pereira
Software Mentions: 2
Published: almost 4 years ago
10.1186/s13229-017-0130-3
Leveraging blood serotonin as an endophenotype to identify de novo and rare variants involved in autism
Cited by: 44
Author(s): Rui Chen, Lea K. Davis, Stephen J. Guter, Qiang Wei, Suma Jacob, Melissa H. Potter, Nancy J. Cox, Edwin H. Cook, James S. Sutcliffe, Bingshan Li
Software Mentions: 2
Published: over 7 years ago
10.3390/molecules23071527
Investigations of Structural Requirements for BRD4 Inhibitors through Ligand- and Structure-Based 3D QSAR Approaches
Cited by: 11
Author(s): Adeena Tahir, Rima D. Alharthy, Saadia Naseem, Natasha Mahmood, Mahmood Ahmed, Khuram Shahzad, Muhammad Usman Akhtar, Abdul Hameed, Irfan Sadiq, Haq Nawaz, Muhammad Muddassar
Software Mentions: 2
Published: over 6 years ago
10.3390/molecules23010186
Synthesis, Anti-Proliferative Activity Evaluation and 3D-QSAR Study of Naphthoquinone Derivatives as Potential Anti-Colorectal Cancer Agents
Cited by: 9
Author(s): Julio Acuña, Jhoan Piermattey, Daneiva Caro, Sven Bannwitz, L Barrios, Juan‐Felipe López, Yanet Ocampo, Ricardo Vivas‐Reyes, Fabio Aristizábal, Ricardo Gaitán, Klaus Müller, Luís Franco
Software Mentions: 2
Published: almost 7 years ago
10.3390/molecules24061064
Metabolome and Transcriptome Sequencing Analysis Reveals Anthocyanin Metabolism in Pink Flowers of Anthocyanin-Rich Tea (Camellia sinensis)
Cited by: 49
Author(s): Dylan O’Neill Rothenberg, Haijun Yang, Meiban Chen, Wenting Zhang, Lingyun Zhang
Software Mentions: 2
Published: over 5 years ago
10.3390/molecules25246003
Structure-Based Discovery and Bioactivity Evaluation of Novel Aurora-A Kinase Inhibitors as Anticancer Agents via Docking-Based Comparative Intermolecular Contacts Analysis (dbCICA)
Cited by: 10
Author(s): Majd S. Hijjawi, Reem Fawaz Abutayeh, Mutasem O. Taha
Software Mentions: 2
Published: almost 4 years ago
10.3390/molecules24142564
Integration of Metabolite Profiling and Transcriptome Analysis Reveals Genes Related to Volatile Terpenoid Metabolism in Finger Citron (C. medica var. sarcodactylis)
Cited by: 37
Author(s): Yaying Xu, Changqing Zhu, Changjie Xu, Jun Sun, Donald Grierson, Bo Zhang, Kunsong Chen
Software Mentions: 2
Published: over 5 years ago
10.3390/molecules190914723
Challenges and Opportunities of MicroRNAs in Lymphomas
Cited by: 25
Author(s): Giacoma De Tullio, Valentina Fazio, Nicola Sgherza, Carla Minoia, Simona Serratì, Francesca Merchionne, Giacomo Loseto, Angela Iacobazzi, Antonello Rana, P. Petrillo, Nicola Silvestris, Pasquale Iacopino, Attilio Giacosa
Software Mentions: 2
Published: about 10 years ago
10.3390/molecules24162989
Discovery of Lipid Peroxidation Inhibitors from Bacopa Species Prioritized through Multivariate Data Analysis and Multi-Informative Molecular Networking
Cited by: 8
Author(s): Tongchai Saesong, Pierre‐Marie Allard, Emerson Ferreira Queiroz, Laurence Marcourt, Nitra Nuengchamnong, Prapapan Temkitthawon, Nantaka Khorana, Jean‐Luc Wolfender, Kornkanok Ingkaninan
Software Mentions: 2
Published: over 5 years ago
10.1016/j.molmet.2020.101094
Ozone-induced fetal growth restriction in rats is associated with sexually dimorphic placental and fetal metabolic adaptation
Cited by: 9
Author(s): Colette N. Miller, Janice A. Dye, Andres R. Henriquez, Erica Stewart, Katelyn S. Lavrich, Gleta Carswell, Hongzu Ren, Danielle L. Freeborn, Samantha J. Snow, Mette C. Schladweiler, Judy H. Richards, Prasada Rao S. Kodavanti, Anna Fisher, Brian N. Chorley, Urmila P. Kodavanti
Software Mentions: 2
Published: almost 4 years ago
10.1002/1878-0261.12349
C1q/ <scp>TNF</scp> ‐related peptide 8 ( <scp>CTRP</scp> 8) promotes temozolomide resistance in human glioblastoma
Cited by: 16
Author(s): Thatchawan Thanasupawat, Aleksandra Głogowska, Maxwell Burg, Jerry Krcek, Jason Beiko, Marshall Pitz, Guojun Zhang, Sabine Hombach‐Klonisch, Thomas Klonisch
Software Mentions: 2
Published: over 6 years ago
10.1002/1878-0261.12014
Gene expression panel predicts metastatic‐lethal prostate cancer outcomes in men diagnosed with clinically localized prostate cancer
Cited by: 22
Author(s): Rohina Rubicz, Shanshan Zhao, Jonathan L. Wright, Ilsa M. Coleman, Catherine S. Grasso, Milan S. Geybels, Amy Leonardson, Suzanne Kolb, Craig April, Marina Bibikova, Dean A. Troyer, Raymond S. Lance, Daniel W. Lin, Elaine A. Ostrander, Peter S. Nelson, Jie Fan, Ziding Feng, Janet L. Stanford
Software Mentions: 2
Published: about 8 years ago
10.1002/1878-0261.12561
miRNA expression changes during the course of neoadjuvant bevacizumab and chemotherapy treatment in breast cancer
Cited by: 27
Author(s): Evita M. Lindholm, Miriam Ragle Aure, Mads H. Haugen, Kristine Kleivi Sahlberg, Vessela N. Kristensen, Daniel J. H. Nebdal, Anne‐Lise Børresen‐Dale, Ole Christian Lingjærde, Olav Engebraaten
Software Mentions: 2
Published: about 5 years ago
10.1002/1878-0261.12871
Interaction of transcription factor AP‐2 gamma with proto‐oncogene PELP1 promotes tumorigenesis by enhancing RET signaling
Cited by: 13
Author(s): Junhao Liu, Zexuan Liu, Mengxing Li, Weiwei Tang, Uday P. Pratap, Yiliao Luo, Kristin A. Altwegg, Xiaonan Li, Yi Zou, Hong Zhu, Gangadhara R. Sareddy, Suryavathi Viswanadhapalli, Ratna K. Vadlamudi
Software Mentions: 2
Published: almost 4 years ago
10.1038/s41380-018-0255-6
Integrative approach to sporadic Alzheimer’s disease: deficiency of TYROBP in cerebral Aβ amyloidosis mouse normalizes clinical phenotype and complement subnetwork molecular pathology without reducing Aβ burden
Cited by: 52
Author(s): Jean‐Vianney Haure‐Mirande, Minghui Wang, Mickaël Audrain, Tomas Fanutza, Soong Ho Kim, Szilvia Heja, Ben Readhead, Joel T. Dudley, Robert D. Blitzer, Eric E. Schadt, Bin Zhang, Sam Gandy, Michelle E. Ehrlich
Software Mentions: 2
Published: about 6 years ago
10.15252/msb.20188202
Identification of an oncogenic network with prognostic and therapeutic value in prostate cancer
Cited by: 23
Author(s): Fiorella Magani, Eric R. Bray, María Julia Martínez, Ning Zhao, Valeria A. Copello, Laine M. Heidman, Stephanie Peacock, David J. Wiley, Gennaro D’Urso, Kerry L. Burnstein
Software Mentions: 2
Published: over 6 years ago
10.3390/v10110649
Characterizing the Different Effects of Zika Virus Infection in Placenta and Microglia Cells
Cited by: 15
Author(s): Maria del Pilar Martinez Viedma, Brett E. Pickett
Software Mentions: 2
Published: about 6 years ago
10.12688/wellcomeopenres.14867.2
Tissue and host species-specific transcriptional changes in models of experimental visceral leishmaniasis
Cited by: 17
Author(s): Helen Ashwin, Karlheinz Seifert, Sarah Forrester, Najmeeyah Brown, Sandy MacDonald, Sally James, Dimitrios Lagos, Jon Timmis, Jeremy C. Mottram, Simon L. Croft, Paul M. Kaye
Software Mentions: 2
Published: almost 6 years ago
10.3390/pathogens10050504
Drift of the Subgingival Periodontal Microbiome during Chronic Periodontitis in Type 2 Diabetes Mellitus Patients
Cited by: 14
Author(s): И П Балмасова, Evgenii I. Olekhnovich, Ksenia M. Klimina, Anna A. Korenkova, Maria T. Vakhitova, Elmar Babaev, Leyla A. Ovchinnikova, Yakov A. Lomakin, Иван Смирнов, В.Н. Царев, А. M. Mkrtumyan, Alexey A. Belogurov, Alexander G. Gabibov, Elena Ilina, С Д Арутюнов
Software Mentions: 2
Published: over 3 years ago
10.3390/pathogens10081048
Artificial Intelligence in Surveillance, Diagnosis, Drug Discovery and Vaccine Development against COVID-19
Cited by: 36
Author(s): Gunjan Arora, Jayadev Joshi, Rahul Shubhra Mandal, Nitisha Shrivastava, R Virmani, Tavpritesh Sethi
Software Mentions: 2
Published: over 3 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
10.7717/peerj.9462
Expression profile analysis to predict potential biomarkers for glaucoma: BMP1, DMD and GEM
Cited by: 4
Author(s): Dao wei Zhang, Shenghai Zhang, Jihong Wu
Software Mentions: 2
Published: about 4 years ago
10.7717/peerj.11278
The paeonol target gene autophagy-related 5 has a potential therapeutic value in psoriasis treatment
Cited by: 1
Author(s): Qian Zhang, Hongqiao Shi, Jiaan Zhang, Chenxue Jiang, Chunxiang Zhou
Software Mentions: 2
Published: over 3 years ago
10.7717/peerj.9784
Distribution, evolution and expression of GATA-TFs provide new insights into their functions in light response and fruiting body development of Tolypocladium guangdongense
Cited by: 2
Author(s): Chenghua Zhang, Jinjie Wang, Wang-Qiu Deng, Tai­-Hui Li
Software Mentions: 2
Published: about 4 years ago
10.7717/peerj.4935
High similarity in the microbiota of cold-water sponges of the Genus <i>Mycale</i> from two different geographical areas
Cited by: 28
Author(s): César Cárdenas, Marcelo González-Aravena, Alejandro Font, Jon Thomassen Hestetun, Eduardo Hajdu, Nicole Trefault, Maja Malmberg, Erik Bongcam‐Rudloff
Software Mentions: 2
Published: over 6 years ago
10.7717/peerj.9000
Identification of key miRNAs in the progression of hepatocellular carcinoma using an integrated bioinformatics approach
Cited by: 3
Author(s): Qi Zheng, Xiaoyong Wei, Jun Rao, Cuncai Zhou
Software Mentions: 2
Published: over 4 years ago
10.7717/peerj.6355
New insight into the phylogeographic pattern of<i>Liriodendron chinense</i>(Magnoliaceae) revealed by chloroplast DNA: east–west lineage split and genetic mixture within western subtropical China
Cited by: 10
Author(s): Aihong Yang, Yongda Zhong, Shujuan Liu, Lipan Liu, Tengyun Liu, Yanqiang Li, Fang Yu
Software Mentions: 2
Published: almost 6 years ago
10.7717/peerj.5460
Spatio–temporal variation in stable isotope signatures (δ<sup>13</sup>C and δ<sup>15</sup>N) of sponges on the Saba Bank
Cited by: 8
Author(s): Fleur C. van Duyl, Benjamin Mueller, H.W.G. Meesters
Software Mentions: 2
Published: over 6 years ago
10.7717/peerj.4210
Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak
Cited by: 58
Author(s): Jason C Kwong, Courtney R Lane, Finn Romanes, Anders Gonçalves da Silva, Marion Easton, Katie Cronin, Mary Jo Waters, Takehiro Tomita, Kerrie Stevens, Mark B. Schultz, Sarah L. Baines, Norelle L Sherry, Glen P. Carter, Andre Mu, Michelle Sait, Susan A Ballard, Torsten Seemann, Timothy P. Stinear, Benjamin P Howden
Software Mentions: 2
Published: almost 7 years ago
10.7717/peerj.6472
Metacommunity patterns of Amazonian Odonata: the role of environmental gradients and major rivers
Cited by: 14
Author(s): Fernanda Alves‐Martins, Leandro Schlemmer Brasil, Leandro Juen, Paulo de Marco Júnior, Juliana Stropp, Joaquín Hortal
Software Mentions: 2
Published: over 5 years ago
10.3390/pharmaceutics11060264
Scale-Up Strategy in Quality by Design Approach for Pharmaceutical Blending Process with Discrete Element Method Simulation
Cited by: 12
Author(s): Su Bin Yeom, Du Hyung Choi
Software Mentions: 2
Published: over 5 years ago
10.3390/pharmaceutics13040545
Drug Repurposing for COVID-19 Treatment by Integrating Network Pharmacology and Transcriptomics
Cited by: 15
Author(s): Danyang Liu, Jiachen Liu, Shuang Liang, Xiang-He Meng, Jonathan Greenbaum, Hong‐Mei Xiao, Lijun Tan, Hong‐Wen Deng
Software Mentions: 2
Published: over 3 years ago
10.3390/pharmaceutics13010080
Control Strategy for Process Development of High-Shear Wet Granulation and Roller Compaction to Prepare a Combination Drug Using Integrated Quality by Design
Cited by: 3
Author(s): Ji Yeon Kim, Myung Hee Chun, Du Hyung Choi
Software Mentions: 2
Published: almost 4 years ago
10.1111/pce.13078
Complex bud architecture and cell-specific chemical patterns enable supercooling of<i>Picea abies</i>bud primordia
Cited by: 34
Author(s): Edith Kuprian, Caspar Munkler, Anna Resnyak, Sonja Zimmermann, Tan D. Tuong, Notburga Gierlinger, Thomas Müller, David P. Livingston, Gilbert Neuner
Software Mentions: 2
Published: about 7 years ago
10.1007/s11103-021-01121-3
Genome-wide identification and characterization of long non-coding RNAs involved in flag leaf senescence of rice
Cited by: 18
Author(s): Xiaoping Huang, Hongyu Zhang, Qiang Wang, Rong Guo, Liping Wei, Haiyan Song, Weigang Kuang, Jiang-Lin Liao, Yongji Huang, Zhaohai Wang
Software Mentions: 2
Published: almost 4 years ago
10.3390/plants8100422
Exploration of Floral Volatile Organic Compounds in Six Typical Lycoris taxa by GC-MS
Cited by: 13
Author(s): Tingting Shi, Yuanzheng Yue, Man Shi, Min Chen, Xia Yang, Lianggui Wang
Software Mentions: 2
Published: about 5 years ago
10.3390/plants9080977
Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed
Cited by: 9
Author(s): Lin Ai, Jinqi Ma, Fei Xu, Wen Xu, Huanhuan Jiang, Haoran Zhang, Cunmin Qu, Lijuan Wei, Jiana Li
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pbio.2002176
Dynamic transcriptome changes during adipose tissue energy expenditure reveal critical roles for long noncoding RNA regulators
Cited by: 67
Author(s): Zhiqiang Bai, Xiaoran Chai, Myeong Jin Yoon, Hye-Jin Kim, Kinyui Alice Lo, Zhichun Zhang, Dan Xu, Diana Teh Chee Siang, Arcinas Camille Esther Walet, Shaohai Xu, Sook-Yoong Chia, Peng Chen, Hongyuan Yang, Sujoy Ghosh, Li Sun
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pbio.3000324
DPPA2/4 and SUMO E3 ligase PIAS4 opposingly regulate zygotic transcriptional program
Cited by: 71
Author(s): Yao-Long Yan, Chao Zhang, Jun Hao, Xuelian Wang, Ming Jia, Mi Li, Jie Na, Xinli Hu, Yangming Wang
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pcbi.1005617
Relating dynamic brain states to dynamic machine states: Human and machine solutions to the speech recognition problem
Cited by: 7
Author(s): Cai Wingfield, Li Su, Xunying Liu, Chao Zhang, Philip C. Woodland, Andrew Thwaites, Elisabeth Fonteneau, William D. Marslen–Wilson
Software Mentions: 2
Published: about 7 years ago
10.1371/journal.pcbi.1009022
Inclusion of maintenance energy improves the intracellular flux predictions of CHO
Cited by: 4
Author(s): Diana Széliová, Jerneja Štor, Isabella Thiel, Marcus Weinguny, Michael Hanscho, Gabriele Lhota, Nicole Borth, Jürgen Zanghellini, David E. Ruckerbauer, Isabel Rocha
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pcbi.1003375
Detecting Genetic Association of Common Human Facial Morphological Variation Using High Density 3D Image Registration
Cited by: 50
Author(s): Shouneng Peng, Jingze Tan, Sile Hu, Hang Zhou, Jing Guo, Jin Li, Kun Tang
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pcbi.1000312
Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization
Cited by: 167
Author(s): Ines Thiele, Neema Jamshidi, Ronan M. T. Fleming, Bernhard Ø. Palsson
Software Mentions: 2
Published: over 15 years ago
10.1371/journal.pcbi.1002705
Coupling between Catalytic Loop Motions and Enzyme Global Dynamics
Cited by: 43
Author(s): Zeynep Kurkcuoglu, Ahmet Bakan, Duygu Kocaman, İvet Bahar, Pemra Doruker
Software Mentions: 2
Published: about 12 years ago
10.1371/journal.pcbi.1008942
The landscape of metabolic pathway dependencies in cancer cell lines
Cited by: 7
Author(s): James H. Joly, Brandon T.L. Chew, Nicholas A. Graham
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pcbi.1000306
Mechanical Network in Titin Immunoglobulin from Force Distribution Analysis
Cited by: 66
Author(s): Wolfram Stacklies, M. Cristina Vega, Matthias Wilmanns, Frauke Gräter
Software Mentions: 2
Published: over 15 years ago
10.1371/journal.pgen.1004502
Integrative Genomics Reveals Novel Molecular Pathways and Gene Networks for Coronary Artery Disease
Cited by: 176
Author(s): Ville-Petteri Mäkinen, Mete Civelek, Qingying Meng, Bin Zhang, Jun Zhu, Candace Levian, Tianxiao Huan, Ayellet V. Segrè, Sujoy Ghosh, Juan C. Vivar, Majid Nikpay, Alexandre F.R. Stewart, Christopher P. Nelson, Christina Willenborg, Jeanette Erdmann, Stefan Blakenberg, Christopher J. O’Donnell, Winfried März, Reijo Laaksonen, Stephen E. Epstein, Sekar Kathiresan, Svati H. Shah, Stanley L. Hazen, Muredach P. Reilly, Aldons J. Lusis, Nilesh J. Samani, Heribert Schunkert, Thomas Quertermous, Ruth McPherson, Xia Yang, Themistocles L. Assimes
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pgen.1008279
A functional regulatory variant of MYH3 influences muscle fiber-type composition and intramuscular fat content in pigs
Cited by: 59
Author(s): In-Cheol Cho, Hee-Bok Park, Jungoh Ahn, Sang‐Hyun Han, Jae-Bong Lee, Hyun‐Tae Lim, Chae-Kyoung Yoo, Eun Ji Jung, Dong Hwan Kim, Wu-Sheng Sun, Yuliaxis Ramayo-Caldas, Sang-Geum Kim, Yoon‐Suk Kang, Yoo-Kyung Kim, Hyun-Sook Shin, Pil‐Nam Seong, In-Sul Hwang, Beom-Young Park, Seongsoo Hwang, Sung-Soo Lee, Youn-Chul Ryu, Jun Heon Lee, Moon-Suck Ko, Kichoon Lee, Gerhard Andersson, Miguel Pérez‐Enciso, Jeong-Woong Lee
Software Mentions: 2
Published: about 5 years ago
10.1371/journal.pgen.1006143
Conservation of Distinct Genetically-Mediated Human Cortical Pattern
Cited by: 14
Author(s): Qian Peng, Andrew J. Schork, Hauke Bartsch, Min‐Tzu Lo, Matthew S. Panizzon, Genetics Study, Alzheimer’s Disease Neuroimaging Initiative, Lars T. Westlye, William S. Kremen, Terry L. Jernigan, Stéphanie Le Hellard, Vidar M. Steen, Thomas Espeseth, Matt Huentelman, Asta Håberg, Ingrid Agartz, Srdjan Djurovic, Ole A. Andreassen, Anders M. Dale, Nicholas J. Schork, Chi‐Hua Chen
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pgen.0030096
Network-Based Analysis of Affected Biological Processes in Type 2 Diabetes Models
Cited by: 169
Author(s): Manway Liu, Arthur Liberzon, Sek Won Kong, Weil Lai, Peter J. Park, Isaac S. Kohane, Simon Kasif
Software Mentions: 2
Published: over 17 years ago
10.1371/journal.pgen.1003617
Bacterial Adaptation through Loss of Function
Cited by: 192
Author(s): Alison K. Hottes, Peter L. Freddolino, Anupama Khare, Zachary N. Donnell, Julia Liu, Saeed Tavazoie
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pgen.1004768
SCL, LMO1 and Notch1 Reprogram Thymocytes into Self-Renewing Cells
Cited by: 54
Author(s): Bastien Gerby, Cédric Tremblay, Mathieu Tremblay, Shanti Rojas-Sutterlin, Sabine Herblot, Josée Hébert, Guy Sauvageau, Sébastien Lemieux, Éric Lécuyer, Diogo Veiga, Trang Hoang
Software Mentions: 2
Published: almost 10 years ago
10.1371/journal.pone.0253442
Joint representation of color and form in convolutional neural networks: A stimulus-rich network perspective
Cited by: 7
Author(s): JohnMark Taylor, Yaoda Xu
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0096153
Transcriptome Profiling of Human Ulcerative Colitis Mucosa Reveals Altered Expression of Pathways Enriched in Genetic Susceptibility Loci
Cited by: 8
Author(s): Christopher J. Cardinale, Zhi Wei, Jin Li, Junfei Zhu, Mengnan Gu, Robert N. Baldassano, Struan F.A. Grant, Hákon Hákonarson
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0117029
Functional Network Overlap as Revealed by fMRI Using sICA and Its Potential Relationships with Functional Heterogeneity, Balanced Excitation and Inhibition, and Sparseness of Neuron Activity
Cited by: 17
Author(s): Jiansong Xu, Vince D. Calhoun, Patrick D. Worhunsky, Hui Xiang, Jian Li, John T. Wall, Godfrey D. Pearlson, Marc N. Potenza
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0230392
High-mobility group box 1 fragment suppresses adverse post-infarction remodeling by recruiting PDGFRα-positive bone marrow cells
Cited by: 13
Author(s): Tetsushi Goto, Katsuto Tamai, Ryohei Matsuura, Takashi Kido, Toru Kuratani, Kazuo Shimamura, Ryoto Sakaniwa, Akira Harada, Yoshiki Sawa
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pone.0130326
Bayesian Spatial NBDA for Diffusion Data with Home-Base Coordinates
Cited by: 3
Author(s): Glenna Nightingale, Kevin N. Laland, William Hoppitt, Peter Nightingale
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0124806
Net Clinical Benefit of Oral Anticoagulants: A Multiple Criteria Decision Analysis
Cited by: 20
Author(s): Jason C. Hsu, Cheng Yang Hsieh, Yea Huei Kao Yang, Christine Y. Lu
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0202751
Long length of stay at the emergency department is mostly caused by organisational factors outside the influence of the emergency department: A root cause analysis
Cited by: 42
Author(s): Babiche E. J. M. Driesen, Bauke H.G. Van Riet, Lisa Verkerk, H. Jaap Bonjer, Hanneke Merten, Prabath W.B. Nanayakkara
Software Mentions: 2
Published: about 6 years ago
10.1371/journal.pone.0177513
An integrative analysis of tissue-specific transcriptomic and metabolomic responses to short-term dietary methionine restriction in mice
Cited by: 30
Author(s): Sujoy Ghosh, Laura A. Forney, Desiree Wanders, Kirsten P. Stone, Thomas W. Gettys
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pone.0055137
Construction and Analysis of the Model of Energy Metabolism in E. coli
Cited by: 4
Author(s): Zixiang Xu, Xiao Sun, Jibin Sun
Software Mentions: 2
Published: almost 12 years ago
10.1371/journal.pone.0088896
Long-Term Effects of Gestational Nicotine Exposure and Food-Restriction on Gene Expression in the Striatum of Adolescent Rats
Cited by: 5
Author(s): Nicholas E. Ilott, Tomasz Schneider, Jonathan Mill, Leonard C. Schalkwyk, Giovana Brolese, Lisiane Bizarro, I. P. Stolerman, Emma Dempster, Philip Asherson
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pone.0063644
Identification of Altered Metabolic Pathways in Plasma and CSF in Mild Cognitive Impairment and Alzheimer’s Disease Using Metabolomics
Cited by: 338
Author(s): Eugenia Trushina, Tumpa Dutta, Xuan Mai T. Persson, Michelle M. Mielke, Ronald C. Petersen
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0231021
Exploitation of local and global information in predictive processing
Cited by: 1
Author(s): Daniel S. Kluger, Nico Broers, Marlen A. Roehe, Moritz F. Wurm, Niko A. Busch, Ricarda Ines Schubotz
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pone.0106050
Tau Overexpression Impacts a Neuroinflammation Gene Expression Network Perturbed in Alzheimer’s Disease
Cited by: 87
Author(s): Paul D. Wes, Amy Easton, John P. Corradi, Donna M. Barten, Nino Devidze, Lynn B. DeCarr, Amy Truong, Aiqing He, Nestor X. Barrezueta, Craig Polson, Clotilde Bourin, Marianne E. Flynn, Stefanie Keenan, Regina Lidge, Jere E. Meredith, JoAnne E. Natale, Sethu Sankaranarayanan, Gregory Cadelina, Charlie Albright, Angela Cacace
Software Mentions: 2
Published: about 10 years ago
10.1371/journal.pone.0211095
Mapping and quantification of ferruginous outcrop savannas in the Brazilian Amazon: A challenge for biodiversity conservation
Cited by: 34
Author(s): Pedro Walfir M. Souza-Filho, Tereza Cristina Giannini, Rodolfo Jaffé, Ana María Giulietti, Diogo C. Santos, Wilson R. Nascimento, José Tasso Felix Guimarães, Marlene Furtado da Costa, Vera Lúcia Imperatriz-Fonseca, José Oswaldo Siqueira
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pone.0087225
Nanoscale Effects of Ethanol and Naltrexone on Protein Organization in the Plasma Membrane Studied by Photoactivated Localization Microscopy (PALM)
Cited by: 24
Author(s): Steven J. Tobin, Eliedonna E. Cacao, Daniel Wing Wo Hong, Lars Terenius, Vladana Vukojević, Tijana Jovanovic-Talisman
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pone.0023525
OASIS: Online Application for the Survival Analysis of Lifespan Assays Performed in Aging Research
Cited by: 256
Author(s): Jae-Seong Yang, Hyun Jun Nam, Mihwa Seo, Seong Kyu Han, Y. S. Choi, Hong Gil Nam, Seung-Jae Lee, Sanguk Kim
Software Mentions: 2
Published: over 13 years ago
10.1371/journal.pone.0065324
To Clone or Not to Clone? Induced Pluripotent Stem Cells Can Be Generated in Bulk Culture
Cited by: 34
Author(s): Charlotte A. Willmann, Hatim Hemeda, Lisa A. Pieper, Michael Lenz, Jie Qin, Sylvia Joussen, Stephanie Sontag, Paul Wanek, Bernd Denecke, H Schüler, Martin Zenke, Wolfgang Wagner
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0157893
Draft Genomes of Anopheles cracens and Anopheles maculatus: Comparison of Simian Malaria and Human Malaria Vectors in Peninsular Malaysia
Cited by: 7
Author(s): Yee Ling Lau, Wenn-Chyau Lee, Junhui Chen, Zhisheng Zhong, Jianbo Jian, Amirah Amir, Fei Wen Cheong, Jia-Siang Sum, Mun-Yik Fong
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0020763
A Systems Level, Functional Genomics Analysis of Chronic Epilepsy
Cited by: 63
Author(s): Kellen D. Winden, Stanislav L. Karsten, Anatol Bragin, Lili C. Kudo, Lauren Gehman, Josephine Ruidera, Daniel H. Geschwind, Jerome Engel
Software Mentions: 2
Published: over 13 years ago
10.1371/journal.pone.0107559
Gene Expression and Pathway Analysis of Effects of the CMAH Deactivation on Mouse Lung, Kidney and Heart
Cited by: 15
Author(s): Deug-Nam Kwon, Byungsoo Chang, Jin‐Hoi Kim
Software Mentions: 2
Published: about 10 years ago
10.1371/journal.pone.0210008
Constraints-based analysis identifies NAD+ recycling through metabolic reprogramming in antibiotic resistant Chromobacterium violaceum
Cited by: 10
Author(s): Deepanwita Banerjee, Anu Raghunathan
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pone.0193271
Placental CpG methylation of infants born extremely preterm predicts cognitive impairment later in life
Cited by: 26
Author(s): Sloane K. Tilley, Elizabeth M. Martin, Lisa Smeester, Robert M. Joseph, Karl Kuban, Timothy Heeren, Olaf Dammann, T. Michael O’Shea, Rebecca C. Fry
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0211502
Switching between reading tasks leads to phase-transitions in reading times in L1 and L2 readers
Cited by: 3
Author(s): Sebastian Wallot, Jun Taek Lee, Damian G. Kelty-Stephen
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pone.0064181
Suppression and Activation of the Malignant Phenotype by Extracellular Matrix in Xenograft Models of Bladder Cancer: A Model for Tumor Cell “Dormancy”
Cited by: 15
Author(s): Robert E. Hurst, Paul Hauser, Kimberly D. Kyker, Jonathan E. Heinlen, Jason P. Hodde, Michael C. Hiles, Stanley D. Kosanke, Mikhail G. Dozmorov, Michael A. Ihnat
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0159790
Phylogeography of Libanotis buchtormensis (Umbelliferae) in Disjunct Populations along the Deserts in Northwest China
Cited by: 7
Author(s): Ping Wang, Xianzhi Zhang, Nan Tang, Jianjun Liu, Liang Xu, Kai Wang
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0160574
Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers
Cited by: 15
Author(s): Michelle Davison, Todd J. Treangen, Sergey Koren, Mihai Pop, Devaki Bhaya
Software Mentions: 2
Published: about 8 years ago
10.1371/journal.pone.0164627
Comparing Eye Tracking with Electrooculography for Measuring Individual Sentence Comprehension Duration
Cited by: 13
Author(s): Jana Müller, Dorothea Wendt, Birger Kollmeier, Thomas Brand
Software Mentions: 2
Published: about 8 years ago
10.1371/journal.pone.0096841
HaplotypeCN: Copy Number Haplotype Inference with Hidden Markov Model and Localized Haplotype Clustering
Cited by: 3
Author(s): Yen-Jen Lin, Yu-Tin Chen, Shu-Ni Hsu, Chieh Yu Peng, Chuan‐Yi Tang, Tzu‐Chen Yen, Wu‐Chiao Hsieh
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0134014
Flux Balance Analysis with Objective Function Defined by Proteomics Data—Metabolism of Mycobacterium tuberculosis Exposed to Mefloquine
Cited by: 21
Author(s): Daniel Montezano, Laura Meek, Rashmi Gupta, Luiz E. Bermudez, J.C.M. Bermudez
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0011031
Acetaminophen Modulates the Transcriptional Response to Recombinant Interferon-β
Cited by: 16
Author(s): Aaron Farnsworth, Anathea S. Flaman, Shiv S. Prasad, Caroline Gravel, Andrew Williams, Carole L. Yauk, Xuguang Li
Software Mentions: 2
Published: over 14 years ago
10.1371/journal.pone.0151436
Understory Plant Community Composition Is Associated with Fine-Scale Above- and Below-Ground Resource Heterogeneity in Mature Lodgepole Pine (Pinus contorta) Forests
Cited by: 16
Author(s): Anne C.S. McIntosh, S. Ellen Macdonald, Sylvie A. Quideau
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0019328
Identification of Hyaloperonospora arabidopsidis Transcript Sequences Expressed during Infection Reveals Isolate-Specific Effectors
Cited by: 57
Author(s): Adriana Cabral, Joost H. M. Stassen, Michael Seidl, Jaqueline Bautor, Jane E. Parker, Guido Van den Ackerveken
Software Mentions: 2
Published: over 13 years ago
10.1002/ctm2.187
Tumor microenvironment characterization in head and neck squamous carcinoma reveals distinct genomic alterations and clinical outcomes
Cited by: 2
Author(s): Run Shi, Xuanwen Bao, Jing Sun, Shun Lü, Claus Belka, Minglun Li
Software Mentions: 2
Published: about 4 years ago
10.1186/s40169-017-0174-1
Post‐zygotic genomic changes in glutamate and dopamine pathway genes may explain discordance of monozygotic twins for schizophrenia
Cited by: 11
Author(s): Christina A Castellani, M.G. Melka, Jane L. Gui, Anthony J. Gallo, Richard O’Reilly, Shiva M. Singh
Software Mentions: 2
Published: almost 7 years ago
10.1002/ctm2.325
Integrative lncRNA–mRNA co‐expression network analysis identifies novel lncRNA E2F3‐IT1 for rheumatoid arthritis
Cited by: 6
Author(s): Long‐Fei Wu, Xing‐Bo Mo, Jin-Bo He, Pei He, Xin Lu, Hong‐Wen Deng, Fei‐Yan Deng, Shu‐Feng Lei
Software Mentions: 2
Published: almost 4 years ago
10.1038/s42003-020-0821-8
New insight into the molecular mechanism of colour differentiation among floral segments in orchids
Cited by: 60
Author(s): Bai Jun Li, Bao Qiang Zheng, Jie Yu Wang, Wen Chieh Tsai, Hsiao‐Chi Lu, Long−Hai Zou, Wei Xiao, Di Yang Zhang, Hong Juan Qiao, Zhong‐Jian Liu, Yan Wang
Software Mentions: 2
Published: over 4 years ago
10.1038/s42003-019-0618-9
Single-cell RNA-sequencing analysis of estrogen- and endocrine-disrupting chemical-induced reorganization of mouse mammary gland
Cited by: 28
Author(s): Noriko Kanaya, Gregory Chang, Xiwei Wu, Kohei Saeki, Lauren Bernal, Hyun-Jeong Shim, Jinhui Wang, Charles Warden, Takuro Yamamoto, Jay Li, June-Soo Park, Timothy W. Synold, Steve Vonderfecht, Michele Rakoff, Susan L. Neuhausen, Shiuan Chen
Software Mentions: 2
Published: about 5 years ago
10.1038/s42003-020-1009-y
Population genomics of Staphylococcus pseudintermedius in companion animals in the United States
Cited by: 23
Author(s): Joshua T. Smith, Sharlene Amador, Colin J. McGonagle, David B. Needle, R. J. Gibson, Cheryl P. Andam
Software Mentions: 2
Published: over 4 years ago
10.1155/2007/58253
Canonical Decomposition of Ictal Scalp EEG and Accurate Source Localisation: Principles and Simulation Study
Cited by: 36
Author(s): Maarten De Vos, Lieven De Lathauwer, Bart Vanrumste, Sabine Van Huffel, Wim Van Paesschen
Software Mentions: 2
Published: almost 18 years ago
10.1155/2021/5511598
The Gene Coexpression Analysis Identifies Functional Modules Dynamically Changed After Traumatic Brain Injury
Cited by: 3
Author(s): Zhi-hui Zhao, Dong-po Wei, Ruizhe Zheng, Tinghua Peng, Xiang Xiao, Fusheng Li
Software Mentions: 2
Published: over 3 years ago
10.1186/s12962-018-0124-9
Combining A4R and MCDA in priority setting for health
Cited by: 4
Author(s): Norman Daniels
Software Mentions: 2
Published: about 6 years ago