pypi: analysis | Projects | Ecosyste.ms: Papers

10.7717/peerj.7015

Metabolic traits specific for lipid-overproducing strain of Mucor circinelloides 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 Mycale 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 ofLiriodendron chinense(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 (δ13C and δ15N) 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 ofPicea abiesbud 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: over 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

10.1016/j.coisb.2019.04.002

Footprint-based functional analysis of multiomic data
Cited by: 32
Author(s): Aurélien Dugourd, Julio Sáez-Rodríguez
Software Mentions: 2
Published: over 5 years ago

10.1007/s11926-019-0810-4

New Attempts to Define and Clarify Lupus
Cited by: 18
Author(s): Marta E. Alarcón‐Riquelme
Software Mentions: 2
Published: over 5 years ago

10.1093/database/bau030

'In silico expression analysis', a novel PathoPlant web tool to identify abiotic and biotic stress conditions associated with specific cis-regulatory sequences
Cited by: 18
Author(s): Julio C. Bolívar, Fabian Machens, Yuri Brill, Artyom Romanov, Lorenz Bülow, Reinhard Hehl
Software Mentions: 2
Published: over 10 years ago

10.1007/s00125-020-05107-6

Metabolic alterations in immune cells associate with progression to type 1 diabetes
Cited by: 37
Author(s): Partho Sen, Alex M. Dickens, M.A. López-Bascón, Tuomas Lindeman, Esko Kemppainen, Santosh Lamichhane, Tuukka Rönkkö, Jorma Ilonen, Jorma Toppari, Riitta Veijola, Heikki Hyöty, Tuulia Hyötyläinen, Mikael Knip, Matej Orešič
Software Mentions: 2
Published: almost 5 years ago

10.3390/diagnostics10080598

Somatostatin Receptor PET/CT Imaging for the Detection and Staging of Pancreatic NET: A Systematic Review and Meta-Analysis
Cited by: 25
Author(s): Matteo Bauckneht, Domenico Albano, Salvatore Annunziata, Giulia Santo, Priscilla Guglielmo, Viviana Frantellizzi, Alessia Branca, Cristina Ferrari, Alessandro Vento, Alessia Mirabile, Anna Nappi, Laura Evangelista, Pierpaolo Alongi, Riccardo Laudicella
Software Mentions: 2
Published: over 4 years ago

10.1155/2019/3491852

Metabolomics Analysis in Serum from Patients with Colorectal Polyp and Colorectal Cancer by 1H-NMR Spectrometry
Cited by: 51
Author(s): Jinping Gu, Yaqing Xiao, Dan Shu, Xianrui Liang, Xiaomin Hu, Yuanyuan Xie, Donghai Lin, Hua Li
Software Mentions: 2
Published: over 5 years ago

10.1242/dmm.039578

Reversion of tumor hepatocytes to normal hepatocytes during liver tumor regression in an oncogene transgenic zebrafish model
Cited by: 12
Author(s): Yan Li, Ira Agrawal, Zhiyuan Gong
Software Mentions: 2
Published: almost 6 years ago

10.1242/dmm.033043

SIL1, the ER Hsp70 co-chaperone, plays a critical role in maintaining skeletal muscle proteostasis and physiology
Cited by: 13
Author(s): Viraj P. Ichhaporia, Jieun Kim, Kanisha Kavdia, Peter Vogel, Linda H. Horner, Sharon Frase, Linda M. Hendershot
Software Mentions: 2
Published: almost 7 years ago

10.1242/dmm.017889

Acute upregulation of hedgehog signaling in mice causes differential effects on cranial morphology
Cited by: 11
Author(s): Nandini Singh, Tara Dutka, Benjamin Devenney, Kazuhiko Kawasaki, Roger H. Reeves, Joan T. Richtsmeier
Software Mentions: 2
Published: almost 10 years ago

10.1002/emmm.201302558

Triple negative breast cancer initiating cell subsets differ in functional and molecular characteristics and in γ‐secretase inhibitor drug responses
Cited by: 58
Author(s): Diana J. Azzam, Dekuang Zhao, Junjun Sun, Andy J. Minn, Prathibha Ranganathan, Katherine Drews-Elger, Xiaoqing Han, Manuel Picón-Ruiz, Candace A. Gilbert, Seth A. Wander, Anthony J. Capobianco, Dorraya El-Ashry, Joyce M. Slingerland
Software Mentions: 2
Published: about 11 years ago

10.1002/embr.201337642

Extensive regulation of the non‐coding transcriptome by hypoxia: role of <scp>HIF</scp> in releasing paused <scp>RNA</scp> pol2
Cited by: 138
Author(s): Hani Choudhry, Johannes Schödel, Spyros Oikonomopoulos, Carme Camps, Steffen Grampp, Adrian L. Harris, Peter J. Ratcliffe, Jiannis Ragoussis, David R. Mole
Software Mentions: 2
Published: almost 11 years ago

10.1002/ece3.5381

Drift versus selection as drivers of phenotypic divergence at small spatial scales: The case of Belgjarskógur threespine stickleback
Cited by: 10
Author(s): Mathew Seymour, Katja Räsänen, Bjarni K. Kristjánsson
Software Mentions: 2
Published: over 5 years ago

10.1002/ece3.7107

The influence of nutrient enrichment on riverine food web function and stability
Cited by: 10
Author(s): Adam D. Canning, Russell G. Death
Software Mentions: 2
Published: almost 4 years ago

10.1002/ece3.2648

Morphological divergence of lake and streamPhoxinusof Northern Italy and the Danube basin based on geometric morphometric analysis
Cited by: 24
Author(s): David Ramler, Anja Palandačić, Giovanni B. Delmastro, Josef Wanzenböck, Harald Ahnelt
Software Mentions: 2
Published: almost 8 years ago

10.1002/ece3.6762

Genetic diversity, population structure, and gene flow analysis of lowland bamboo [Oxytenanthera abyssinica (A. Rich.) Munro] in Ethiopia
Cited by: 16
Author(s): Oumer Abdie Oumer, Kifle Dagne, Tileye Feyissa, Kassahun Tesfaye, Jayaraman Durai, Muhammad Zeeshan Hyder
Software Mentions: 2
Published: about 4 years ago

10.3390/e22091030

TMEA: A Thermodynamically Motivated Framework for Functional Characterization of Biological Responses to System Acclimation
Cited by: 5
Author(s): Kevin Schneider, Benedikt Venn, Timo Mühlhaus
Software Mentions: 2
Published: about 4 years ago

10.3390/e20080576

Optimal Placement of Pressure Gauges for Water Distribution Networks Using Entropy Theory Based on Pressure Dependent Hydraulic Simulation
Cited by: 6
Author(s): Do Guen Yoo, Dong Eil Chang, Song Yangho, Jung Ho Lee
Software Mentions: 2
Published: over 6 years ago

10.1289/ehp.10216

Nanosize Titanium Dioxide Stimulates Reactive Oxygen Species in Brain Microglia and Damages Neurons in Vitro
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Author(s): Thomas Long, Julianne Tajuba, Preethi Sama, Navid B. Saleh, Carol D. Swartz, Joel Parker, Susan Hester, Gregory V. Lowry, Bellina Veronesi
Software Mentions: 2
Published: about 17 years ago

10.1186/s12199-021-00932-6

Replacing school and out-of-school sedentary behaviors with physical activity and its associations with adiposity in children and adolescents: a compositional isotemporal substitution analysis
Cited by: 15
Author(s): Aleš Gába, Jan Dygrýn, Nikola Štefelová, Lukáš Rubín, Karel Hron, Lukáš Jakubec
Software Mentions: 2
Published: almost 4 years ago

10.1021/acs.est.0c02387

Log Mean Divisia Index Decomposition Analysis of the Demand for Building Materials: Application to Concrete, Dwellings, and the U.K.
Cited by: 10
Author(s): He He, Rupert J. Myers
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13072-019-0310-9

Virtual methylome dissection facilitated by single-cell analyses
Cited by: 3
Author(s): Liduo Yin, Ye Luo, Xiguang Xu, Shiyu Wen, Xiaowei Wu, Xuemei Lu, Hehuang Xie
Software Mentions: 2
Published: about 5 years ago

10.3390/epigenomes4040024

Simplified MethylRAD Sequencing to Detect Changes in DNA Methylation at Enhancer Elements in Differentiating Embryonic Stem Cells
Cited by: 3
Author(s): Debapriya Saha, Allison B Norvil, Nadia A. Lanman, Humaira Gowher
Software Mentions: 2
Published: about 4 years ago

10.1093/emph/eoaa003

Spondylolysis and spinal adaptations for bipedalism
Cited by: 8
Author(s): Kimberly A. Plomp, Keith Dobney, Mark Collard
Software Mentions: 2
Published: almost 5 years ago

10.3892/etm.2013.1392

A study exploring critical pathways in clear cell renal cell carcinoma
Cited by: 12
Author(s): Zisan Zeng, Tengcheng Que, Jiange Zhang, Yanling Hu
Software Mentions: 2
Published: about 11 years ago

10.3389/fbioe.2020.00239

Current Status and Future Prospects of Genome-Scale Metabolic Modeling to Optimize the Use of Mesenchymal Stem Cells in Regenerative Medicine
Cited by: 11
Author(s): Þóra Björg Sigmarsdóttir, Sarah McGarrity, Óttar Rolfsson, James T. Yurkovich, Ólafur E. Sigurjónsson
Software Mentions: 2
Published: over 4 years ago

10.3389/fcell.2020.604627

Identification of a Gene Signature for Renal Cell Carcinoma–Associated Fibroblasts Mediating Cancer Progression and Affecting Prognosis
Cited by: 24
Author(s): Bitian Liu, Xiaonan Chen, Yunhong Zhan, Bin Wu, Pan Shen
Software Mentions: 2
Published: almost 4 years ago

10.3389/fcell.2021.622519

Connecting the Dots: Resolving the Bone Marrow Niche Heterogeneity
Cited by: 41
Author(s): Igor Dolgalev, Anastasia Tikhonova
Software Mentions: 2
Published: over 3 years ago

Projects: pypi: analysis

Papers Mentioning analysis 2,036