pypi: analysis | Projects | Ecosyste.ms: Papers

10.3389/fgene.2021.721873

Screening of DNA Damage Repair Genes Involved in the Prognosis of Triple-Negative Breast Cancer Patients Based on Bioinformatics
Cited by: 4
Author(s): Nan Wang, Yuanting Gu, Jiangrui Chi, Xinwei Li, Youyi Xiong, Chaochao Zhong, Fang Wang, Xinxing Wang, Lin Li
Software Mentions: 5
Published: over 3 years ago

10.1186/s10020-021-00343-x

Long non-coding RNA profile study identifies a metabolism-related signature for colorectal cancer
Cited by: 19
Author(s): Yongqu Lu, Wendong Wang, Zhenzhen Liu, Junren Ma, Xin Zhou, Wei Fu
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-018-36840-z

Identification of candidate neoantigens produced by fusion transcripts in human osteosarcomas
Cited by: 28
Author(s): Susan K. Rathe, Flavia E. Popescu, James E. Johnson, Adrienne L. Watson, Tracy A. Marko, Branden S. Moriarity, John R. Ohlfest, David A. Largaespada
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-018-38209-8

Differentially expressed gene networks, biomarkers, long noncoding RNAs, and shared responses with cocaine identified in the midbrains of human opioid abusers
Cited by: 30
Author(s): Manal H. Saad, Matthew Rumschlag, Michael H. Guerra, Candace Savonen, Alaina M Jaster, Philip D. Olson, Adnan Alazizi, Francesca Luca, Roger Piqué-Regi, Carl J. Schmidt, Michael J. Bannon
Software Mentions: 5
Published: almost 6 years ago

10.1111/jcmm.16469

m6A regulator‐mediated RNA methylation modification patterns are involved in immune microenvironment regulation of periodontitis
Cited by: 57
Author(s): Xiaoqi Zhang, Shizhen Zhang, Xinyu Yan, Yue Shan, Ling Lü, Jing Zhou, Qianyun Kuang, Minqi Li, Hu Long, Wenli Lai
Software Mentions: 5
Published: over 3 years ago

10.1186/s12919-018-0130-0

Network analysis of drug effect on triglyceride-associated DNA methylation
Cited by: 5
Author(s): Elise Lim, Hanfei Xu, Peitao Wu, Daniel Posner, Jiayi Wu, Gina M. Peloso, Achilleas Pitsillides, Anita L. DeStefano, L. Adrienne Cupples, Ching‐Ti Liu
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0208917

The hindgut microbiota of praying mantids is highly variable and includes both prey-associated and host-specific microbes
Cited by: 6
Author(s): Kara Tinker, Elizabeth A. Ottesen
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0070433

Genome-Wide Expression of Transcriptomes and Their Co-Expression Pattern in Subtropical Maize (Zea mays L.) under Waterlogging Stress
Cited by: 54
Author(s): Nepolean Thirunavukkarasu, Firoz Hossain, Sweta Mohan, Kaliyugam Shiriga, Swati Mittal, R.C. Sharma, Rita Singh, H. S. Gupta
Software Mentions: 5
Published: over 11 years ago

10.1007/s00420-020-01610-w

Can a metric combining arm elevation and trapezius muscle activity predict neck/shoulder pain? A prospective cohort study in construction and healthcare
Cited by: 4
Author(s): Suzanne L. Merkus, Svend Erik Mathiassen, Lars-Kristian Lunde, Markus Koch, Morten Wærsted, Mikael Forsman, Stein Knardahl, Kaj Bo Veiersted
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13041-020-00603-7

Ocular hypertension suppresses homeostatic gene expression in optic nerve head microglia of DBA/2 J mice
Cited by: 28
Author(s): James R. Tribble, Jeffrey M. Harder, Pete A. Williams, Simon W. M. John
Software Mentions: 5
Published: over 4 years ago

10.1007/s11357-021-00329-x

Are the 50’s, the transition decade, in choroid plexus aging?
Cited by: 5
Author(s): Ana Carolina Tahira, Fernanda Marques, Bianca Cristina Garcia Lisbôa, Arthur Sant’Anna Feltrin, André Rocha Barbosa, Kátia C. Oliveira, Carlos Alberto de Bragança Pereira, Renata Leite, Lea T. Grinberg, Cláudia Kimie Suemoto, Renata Eloah de Lucena Ferretti‐Rebustini, Carlos Augusto Pasqualucci, Wilson Jacob‐Filho, Helena Brentani, Joana Almeida Palha
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13059-016-0902-7

Comparative transcriptomics reveals the conserved building blocks involved in parallel evolution of diverse phenotypic traits in ants
Cited by: 67
Author(s): Claire Morandin, Mandy M. Y. Tin, Sílvia Abril, Crisanto Gómez, Luigi Pontieri, Morten Schiøtt, Liselotte Sundström, Kazuki Tsuji, Jes S. Pedersen, Heikki Helanterä, Alexander S. Mikheyev
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0022176

Time-Resolved Human Kinome RNAi Screen Identifies a Network Regulating Mitotic-Events as Early Regulators of Cell Proliferation
Cited by: 9
Author(s): Jitao David Zhang, Cindy Körner, Stephanie Bechtel, Christian Bender, Ioanna Keklikoglou, Christian Schmidt, Anja Irsigler, Ute Ernst, Özgür Şahin, Stefan Wiemann, Ulrich Tschulena
Software Mentions: 5
Published: over 13 years ago

10.18632/aging.102697

Identification of a nomogram based on long non-coding RNA to improve prognosis prediction of esophageal squamous cell carcinoma
Cited by: 45
Author(s): Wenli Li, Jun Li, Hetong Zhao
Software Mentions: 5
Published: almost 5 years ago

10.1111/jcmm.15205

Characterization of the relationship between FLI1 and immune infiltrate level in tumour immune microenvironment for breast cancer
Cited by: 14
Author(s): Shiyuan Wang, Yakun Wang, Changhong Yu, Yiyin Cao, Yao Yu, Yi Pan, Dongqing Su, Qianzi Lu, Weihao Yang, Yongchun Zuo, Lei Yang
Software Mentions: 5
Published: over 4 years ago

10.1186/s12979-020-00182-0

Effect of aging on the transcriptomic changes associated with the expression of the HERV-K (HML-2) provirus at 1q22
Cited by: 11
Author(s): Arttu Autio, Tapio Nevalainen, Binisha H. Mishra, Marja Jylhä, Heini Flinck, Mikko Hurme
Software Mentions: 5
Published: over 4 years ago

10.1002/1878-0261.12706

Ribonucleotide reductase small subunit M2 is a master driver of aggressive prostate cancer
Cited by: 17
Author(s): Ying Z. Mazzu, Joshua Armenia, Subhiksha Nandakumar, Goutam Chakraborty, Yuki Yoshikawa, Lina Jehane, Gwo‐Shu Mary Lee, Mohammad Atiq, Nabeela Khan, Nikolaus Schultz, Philip W. Kantoff
Software Mentions: 5
Published: over 4 years ago

10.3389/fonc.2020.00368

Expression Profile and Prognostic Values of HOXA Family Members in Laryngeal Squamous Cell Cancer
Cited by: 20
Author(s): Jinyun Li, Meng Ye, Chongchang Zhou
Software Mentions: 5
Published: over 4 years ago

10.3389/fpls.2019.01373

Quantitative Trait Locus Analysis of Leaf Morphology Indicates Conserved Shape Loci in Grapevine
Cited by: 21
Author(s): Elizabeth Demmings, Brigette R. Williams, Cheng‐Ruei Lee, Paola Barba, Shanshan Yang, Chin-Feng Hwang, Bruce I. Reisch, Daniel H. Chitwood, Jason P. Londo
Software Mentions: 5
Published: about 5 years ago

10.3389/fonc.2021.675104

ALOX5AP Predicts Poor Prognosis by Enhancing M2 Macrophages Polarization and Immunosuppression in Serous Ovarian Cancer Microenvironment
Cited by: 13
Author(s): Yu‐Tao Xiang, Li-Mei An, Xiangxiang Wang, Chenyi Zhang, Wei Huang, Ce Sun, Rongrong Li, Hongbing Ma, Hongyan Wang, Min Gao
Software Mentions: 5
Published: over 3 years ago

10.1186/s13024-018-0282-4

Deep proteomic network analysis of Alzheimer’s disease brain reveals alterations in RNA binding proteins and RNA splicing associated with disease
Cited by: 147
Author(s): Erik C. B. Johnson, Eric B. Dammer, Duc M. Duong, Luming Yin, Madhav Thambisetty, Juan C. Troncoso, James J. Lah, Aĺlan I. Levey, Nicholas T. Seyfried
Software Mentions: 5
Published: about 6 years ago

10.3390/metabo11080488

Investigating Global Lipidome Alterations with the Lipid Network Explorer
Cited by: 17
Author(s): Nikolai Köhler, Tim Rose, Lisa Falk, Josch Pauling
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-021-84407-2

Premating barriers in young sympatric snail species
Cited by: 6
Author(s): Arina L. Maltseva, Marina A. Varfolomeeva, Arseniy Lobov, Polina Tikanova, Egor A. Repkin, Irina Y. Babkina, Marina Panova, Natalia A. Mikhailova, Andrei I. Granovitch
Software Mentions: 5
Published: over 3 years ago

10.1186/s13024-020-00412-5

A novel systems biology approach to evaluate mouse models of late-onset Alzheimer’s disease
Cited by: 36
Author(s): Christoph Preuß, Ravi S. Pandey, Erin Piazza, Alexander D. Fine, Asli Uyar, Thanneer M. Perumal, Dylan Garceau, Kevin P. Kotredes, Huw Williams, Lara M. Mangravite, Bruce T. Lamb, Adrian L. Oblak, Gareth R. Howell, Michael Sasner, Benjamin A. Logsdon, Gregory W. Carter
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0215987

Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic data
Cited by: 18
Author(s): Yu Kong, Deepa Rastogi, Cathal Seoighe, John M. Greally, Masako Suzuki
Software Mentions: 5
Published: over 5 years ago

10.1016/j.cell.2019.05.047

Neutrophils Driving Unconventional T Cells Mediate Resistance against Murine Sarcomas and Selected Human Tumors
Cited by: 147
Author(s): Andrea Ponzetta, Roberta Carriero, Silvia Carnevale, Marialuisa Barbagallo, Martina Molgora, Chiara Perucchini, Elena Magrini, Francesca Gianni, Paolo Kunderfranco, Nadia Polentarutti, Fabio Pasqualini, Sabrina Di Marco, Domenico Supino, Clelia Peano, Ferdinando Carlo Maria Cananzi, Piergiuseppe Colombo, Silvana Pilotti, Suliman Yousef Alomar, Eduardo Bonavita, Maria Rosaria Galdiero, Cecília Garlanda, Alberto Mantovani, Sébastien Jaillon
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pntd.0005693

Evolution and spread of Venezuelan equine encephalitis complex alphavirus in the Americas
Cited by: 53
Author(s): Naomi L. Forrester, Joel O. Wertheim, Vivian G. Dugan, Albert J. Auguste, David L. Lin, Alexandra Adams, Rubing Chen, Rodion Gorchakov, Grace Leal, José G. Estrada-Franco, Jyotsna Pandya, Rebecca Halpin, Kumar Hari, Ravi Jain, Timothy B. Stockwell, Suman Das, David E. Wentworth, Martin D. Smith, Sergei L. Kosakovsky Pond, Scott C. Weaver
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0064747

CD14 −159 C>T Gene Polymorphism with Increased Risk of Tuberculosis: Evidence from a Meta-Analysis
Cited by: 18
Author(s): Mohammed Y. Areeshi, Raju K. Mandal, Aditya K. Panda, Shekhar Chandra Bisht, Shafiul Haque
Software Mentions: 5
Published: over 11 years ago

10.3389/fmolb.2021.633299

Identification of Lymph Node Metastasis–Related Key Genes and Prognostic Risk Model in Bladder Cancer by Co-Expression Analysis
Cited by: 8
Author(s): Cheng Luo, Bin Huang, Yukun Wu, Yadong Xu, Wei Ou, Junxing Chen, Lingwu Chen
Software Mentions: 5
Published: over 3 years ago

10.1038/s41385-020-0305-7

γδ T cells compose a developmentally regulated intrauterine population and protect against vaginal candidiasis
Cited by: 32
Author(s): Leticia Monin, Dmitry S. Ushakov, Henriette Arnesen, Nourdine Bah, Anett Jandke, Miguel Muñoz-Ruiz, Joana Carvalho, Susan Joseph, Bruna Almeida, M. J. Green, Emma Nye, Shoji Hatano, Yasunobu Yoshikai, Michael Curtis, Harald Carlsen, Ulrich Steinhoff, Preben Boysen, Adrian Hayday
Software Mentions: 5
Published: about 4 years ago

10.3389/fmicb.2021.699797

Marked Seasonal Variation in Structure and Function of Gut Microbiota in Forest and Alpine Musk Deer
Cited by: 32
Author(s): Feng Jiang, Hongmei Gao, Wen Qin, Pengfei Song, Haijing Wang, Jingjie Zhang, Daoxin Liu, Dong Wang, Tongzuo Zhang
Software Mentions: 5
Published: about 3 years ago

10.18632/aging.102665

Prognostic potential of PRPF3 in hepatocellular carcinoma
Cited by: 27
Author(s): Yinlan Liu, Yuhan Yang, Yan Luo, Juan Wang, Xiangyun Lu, Zongxing Yang, Jin Yang
Software Mentions: 5
Published: almost 5 years ago

10.1002/cam4.3959

IBSP, a potential recurrence biomarker, promotes the progression of colorectal cancer via Fyn/β‐catenin signaling pathway
Cited by: 8
Author(s): Cheng Yan, Ying Qin, Mengmeng Dai, Liping Liu, Yicheng Ni, Qiao Sun, Lulu Li, Yaoyao Zhou, Cheng Qiu, Yuyang Jiang
Software Mentions: 5
Published: over 3 years ago

10.18632/aging.102373

Bioinformatic profiling of prognosis-related genes in the breast cancer immune microenvironment
Cited by: 29
Author(s): Fang Bai, Yu-Chun Jin, Peng Zhang, Hongliang Chen, Yi‐Peng Fu, Mingdi Zhang, Zhen Weng, Kangning Wu
Software Mentions: 5
Published: about 5 years ago

10.1002/cam4.4054

Identification of a novel six‐gene signature with potential prognostic and therapeutic value in cervical cancer
Cited by: 11
Author(s): Xinyu Qu, Zhiwen Shi, Jingjing Guo, Chenyan Guo, Junjun Qiu, Keqin Hua
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pone.0024351

Molecular Insights into Reprogramming-Initiation Events Mediated by the OSKM Gene Regulatory Network
Cited by: 63
Author(s): Nancy Mah, Ying Wang, Mei-Chih Liao, Alessandro Prigione, Justyna Józefczuk, Björn Lichtner, Katharina Wolfrum, Manuela Haltmeier, Max Flöttmann, Martin H. Schaefer, Alexander Hahn, Ralf Mrowka, Edda Klipp, Miguel A. Andrade‐Navarro, James Adjaye
Software Mentions: 5
Published: about 13 years ago

10.1186/1471-2164-13-351

The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline-adapted archaeon
Cited by: 38
Author(s): Kusum Sharma, Nicholas Gillum, J Lomax Boyd, Amy K. Schmid
Software Mentions: 5
Published: over 12 years ago

10.1186/s40478-018-0614-1

Transcriptomic and epigenetic profiling of ‘diffuse midline gliomas, H3 K27M-mutant’ discriminate two subgroups based on the type of histone H3 mutated and not supratentorial or infratentorial location
Cited by: 78
Author(s): David Castel, Cathy Philippe, Thomas Kergrohen, Martin Sill, Jane Merlevede, E. Barret, Stéphanie Puget, Christian Sainte‐Rose, Christof M. Kramm, Chris Jones, Pascale Varlet, Stefan M. Pfister, Jacques Grill, David Jones, Marie‐Anne Debily
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pcbi.0030132

Novel Algorithms Reveal Streptococcal Transcriptomes and Clues about Undefined Genes
Cited by: 14
Author(s): Patricia Ryan, Brian W. Kirk, Chad W. Euler, Raymond Schuch, Vincent A. Fischetti
Software Mentions: 5
Published: over 17 years ago

10.1155/2020/3451610

A Pipeline to Call Multilevel Expression Changes between Cancer and Normal Tissues and Its Applications in Repurposing Drugs Effective for Gastric Cancer
Cited by: 3
Author(s): Wei Gao, Jun Yang, Changhua Zhuo, Sha Huang, Lin Jia, Guangfeng Wu, Min Zhou
Software Mentions: 5
Published: over 4 years ago

10.1038/s42003-020-0914-4

Birds have peramorphic skulls, too: anatomical network analyses reveal oppositional heterochronies in avian skull evolution
Cited by: 29
Author(s): Olivia Plateau, Christian Foth
Software Mentions: 5
Published: over 4 years ago

10.1111/pbi.13236

Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton ( <i>Gossypium hirsutum</i> )
Cited by: 42
Author(s): Syed Shan-e-Ali Zaidi, Rubab Zahra Naqvi, Muhammad Asif, Susan R. Strickler, Sara Shakir, Muhammad Shafiq, Ayesha Khan, Imran Amin, Bharat Mishra, M. Shahid Mukhtar, Brian E. Scheffler, Jodi A. Scheffler, Lukas A. Mueller, Shahid Mansoor
Software Mentions: 5
Published: about 5 years ago

10.1155/2020/7575862

Coexpression Network Analysis of Genes Related to the Characteristics of Tumor Stemness in Triple-Negative Breast Cancer
Cited by: 11
Author(s): Huandan Suo, Tao Zuo, Lei Zhang, Zining Jin, Xiaoying Li, Wei Ma, Zhen Wang, Yue Qiu, Feng Jin, Bin Chen, Yu Cao
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-017-3936-7

Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire
Cited by: 35
Author(s): Michael Giolai, Pirita Paajanen, Walter Verweij, Kamil Witek, Jonathan D. G. Jones, Matt Clark
Software Mentions: 5
Published: over 7 years ago

10.1186/s13062-015-0088-z

The human disease network in terms of dysfunctional regulatory mechanisms
Cited by: 22
Author(s): Jing Yang, Sujuan Wu, Wentao Dai, Yixue Li, Yuanyuan Li
Software Mentions: 5
Published: about 9 years ago

10.1093/bioinformatics/btx179

<i>Fuento</i>: functional enrichment for bioinformatics
Cited by: 5
Author(s): David Tobias Weichselbaum, Bojan Žagrović, Anton A. Polyansky
Software Mentions: 5
Published: over 7 years ago

10.1093/brain/awaa242

Functional gene networks reveal distinct mechanisms segregating in migraine families
Cited by: 14
Author(s): Anne Marie Rasmussen, Lisette J. A. Kogelman, David M. Kristensen, Mona Ameri Chalmer, Jes Olesen, Thomas Folkmann Hansen
Software Mentions: 5
Published: about 4 years ago

10.7554/eLife.51373

PHF19 mediated regulation of proliferation and invasiveness in prostate cancer cells
Cited by: 18
Author(s): Payal Jain, Cecilia Ballaré, Enrique Blanco, Pedro Vizán, Luciano Di Croce
Software Mentions: 5
Published: over 4 years ago

10.7717/peerj.11321

Identification of key genes and biological processes contributing to colitis associated dysplasia in ulcerative colitis
Cited by: 5
Author(s): Di Zhang, Pengguang Yan, Tian Han, Xiaoyun Cheng, Jingnan Li
Software Mentions: 5
Published: over 3 years ago

10.3390/cells9030622

The G Protein-Coupled Estrogen Receptor (GPER) Expression Correlates with Pro-Metastatic Pathways in ER-Negative Breast Cancer: A Bioinformatics Analysis
Cited by: 26
Author(s): Marianna Talia, Ernestina Marianna De Francesco, Damiano Cosimo Rigiracciolo, Maria Grazia Muoio, Lucia Muglia, Marcello Maggiolini, Andrew H. Sims
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.60100

Sequential perturbations to mouse corticogenesis following in utero maternal immune activation
Cited by: 15
Author(s): Cesar P Canales, Myka L. Estes, Karol Cichewicz, Kartik Angara, John Paul Aboubechara, Scott A. Cameron, Kathryn Prendergast, Linda Su-Feher, Iva Zdilar, Ellie J Kreun, Emma C Connolly, Jin Myeong Seo, Jack B Goon, Kathleen Farrelly, Tyler W. Stradleigh, Deborah van der List, Lori Haapanen, Judy Van de Water, Daniel Vogt, A. Kimberley McAllister, A. Nord
Software Mentions: 5
Published: over 3 years ago

10.3390/ijms19010071

Transcriptome-Wide Identification and Characterization of Potato Circular RNAs in Response to Pectobacterium carotovorum Subspecies brasiliense Infection
Cited by: 42
Author(s): Ran Zhou, Yong‐Guan Zhu, Jiao Zhao, Zhengwu Fang, Shuping Wang, Jia Yin, Chu Zhang, Dongfang Ma
Software Mentions: 5
Published: almost 7 years ago

10.1016/j.celrep.2020.107691

Expression of RUNX1-ETO Rapidly Alters the Chromatin Landscape and Growth of Early Human Myeloid Precursor Cells
Cited by: 17
Author(s): Monica Nafria, Peter Keane, Elizabeth Ng, Edouard G. Stanley, Andrew G. Elefanty, Constanze Bonifer
Software Mentions: 5
Published: over 4 years ago

10.1042/BSR20191547

Transcriptome profiling of digital flexor tendons after injury in a chicken model
Cited by: 1
Author(s): Wenfei Mao, Yancun Yu, Chen Chen, Ya Fang Wu
Software Mentions: 5
Published: over 4 years ago

10.7717/peerj.9658

A prognostic gene model of immune cell infiltration in diffuse large B-cell lymphoma
Cited by: 9
Author(s): Hao Zhou, Chang Zheng, Desheng Huang
Software Mentions: 5
Published: over 4 years ago

10.1038/s41419-021-03450-z

ECT2 overexpression promotes the polarization of tumor-associated macrophages in hepatocellular carcinoma via the ECT2/PLK1/PTEN pathway
Cited by: 26
Author(s): Dafeng Xu, Yu Wang, Junzhen Wu, Zhensheng Zhang, Jiacheng Chen, Mingwei Xie, Rong Tang, Cheng Chen, Liang Chen, Shaomin Lin, Xiangxiang Luo, Jinfang Zheng
Software Mentions: 5
Published: almost 4 years ago

10.1128/mSystems.00579-19

Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies
Cited by: 48
Author(s): Cecilia Noecker, Hsuan-Chao Chiu, Christopher A. McNally, Elhanan Borenstein
Software Mentions: 5
Published: almost 5 years ago

10.7150/ijbs.45693

Cancer stem cell property and gene signature in bone-metastatic Breast Cancer cells
Cited by: 7
Author(s): An Luo, Yue Xu, Shujun Li, Jinxia Bao, Jianrong Lu, Nan Ding, Qian Zhao, Yuting Fu, Fei Liu, William C. Cho, Xunbin Wei, Haiyun Wang, Zuoren Yu
Software Mentions: 5
Published: almost 5 years ago

10.1128/mBio.01457-20

Kaposi’s Sarcoma-Associated Herpesvirus Drives a Super-Enhancer-Mediated Survival Gene Expression Program in Primary Effusion Lymphoma
Cited by: 13
Author(s): Mark Manzano, Thomas Guenther, Honglyoul Ju, John Nicholas, Elizabeth T. Bartom, Adam Grundhoff, Eva Gottwein
Software Mentions: 5
Published: about 4 years ago

10.3390/cancers12061487

Only Hematopoietic Stem and Progenitor Cells from Cord Blood Are Susceptible to Malignant Transformation by MLL-AF4 Translocations
Cited by: 12
Author(s): Kathy-Ann Secker, Lukas Bruns, Hildegard Keppeler, Johan Jeong, Thomas Hentrich, Julia M. Schulze‐Hentrich, Barbara Mankel, Falko Fend, Dominik Schneidawind, Corina Schneidawind
Software Mentions: 5
Published: over 4 years ago

10.1128/mSphere.00521-18

Marginal Zinc Deficiency and Environmentally Relevant Concentrations of Arsenic Elicit Combined Effects on the Gut Microbiome
Cited by: 32
Author(s): Christopher A. Gaulke, John Rolshoven, Carmen P. Wong, Laurie G. Hudson, Emily Ho, Thomas J. Sharpton
Software Mentions: 5
Published: almost 6 years ago

10.1155/2021/6633442

The Construction and Comprehensive Analysis of Inflammation-Related ceRNA Networks and Tissue-Infiltrating Immune Cells in Ulcerative Colitis Progression
Cited by: 8
Author(s): Jiawei Lu, Aimaier Rouzigu, Li-Hong Teng, Weili Liu
Software Mentions: 5
Published: over 3 years ago

10.7150/thno.57775

Machine learning-assisted immune profiling stratifies peri-implantitis patients with unique microbial colonization and clinical outcomes
Cited by: 20
Author(s): Chin-Wei Wang, Yuning Hao, Riccardo Di Gianfilippo, James V. Sugai, Jiaqian Li, Wang Gong, Kenneth S. Kornman, Hom‐Lay Wang, Nobuhiko Kamada, Yuying Xie, William V. Giannobile, Yu Lei
Software Mentions: 5
Published: almost 4 years ago

10.1002/2211-5463.13134

Identification of hub lncRNAs in head and neck cancer based on weighted gene co‐expression network analysis and experiments
Cited by: 13
Author(s): Longquan Shao
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-021-86294-z

Development of a novel transcription factors-related prognostic signature for serous ovarian cancer
Cited by: 5
Author(s): Lei He, Nayiyuan Wu, Zhaoyi Liu, Yongchang Chen, Quan Cheng, Jing Wang
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0122339

The Active Tamoxifen Metabolite Endoxifen (4OHNDtam) Strongly Down-Regulates Cytokeratin 6 (CK6) in MCF-7 Breast Cancer Cells
Cited by: 4
Author(s): Thomas Helland, Jennifer Gjerde, Simon N. Dankel, Ingvild S. Fenne, Linn Skartveit, Andreas Drangevåg, Olivera Bozickovic, Marianne Hauglid Flågeng, Håvard Søiland, Gunnar Mellgren, Ernst A. Lien
Software Mentions: 4
Published: over 9 years ago

10.1186/s13024-018-0254-8

Identification and therapeutic modulation of a pro-inflammatory subset of disease-associated-microglia in Alzheimer’s disease
Cited by: 227
Author(s): Srikant Rangaraju, Eric B. Dammer, Syed Ali Raza, Priyadharshini Rathakrishnan, Hailian Xiao, Tianwen Gao, Duc M. Duong, Michael W. Pennington, James J. Lah, Nicholas T. Seyfried, Aĺlan I. Levey
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-37284-1

A gene expression signature in developing Purkinje cells predicts autism and intellectual disability co-morbidity status
Cited by: 12
Author(s): Harry Clifford, Anna Dulneva, Chris P. Ponting, Wilfried Haerty, Esther B. E. Becker
Software Mentions: 4
Published: almost 6 years ago

10.18632/aging.101691

SNCA overexpression disturbs hippocampal gene expression trajectories in midlife
Cited by: 6
Author(s): Thomas Hentrich, Zinah Wassouf, Olaf Rieß, Julia M. Schulze‐Hentrich
Software Mentions: 4
Published: almost 6 years ago

10.1111/jcmm.16343

Prognostic values and immune suppression of the S100A family in pancreatic cancer
Cited by: 23
Author(s): Hongkai Zhuang, Xinming Chen, Fengying Dong, Zedan Zhang, Zixuan Zhou, Zuyi Ma, Shanzhou Huang, Bin Chen, Chuanzhao Zhang
Software Mentions: 4
Published: almost 4 years ago

10.1111/jcmm.16573

Development and validation of glycolysis‐related prognostic score for prediction of prognosis and chemosensitivity of pancreatic ductal adenocarcinoma
Cited by: 7
Author(s): Xiuping Zhang, Qinjunjie Chen, Qu Liu, Yang Wang, Fei Wang, Zhiming Zhao, Guodong Zhao, Wan Yee Lau, Yinghong Gao, Rong Liu
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-64623-y

Comparative analysis of MACROD1, MACROD2 and TARG1 expression, localisation and interactome
Cited by: 20
Author(s): Roko Žaja, Gülcan Aydin, Barbara E. Lippok, Regina Feederle, Bernhard Lüscher, Karla L. H. Feijs
Software Mentions: 4
Published: over 4 years ago

10.7150/jca.39723

Weighted gene co-expression network analysis identified MYL9 and CNN1 are associated with recurrence in colorectal cancer
Cited by: 15
Author(s): Qiu Xiao, Shen-Hong Cheng, Fei Xu, Jinwen Yin, Liyang Wang, Xinyou Zhang
Software Mentions: 4
Published: almost 5 years ago

10.7150/jca.56506

Identification of Hub Genes and Small Molecule Drugs Associated with Acquired Resistance to Gefitinib in Non-Small Cell Lung Cancer
Cited by: 8
Author(s): Guangda Li, You-Zhi Ma, Mingwei Yu, Xiaoxiao Li, Xinjie Chen, Yu Tang Gao, Pei-Yu Cheng, Gan‐Lin Zhang, Xiaomin Wang
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12885-015-1179-z

Prediction of long noncoding RNA functions with co-expression network in esophageal squamous cell carcinoma
Cited by: 57
Author(s): Yibin Hao, Wei Wu, Fachun Shi, Rodrigo Juliani Siqueira Dalmolin, Ming Yan, Fei Tian, Xiaobing Chen, Guoyong Chen, Wei Cao
Software Mentions: 4
Published: over 9 years ago

10.1186/s12870-020-02637-4

Revealing the full-length transcriptome of caucasian clover rhizome development
Cited by: 13
Author(s): Xiujie Yin, Kun Yi, Yihang Zhao, Yue Hu, Li Xu, Taotao He, Jiaxue Liu, Guowen Cui
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0246367

Multi-omic modelling of inflammatory bowel disease with regularized canonical correlation analysis
Cited by: 6
Author(s): Lluís Revilla, Aida Mayorgas, A M Corraliza, Maria Carme Masamunt, Amira Metwaly, Dirk Haller, Eva Tristán, Anna Carrasco, María Esteve, Julián Panés, Elena Ricart, Juan José Lozano, Azucena Salas
Software Mentions: 4
Published: almost 4 years ago

10.1186/s42523-021-00098-0

The microbiota of healthy dogs demonstrates individualized responses to synbiotic supplementation in a randomized controlled trial
Cited by: 6
Author(s): Jirayu Tanprasertsuk, Aashish R. Jha, Justin Shmalberg, Roshonda B. Jones, Lee M. Perry, Heather Maughan, Ryan W. Honaker
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0048996

Statistical Object Data Analysis of Taxonomic Trees from Human Microbiome Data
Cited by: 17
Author(s): Patricio S. La Rosa, Berkley Shands, Elena Deych, Yanjiao Zhou, Erica Sodergren, George M. Weinstock, William D. Shannon
Software Mentions: 4
Published: about 12 years ago

10.1186/s12915-020-00775-7

Parkinson’s disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions
Cited by: 114
Author(s): Federico Baldini, Johannes Hertel, Estelle Sandt, Cyrille C. Thinnes, Lorieza Neuberger-Castillo, Lukas Pavelka, Fay Betsou, Rejko Krüger, Ines Thiele
Software Mentions: 4
Published: over 4 years ago

10.1186/s12915-020-00862-9

Genome-enabled insights into the biology of thrips as crop pests
Cited by: 44
Author(s): Dorith Rotenberg, Aaron A. Baumann, Sulley Ben-Mahmoud, Olivier Christiaens, Wannes Dermauw, Panagiotis Ioannidis, Chris G.C. Jacobs, Iris M. Vargas Jentzsch, Jonathan E. Oliver, Monica Poelchau, Swapna Priya Rajarapu, Derek J. Schneweis, Simon Snoeck, Clauvis Nji Tizi Taning, Dong Wei, Shirani M. K. Widana Gamage, Daniel Hughes, Shwetha C. Murali, Samuel T. Bailey, Nicolás Bejerman, Christopher J. Holmes, Emily C. Jennings, Andrew J. Rosendale, Andrew E. Rosselot, Kaylee Hervey, Brandi A. Schneweis, Sammy Cheng, Christopher P. Childers, Felipe A. Simão, Ralf G. Dietzgen, Hsu Chao, Huyen Dinh, Harshavardhan Doddapaneni, Shannon Dugan, Yi Han, Sandra L. Lee, Donna M. Muzny, Jiaxin Qu, Kim C. Worley, Joshua B. Benoit, Markus Friedrich, Jeffery W. Jones, Kristen A. Panfilio, Yoonseong Park, Hugh M. Robertson, Guy Smagghe, Diane E. Ullman, Maurijn van der Zee, Thomas Van Leeuwen, Jan A. Veenstra, Robert M. Waterhouse, Matthew T. Weirauch, John H. Werren, Anna E. Whitfield, Evgeny M. Zdobnov, Richard A. Gibbs, Stephen Richards
Software Mentions: 4
Published: about 4 years ago

10.1186/s13073-018-0551-4

Genetic variants associated with Alzheimer’s disease confer different cerebral cortex cell-type population structure
Cited by: 42
Author(s): Zeran Li, Jorge L. Del-Águila, Umber Dube, John Budde, Rita Martinez, Kathleen Black, Qingli Xiao, Nigel J. Cairns, Joseph D. Dougherty, Lee J, John C. Morris, Randall J. Bateman, Celeste M. Karch, Carlos Cruchaga, Oscar Harari
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0226057

Estrogen receptor β exerts tumor suppressive effects in prostate cancer through repression of androgen receptor activity
Cited by: 16
Author(s): Surendra Chaurasiya, Scott Widmann, Cindy Botero, Chin-Yo Lin, Jan‐Åke Gustafsson, Anders Ström
Software Mentions: 4
Published: over 4 years ago

10.1186/s13073-019-0638-6

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data
Cited by: 628
Author(s): Francesca Finotello, Clemens Mayer, Christina Plattner, Gerhard Laschober, Dietmar Rieder, Hubert Hackl, Anne Krogsdam, Zuzana Loncová, Wilfried Posch, Doris Wilflingseder, Sieghart Sopper, Marieke E. Ijsselsteijn, Thomas P. Brouwer, Douglas B. Johnson, Yaomin Xu, Yu Wang, Melinda E. Sanders, Mónica Valéria Estrada, Paula I. Ericsson-Gonzalez, Pornpimol Charoentong, Justin M. Balko, Noel F.C.C. de Miranda, Zlatko Trajanoski
Software Mentions: 4
Published: over 5 years ago

10.1038/s41438-020-00416-8

Identification of key gene networks controlling organic acid and sugar metabolism during watermelon fruit development by integrating metabolic phenotypes and gene expression profiles
Cited by: 66
Author(s): Muhammad Umer, Luqman Bin Safdar, Haileslassie Gebremeskel, Shengjie Zhao, Pingli Yuan, Huiling Zhu, Mohamed Omar Kaseb, Muhammad Anees, Xingrong Lu, Nan He, Chengsheng Gong, Wenge Liu
Software Mentions: 4
Published: almost 4 years ago

10.1111/jcmm.15650

Combined analysis of RNA‐sequence and microarray data reveals effective metabolism‐based prognostic signature for neuroblastoma
Cited by: 4
Author(s): Xinyao Meng, Chenzhao Feng, Erhu Fang, Jiexiong Feng, Xiang Zhao
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-020-74391-4

Analysis of gene expression from systemic lupus erythematosus synovium reveals myeloid cell-driven pathogenesis of lupus arthritis
Cited by: 9
Author(s): Erika L. Hubbard, Michelle D. Catalina, Sarah Heuer, Prathyusha Bachali, Robert Robl, Nicholas S. Geraci, Amrie C. Grammer, Peter E. Lipsky
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0036161

Effect of Age on Variability in the Production of Text-Based Global Inferences
Cited by: 9
Author(s): Lynne J. Williams, Joseph Dunlop, Hervé Abdi
Software Mentions: 4
Published: over 12 years ago

10.1186/s12915-019-0626-8

Transcriptome, proteome and draft genome of Euglena gracilis
Cited by: 88
Author(s): ThankGod Echezona Ebenezer, Martin Zoltner, Alana Burrell, Anna Nenarokova, Anna M. G. Novák Vanclová, Binod Prasad, Petr Soukal, Carlos Santana-Molina, Ellis C. O’Neill, Nerissa N. Nankissoor, Nithya Vadakedath, Viktor Daiker, Samson O. Obado, Sara Silva Pereira, Andrew P. Jackson, Damien P. Devos, Julius Lukeš, Michael Lebert, Sue Vaughan, Vladimı́r Hampl, Mark Carrington, Michael L. Ginger, Joel B. Dacks, Steven L. Kelly, Mark C. Field
Software Mentions: 4
Published: almost 6 years ago

10.1186/gb-2013-14-11-r125

Transcriptomic classification of genetically engineered mouse models of breast cancer identifies human subtype counterparts
Cited by: 176
Author(s): Adam D. Pfefferle, Jason I. Herschkowitz, Jerry Usary, J. Chuck Harrell, Benjamin T. Spike, Jessica R. Adams, Maria I. Torres-Arzayus, Myles Brown, Sean E. Egan, Geoffrey M. Wahl, Jeffrey M. Rosen, Charles M. Perou
Software Mentions: 4
Published: almost 12 years ago

10.1186/s13059-019-1866-1

547 transcriptomes from 44 brain areas reveal features of the aging brain in non-human primates
Cited by: 25
Author(s): Mingli Li, Shihao Wu, Jinjin Zhang, Hang-Yu Tian, Yong Shao, Zhengbo Wang, David M. Irwin, Jiali Li, Xintian Hu, Dongdong Wu
Software Mentions: 4
Published: almost 5 years ago

10.1007/s00248-017-1108-6

Co-Variation of Bacterial and Fungal Communities in Different Sorghum Cultivars and Growth Stages is Soil Dependent
Cited by: 44
Author(s): Thiago R. Schlemper, Johannes A. van Veen, Eiko E. Kuramae
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0056228

canEvolve: A Web Portal for Integrative Oncogenomics
Cited by: 39
Author(s): Mehmet K. Samur, Zhenyu Yan, Xujun Wang, Qingyi Cao, Nikhil C. Munshi, Li Cheng, Parantu K. Shah
Software Mentions: 4
Published: almost 12 years ago

10.1186/s13326-015-0026-0

Ambiguity and variability of database and software names in bioinformatics
Cited by: 8
Author(s): Geraint Duck, Aleksandar Kovačević, David L. Robertson, Robert Stevens, Goran Nenadić
Software Mentions: 4
Published: over 9 years ago

10.1186/s12983-020-00366-w

Gut transcriptomic changes during hibernation in the greater horseshoe bat (Rhinolophus ferrumequinum)
Cited by: 4
Author(s): Haijian Sun, Jiaying Wang, Yanfeng Xing, Yi-Hsuan Pan, Xiuguang Mao
Software Mentions: 4
Published: over 4 years ago

10.3390/genes10110944

Dissecting the Regulatory Network of Leaf Premature Senescence in Maize (Zea mays L.) Using Transcriptome Analysis of ZmELS5 Mutant
Cited by: 12
Author(s): Mao Chai, Zhanyong Guo, Xia Shi, Yingbo Li, Jian Tang, Zhan‐Hui Zhang
Software Mentions: 4
Published: about 5 years ago

10.1186/s12920-021-00916-z

Identification of super enhancer-associated key genes for prognosis of germinal center B-cell type diffuse large B-cell lymphoma by integrated analysis
Cited by: 6
Author(s): Xi Li, Yan Duan, Yuxia Hao
Software Mentions: 4
Published: over 3 years ago

10.3389/fpls.2021.630243

Identification of Key Gene Networks Associated With Cell Wall Components Leading to Flesh Firmness in Watermelon
Cited by: 11
Author(s): Muhammad Anees, Lei Gao, Muhammad Umer, Pingli Yuan, Huiling Zhu, Xingrong Lu, Nan He, Chengsheng Gong, Mohamed Omar Kaseb, Shengjie Zhao, Wenge Liu
Software Mentions: 4
Published: over 3 years ago

10.1107/S1399004715011426

From deep TLS validation to ensembles of atomic models built from elemental motions
Cited by: 14
Author(s): Alexandre Urzhumtsev, Pavel V. Afonine, A.H. Van Benschoten, James S. Fraser, Paul D. Adams
Software Mentions: 4
Published: over 9 years ago

10.3389/fpls.2020.00574

Decoding Gene Networks Modules That Explain the Recovery of Hymenoglossum cruentum Cav. After Extreme Desiccation
Cited by: 6
Author(s): Enrique Ostria‐Gallardo, Giovanni Larama, Graciela Berríos, Ana Fallard, Ana Gutiérrez-Moraga, Ingo Ensminger, Patrício Manque, Luisa Bascuñán‐Godoy, León A. Bravo
Software Mentions: 4
Published: over 4 years ago

Projects: pypi: analysis

Papers Mentioning analysis 2,036