pypi: heatmap | Projects | Ecosyste.ms: Papers

10.3390/ijms21239157

NF-Y Overexpression in Liver Hepatocellular Carcinoma (HCC)
Cited by: 16
Author(s): Eugenia Bezzecchi, Mirko Ronzio, Roberto Mantovani, Diletta Dolfini
Software Mentions: 15
Published: almost 4 years ago

10.12688/f1000research.8987.2

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
Cited by: 415
Author(s): Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth
Software Mentions: 15
Published: over 8 years ago

10.1186/s12859-016-1260-x

MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps
Cited by: 14
Author(s): Bohdan B. Khomtchouk, John L. Hennessy, Claes Wahlestedt
Software Mentions: 12
Published: about 8 years ago

10.1186/1756-0500-3-81

Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays
Cited by: 17
Author(s): Colin S. Gillespie, Guiyuan Lei, Richard J. Boys, Amanda Greenall, Darren J. Wilkinson
Software Mentions: 11
Published: over 14 years ago

10.3390/cancers11081104

Differential Expression of DNA Repair Genes in Prognostically-Favorable versus Unfavorable Uveal Melanoma
Cited by: 10
Author(s): Mehmet Doğrusöz, Andrea Ruschel Träsel, Jinfeng Cao, Selҫuk Ҫolak, Sake I. van Pelt, Wilma G. M. Kroes, Amina F.A.S. Teunisse, Samar Alsafadi, Sjoerd G. van Duinen, Gregorius P M Luyten, Pieter A. van der Velden, Adriana Amaro, Ulrich Pfeffer, Aart G. Jochemsen, Martine J. Jager
Software Mentions: 11
Published: over 5 years ago

10.1371/journal.ppat.1007945

Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotype
Cited by: 28
Author(s): Bernd Hommel, Aude Sturny-Leclère, Stevenn Volant, Nathanaël Veluppillai, Magalie Duchateau, Chen-Hsin Albert Yu, Véronique Hourdel, Hugo Varet, Mariette Matondo, John R. Perfect, Arturo Casadevall, Françoise Dromer, Alexandre Alanio
Software Mentions: 10
Published: over 5 years ago

10.3389/fonc.2021.704038

Fatty Acid Metabolism-Related lncRNAs Are Potential Biomarkers for Predicting the Overall Survival of Patients With Colorectal Cancer
Cited by: 13
Author(s): Yue Peng, Chang Xu, Jun Wen, Yuanchuan Zhang, Meng Wang, Xiaoxiao Liu, Kang Zhao, Zheng Wang, Yanjun Liu, Tongtong Zhang
Software Mentions: 10
Published: over 3 years ago

10.1007/s00401-020-02187-x

Interleukin-1 promotes autoimmune neuroinflammation by suppressing endothelial heme oxygenase-1 at the blood–brain barrier
Cited by: 44
Author(s): Judith Hauptmann, Lisa Johann, Fédérico Marini, Maja Kitic, E. Colombo, Ilgiz A. Mufazalov, Martin W. Krueger, Khalad Karram, Sonja Moos, Florian Wanke, Florian C. Kurschus, Matthias Klein, Sílvia Cardoso, Johannes Strauß, Subhashini Bolisetty, Fred Lühder, Markus Schwaninger, Harald Binder, Ingo Bechman, Tobias Bopp, Anupam Agarwal, Miguel P. Soares, Tommy Regen, Ari Waisman
Software Mentions: 9
Published: over 4 years ago

10.1371/journal.pone.0255708

Identification of key genes and immune infiltration modulated by CPAP in obstructive sleep apnea by integrated bioinformatics analysis
Cited by: 3
Author(s): Cheng Fan, Sisi Huang, Chunhua Xiang, Tianhui An, Yi Song
Software Mentions: 8
Published: about 3 years ago

10.3390/plants10030550

Phenolic Compounds and Biological Activity of Selected Mentha Species
Cited by: 51
Author(s): Sanja Ćavar Zeljković, Jana Šišková, Karolína Komzáková, Nuria De Diego, K. Kaffková, Petr Tarkowski
Software Mentions: 8
Published: over 3 years ago

10.3390/genes10110937

NF-YA Overexpression in Lung Cancer: LUSC
Cited by: 28
Author(s): Eugenia Bezzecchi, Mirko Ronzio, Diletta Dolfini, Roberto Mantovani
Software Mentions: 8
Published: about 5 years ago

10.1002/1878-0261.12139

Transcription instability in high-risk neuroblastoma is associated with a global perturbation of chromatin domains
Cited by: 4
Author(s): Carlo Zanon, Gian Paolo Tonini
Software Mentions: 8
Published: about 7 years ago

10.1186/s42523-021-00096-2

Salmon gut microbiota correlates with disease infection status: potential for monitoring health in farmed animals
Cited by: 65
Author(s): Davide Bozzi, Jacob Agerbo Rasmussen, Christian Carøe, Harald Sveier, Kristian Nordøy, M. Thomas P. Gilbert, Morten T. Limborg
Software Mentions: 8
Published: over 3 years ago

10.3389/pore.2021.1609825

Clinical Value of TXNDC12 Combined With IDH and 1p19q as Biomarkers for Prognosis of Glioma
Cited by: 4
Author(s): Xinzhuang Wang, Quan Yang, Nan Liu, Qilong Bian, Ming Gao, Xu Hou
Software Mentions: 7
Published: about 3 years ago

10.1186/s13059-021-02372-5

Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1, and TIA1
Cited by: 11
Author(s): Claudia Vivori, Panagiotis Papasaikas, Ralph Stadhouders, Bruno Di Stefano, Anna Ribó Rubio, Clara Berenguer Balaguer, Serena Francesca Generoso, Anna Mallol, José Luis Sardina, Bernhard Payer, Thomas Graf, Juan Valcárcel
Software Mentions: 7
Published: over 3 years ago

10.3390/ani11051442

Agricultural Holdings and Slaughterhouses’ Impact on Patterns of Pathological Findings Observed during Post-Mortem Meat Inspection
Cited by: 5
Author(s): Johannes Klinger, Beate Conrady, Marina Mikula, Annemarie Käsbohrer
Software Mentions: 7
Published: over 3 years ago

10.3389/fmicb.2020.00669

Patterns in Microbial Assemblages Exported From the Meltwater of Arctic and Sub-Arctic Glaciers
Cited by: 20
Author(s): Tyler J. Kohler, Petra Vinšová, Lukáš Falteisek, Jakub D. Žárský, Jacob C. Yde, Jade E. Hatton, Jon R. Hawkings, Guillaume Lamarche-Gagnon, Eran Hood, Karen A. Cameron, Marek Stibal
Software Mentions: 7
Published: over 4 years ago

10.12688/f1000research.6030.2

AGA: Interactive pipeline for reproducible gene expression and DNA methylation data analyses
Cited by: 3
Author(s): Michael Considine, Hilary S. Parker, Yingying Wei, Xaio Xia, Leslie Cope, Michael F. Ochs, Elana J. Fertig
Software Mentions: 7
Published: about 9 years ago

10.3389/fimmu.2021.617163

The Changes of Leukocytes in Brain and Blood After Intracerebral Hemorrhage
Cited by: 14
Author(s): Shuhao Mei, Yijie Shao, Yuanjian Fang, Jianing Lu, Jingwei Zheng, Shenbin Xu, Haijian Wu, Zeyu Sun, Jun Yu, Sheng Chen, Zhen Wang, Jianmin Zhang
Software Mentions: 7
Published: almost 4 years ago

10.1038/srep19899

Global transcriptomic responses of Escherichia coli K-12 to volatile organic compounds
Cited by: 34
Author(s): Pui Yi Yung, Letizia Lo Grasso, Abeed Fatima Mohidin, Enzo Acerbi, Jamie Hinks, Thomas Seviour, Enrico Marsili, Federico M. Lauro
Software Mentions: 7
Published: almost 9 years ago

10.15252/msb.20178041

Molecular transitions in early progenitors during human cord blood hematopoiesis
Cited by: 120
Author(s): Shiwei Zheng, Efthymia Papalexi, Andrew Butler, William Stephenson, Rahul Satija
Software Mentions: 7
Published: over 6 years ago

10.3390/genes11020198

NF-YA Overexpression in Lung Cancer: LUAD
Cited by: 17
Author(s): Eugenia Bezzecchi, Mirko Ronzio, Valentina Semeghini, Valentina Andrioletti, Roberto Mantovani, Diletta Dolfini
Software Mentions: 7
Published: almost 5 years ago

10.1186/s40364-021-00292-x

The REASON score: an epigenetic and clinicopathologic score to predict risk of poor survival in patients with early stage oral squamous cell carcinoma
Cited by: 13
Author(s): Chi T. Viet, Gary Yu, Kesava Asam, Carissa M. Thomas, Angela J. Yoon, Yan Chen Wongworawat, Mina Haghighiabyaneh, Courtney A. Kilkuts, Caitlyn M. McGue, Marcus Couey, Nicholas Callahan, Coleen Doan, Paul C. Walker, Khanh K. Nguyen, Stephanie C. Kidd, Steve C. Lee, Anupama Grandhi, Allen Cheng, Ashish Patel, Elizabeth Philipone, Olivia L. Ricks, Clint Allen, Bradley E. Aouizerat
Software Mentions: 6
Published: over 3 years ago

10.1038/s41398-021-01561-x

Comparison of mouse models reveals a molecular distinction between psychotic illness in PWS and schizophrenia
Cited by: 5
Author(s): Simona Zahova, Trevor Humby, Jennifer R. Davies, Joanne Morgan, Anthony R Isles
Software Mentions: 6
Published: over 3 years ago

10.1038/srep25507

CD36 is expressed in a defined subpopulation of neurons in the olfactory epithelium
Cited by: 31
Author(s): André Machado Xavier, Raissa G. Ludwig, Maíra H. Nagai, Tiago Jonas de Almeida, Hebe Mizuno Watanabe, Marcio Yukio Hirata, Tatiana R. Rosenstock, Fábio Papes, Bettina Malnic, Isaías Glezer
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pone.0204542

NOJAH: NOt Just Another Heatmap for genome-wide cluster analysis
Cited by: 9
Author(s): Manali Rupji, Bhakti Dwivedi, Jeanne Kowalski
Software Mentions: 6
Published: over 5 years ago

10.1186/s12864-021-07812-x

Stage-specific transcriptomic changes in pancreatic α-cells after massive β-cell loss
Cited by: 9
Author(s): Daniel Oropeza, Valentina Cigliola, Agustín Romero, Simona Chera, Santiago A. Rodríguez-Seguí, Pedro Luis Herrera
Software Mentions: 6
Published: over 3 years ago

10.26508/lsa.202000974

GATA transcription factors, SOX17 and TFAP2C, drive the human germ-cell specification program
Cited by: 30
Author(s): Yôji Kojima, Chika Yamashiro, Yusuke Murase, Yukihiro Yabuta, Ikuhiro Okamoto, Chizuru Iwatani, Hideaki Tsuchiya, Masataka Nakaya, Tomoyuki Tsukiyama, Tomonori Nakamura, Takuya Yamamoto, Mitinori Saitou
Software Mentions: 6
Published: almost 4 years ago

10.1038/s41598-018-21161-y

Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response
Cited by: 16
Author(s): Yukie Kashima, Ayako Suzuki, Ying Liu, Masahito Hosokawa, Hiroko Matsunaga, Masamitsu Shirai, Kohji Arikawa, Sumio Sugano, Takashi Kohno, Haruko Takeyama, Katsuya Tsuchihara, Yutaka Suzuki
Software Mentions: 6
Published: over 6 years ago

10.3389/fgene.2020.00992

Identification of the Six-RNA-Binding Protein Signature for Prognosis Prediction in Bladder Cancer
Cited by: 13
Author(s): Yucai Wu, Yi Liu, Anbang He, Bao Guan, Shiming He, Cuijian Zhang, Zhengjun Kang, Yanqing Gong, Xuesong Li, Liqun Zhou
Software Mentions: 6
Published: about 4 years ago

10.3390/plants9040545

Transcriptional Dynamics and Candidate Genes Involved in Pod Maturation of Common Bean (Phaseolus vulgaris L.)
Cited by: 3
Author(s): Cristina Gómez-Martín, Carmen Capel, Ana M. González, Ricardo Lebrón, Fernando J. Yuste‐Lisbona, Michael Hackenberg, José Luis Tejera Oliver, Marta Santalla, Rafael Lozano
Software Mentions: 6
Published: over 4 years ago

10.3389/fmicb.2021.592725

Local Geomorphological Gradients and Land Use Patterns Play Key Role on the Soil Bacterial Community Diversity and Dynamics in the Highly Endemic Indigenous Afrotemperate Coastal Scarp Forest Biome
Cited by: 13
Author(s): Henry Joseph Oduor Ogola, Ramganesh Selvarajan, Memory Tekere
Software Mentions: 6
Published: over 3 years ago

10.1093/gigascience/giz022

Digital expression explorer 2: a repository of uniformly processed RNA sequencing data
Cited by: 41
Author(s): Mark Ziemann, Antony Kaspi, Assam El‐Osta
Software Mentions: 6
Published: over 5 years ago

10.1101/2021.02.23.432450

The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation
Cited by: 4
Author(s): Jordan M. Meyers, Muthukumar Ramanathan, Ronald L. Shanderson, Laura K. Donohue, Ian Ferguson, Margaret Guo, Deepti Rao, Weili Miao, David L. Reynolds, Xue Yang, Yang Zhao, Yen-Yu Yang, Yinsheng Wang, Paul A. Khavari
Software Mentions: 6
Published: over 3 years ago

10.7717/peerj.9478

Cellular heterogeneity map of diverse immune and stromal phenotypes within breast tumor microenvironment
Cited by: 5
Author(s): Yuan Li, Zuhua Chen, Long Wu, Junjie Ye, Wenjing Tao
Software Mentions: 6
Published: over 4 years ago

10.3389/fonc.2021.637023

CXCL5 Has Potential to Be a Marker for Hepatocellular Carcinoma Prognosis and Was Correlating With Immune Infiltrates
Cited by: 8
Author(s): Yuan Nie, Mei-chun Jiang, Cong Liu, Qi Liu, Xuan Zhu
Software Mentions: 6
Published: over 3 years ago

10.1186/1471-2105-13-S16-S10

A tutorial in displaying mass spectrometry-based proteomic data using heat maps
Cited by: 47
Author(s): Melissa Key
Software Mentions: 6
Published: about 12 years ago

10.1155/2020/5831064

Construction and Comprehensive Analyses of a Competing Endogenous RNA Network in Tumor-Node-Metastasis Stage I Hepatocellular Carcinoma
Cited by: 5
Author(s): Xuefeng Gu, Hongbo Li, Ling Sha, Wei Zhao
Software Mentions: 6
Published: almost 5 years ago

10.3389/fpls.2018.00018

Genome-Wide Identification of Cyclic Nucleotide-Gated Ion Channel Gene Family in Wheat and Functional Analyses of TaCNGC14 and TaCNGC16
Cited by: 37
Author(s): Jia Guo, Md. Ashraful Islam, Haocheng Lin, Changan Ji, Yinghui Duan, Peng Liu, Qingdong Zeng, Brad Day, Zhensheng Kang, Jun Guo
Software Mentions: 5
Published: almost 7 years ago

10.3390/microorganisms9040754

Active Rumen Bacterial and Protozoal Communities Revealed by RNA-Based Amplicon Sequencing on Dairy Cows Fed Different Diets at Three Physiological Stages
Cited by: 8
Author(s): Lucia Bailoni, Lisa Carraro, Marco Cardin, Barbara Cardazzo
Software Mentions: 5
Published: over 3 years ago

10.3389/fsurg.2021.665115

Identification and Validation of a Prognostic 5-Protein Signature for Biochemical Recurrence Following Radical Prostatectomy for Prostate Cancer
Cited by: 1
Author(s): Daojun Lv, Zanfeng Cao, Wenjie Li, Haige Zheng, Xiangkun Wu, Yongda Liu, Danan Gu, Guohua Zeng
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.64977

Unique integrated stress response sensors regulate cancer cell susceptibility when Hsp70 activity is compromised
Cited by: 11
Author(s): Sara Sannino, Megan E. Yates, Mark E. Schurdak, Steffi Oesterreich, Adrian V. Lee, Peter Wipf, Jeffrey L. Brodsky
Software Mentions: 5
Published: over 3 years ago

10.3390/ijms22073735

Interplay between Histone and DNA Methylation Seen through Comparative Methylomes in Rare Mendelian Disorders
Cited by: 6
Author(s): Guillaume Velasco, Damien Ulveling, Sophie Rondeau, Pauline Marzin, Motoko Unoki, Valérie Cormier‐Daire, Claire Francastel
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-018-5271-z

Genomic insights into virulence mechanisms of Leishmania donovani: evidence from an atypical strain
Cited by: 23
Author(s): Sumudu R. Samarasinghe, Nilakshi Samaranayake, Udeshika Kariyawasam, Yamuna Deepani Siriwardana, Hideo Imamura, Nadira D. Karunaweera
Software Mentions: 5
Published: almost 6 years ago

10.3389/fonc.2021.633357

Identification of the Prognostic Signatures of Glioma With Different PTEN Status
Cited by: 12
Author(s): Pei Zhang, Xinyi Meng, Liqun Liu, Shengzhen Li, Yang Li, Sakhawat Ali, Shanhu Li, Jichuan Xiong, Xuefeng Li, Shouwei Li, Xia Qin, Lei Dong
Software Mentions: 5
Published: over 3 years ago

10.1186/s12974-019-1418-3

Correlation of alteration of HLA-F expression and clinical characterization in 593 brain glioma samples
Cited by: 36
Author(s): Enshan Feng, Tingyu Liang, Xiaoyong Wang, Juan Du, Kai Tang, Xiaoxuan Wang, Fang Wang, Guoxiang You
Software Mentions: 5
Published: almost 6 years ago

10.3389/fonc.2020.553045

m6A Reader HNRNPA2B1 Promotes Esophageal Cancer Progression via Up-Regulation of ACLY and ACC1
Cited by: 62
Author(s): Huimin Guo, Bei Wang, Kaiyue Xu, Ling Nie, Yao Fu, Zhangding Wang, Qiang Wang, Shouyu Wang, Xiaoping Zou
Software Mentions: 5
Published: about 4 years ago

10.1111/acel.13230

COVID‐19 is an emergent disease of aging
Cited by: 91
Author(s): Didac Santesmasses, José Pedro Castro, Aleksandr Zenin, Anastasia V. Shindyapina, Maxim V. Gerashchenko, Bohan Zhang, Csaba Kerepesi, Sun Hee Yim, П. О. Федичев, Vadim N. Gladyshev
Software Mentions: 5
Published: about 4 years ago

10.3389/fmicb.2021.665858

Multi-Omics Approach Reveals the Potential Core Vaccine Targets for the Emerging Foodborne Pathogen Campylobacter jejuni
Cited by: 6
Author(s): Hai‐Yan Cao, Hanxiao Xu, Ning Cai, Xiang Li, Ren Qiu-fang, Tiantian Zhang, Yusen Zhang, Rui Gao
Software Mentions: 5
Published: over 3 years ago

10.1186/s12935-021-01829-8

Identification of key genes involved in tumor immune cell infiltration and cetuximab resistance in colorectal cancer
Cited by: 4
Author(s): Li Liang, Mengling Liu, Xun Sun, Yunfeng Yuan, Ke Peng, Khalid Rashid, Yiyi Yu, Yuehong Cui, Yanjie Chen, Tianshu Liu
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-017-4100-0

Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates
Cited by: 61
Author(s): Lee M. Yeoh, Christopher D. Goodman, Vanessa Mollard, Geoffrey I. McFadden, Stuart A. Ralph
Software Mentions: 5
Published: about 7 years ago

10.3389/fmolb.2020.566491

Four Immune-Related Long Non-coding RNAs for Prognosis Prediction in Patients With Hepatocellular Carcinoma
Cited by: 15
Author(s): Muqi Li, Minni Liang, Tian Lan, Xiwen Wu, Wenlin Xie, Tielong Wang, Z Chen, Shunli Shen, Baogang Peng
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-020-60065-8

Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation
Cited by: 7
Author(s): Jessica Schira‐Heinen, A. Czapla, Marion Hendricks, Andreas Kloetgen, Wasco Wruck, James Adjaye, Gesine Kögler, Hans Müller, Kai Stühler, Hans‐Ingo Trompeter
Software Mentions: 5
Published: over 4 years ago

10.3390/metabo8040078

Population-Level Analysis to Determine Parameters That Drive Variation in the Plasma Metabolite Profiles
Cited by: 2
Author(s): Mahmoud Al-Majdoub, Katharina Herzog, Bledar Daka, Martin Magnusson, Lennart Råstam, Ulf Lindblad, Peter Sartipy
Software Mentions: 5
Published: about 6 years ago

10.1111/pbi.13085

Development of an integrated 200K <scp>SNP</scp> genotyping array and application for genetic mapping, genome assembly improvement and genome wide association studies in pear (Pyrus)
Cited by: 43
Author(s): Xiaolong Li, Jugpreet Singh, Mengfan Qin, Siwei Li, Xun Zhang, Mingyue Zhang, Awais Khan, Shaoling Zhang
Software Mentions: 5
Published: almost 6 years ago

10.1155/2018/7691794

Differential Expression Profiling of Long Noncoding RNA and mRNA during Osteoblast Differentiation in Mouse
Cited by: 6
Author(s): Minjung Kim, Yi Yin Yu, Ji-Hoi Moon, Insong Koh, Jae Hyung Lee
Software Mentions: 5
Published: almost 7 years ago

10.7717/peerj.5908

Assessing distinct patterns of cognitive aging using tissue-specific brain age prediction based on diffusion tensor imaging and brain morphometry
Cited by: 85
Author(s): Geneviève Richard, Knut-Kristian Kolskår, Anne-Marthe Sanders, Tobias Kaufmann, Anders Petersen, Nhat Trung Doan, Jennifer Monereo Sánchez, Dag Alnæs, Kristine M. Ulrichsen, Erlend S. Dørum, Ole A. Andreassen, Jan Egil Nordvik, Lars T. Westlye
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12860-019-0199-y

Single cell RNA-Seq reveals pre-cDCs fate determined by transcription factor combinatorial dose
Cited by: 14
Author(s): MA Wei-hua, Jaeyop Lee, Daniel Backenroth, Yu Zhou, Erin C. Bush, Peter A. Sims, Kang Liu, Yufeng Shen
Software Mentions: 5
Published: over 5 years ago

10.3390/genes12020292

Comparative Mitogenomics in Hyalella (Amphipoda: Crustacea)
Cited by: 5
Author(s): Francesco Zapelloni, José A. Jurado‐Rivera, Damià Jaume, Carlos Juan, Joan Pons
Software Mentions: 5
Published: almost 4 years ago

10.1038/srep37393

Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer
Cited by: 84
Author(s): Stephan H. Bernhart, Helene Kretzmer, Lesca M. Holdt, Frank Jühling, Ole Ammerpohl, Anke Bergmann, Bernd H. Northoff, Gero Doose, Reiner Siebert, Peter F. Stadler, Steve Hoffmann
Software Mentions: 5
Published: almost 8 years ago

10.7554/eLife.20375

Oral transfer of chemical cues, growth proteins and hormones in social insects
Cited by: 96
Author(s): Adria C LeBoeuf, Patrice Waridel, Colin S. Brent, André Nicolau Aquime Gonçalves, Laure Menin, Daniel Ortiz, Oksana Riba‐Grognuz, Atsuo Koto, Zamira Guerra Soares, Eyal Privman, Eric A. Miska, Richard Benton, Laurent Keller
Software Mentions: 5
Published: almost 8 years ago

10.3389/fmicb.2020.00125

Gut Microbiota Plasticity Influences the Adaptability of Wild and Domestic Animals in Co-inhabited Areas
Cited by: 15
Author(s): Wen Qin, Pengfei Song, Gonghua Lin, YanGan Huang, Lei Wang, Xiaowen Zhou, Shengqing Li, Tongzuo Zhang
Software Mentions: 5
Published: almost 5 years ago

10.3389/fpls.2019.00811

Identification of Loci and Candidate Genes Responsible for Pod Dehiscence in Soybean via Genome-Wide Association Analysis Across Multiple Environments
Cited by: 25
Author(s): Dezhou Hu, Guizhen Kan, Wei Hu, Yali Li, Dejun Hao, Li Xiao, Hui Yang, Zhongyi Yang, Xiaohong He, Fang Huang, Deyue Yu
Software Mentions: 4
Published: over 5 years ago

10.1155/2021/9255494

Developing ZNF Gene Signatures Predicting Radiosensitivity of Patients with Breast Cancer
Cited by: 9
Author(s): Derui Yan, Meifen Shen, Zixuan Du, Jianping Cao, Ye Tian, Ping Zeng, Zaixiang Tang
Software Mentions: 4
Published: about 3 years ago

10.1186/s12859-017-1708-7

Intervene: a tool for intersection and visualization of multiple gene or genomic region sets
Cited by: 322
Author(s): Aziz Khan, Anthony Mathelier
Software Mentions: 4
Published: over 7 years ago

10.1002/ece3.3063

Regulation of gene expression is associated with tolerance of the Arctic copepod Calanus glacialis to <scp>CO</scp> 2 ‐acidified sea water
Cited by: 40
Author(s): Allison Bailey, Pierre De Wit, Peter Thor, Howard I. Browman, Reidun M. Bjelland, Steven Shema, David M. Fields, Jeffrey A. Runge, Cameron Thompson, Haakon Hop
Software Mentions: 4
Published: over 7 years ago

10.3390/microorganisms7100475

Low Temperature (15 °C) Reduces Bacterial Diversity and Prolongs the Preservation Time of Volvariella volvacea
Cited by: 6
Author(s): Xiuling Wang, Shunjie Liu, Mingjie Chen, Changxia Yu, Yan Zhao, Haiyan Yang, Zhe Li, Zhengpeng Li
Software Mentions: 4
Published: about 5 years ago

10.1099/mgen.0.000338

Coinfinder: detecting significant associations and dissociations in pangenomes
Cited by: 33
Author(s): Fiona Whelan, Martin Rusilowicz, James O. McInerney
Software Mentions: 4
Published: over 4 years ago

10.1186/s12865-021-00428-6

Transcriptomics of type 2 diabetic and healthy human neutrophils
Cited by: 8
Author(s): Sarah E. Kleinstein, Jamison McCorrison, A. Razzaque Ahmed, Hatice Hastürk, Thomas E. Van Dyke, Marcelo Freire
Software Mentions: 4
Published: over 3 years ago

10.18632/aging.103172

Overexpression of miR-142-5p inhibits the progression of nonalcoholic steatohepatitis by targeting TSLP and inhibiting JAK-STAT signaling pathway
Cited by: 12
Author(s): Chao Zhou, Pu Wang, Lei Lei, Yi Huang, Yue Wu
Software Mentions: 4
Published: over 4 years ago

10.1155/2021/5345181

Prognostic Implications of Immune-Related Gene Pairs Signatures in Bladder Cancer
Cited by: 3
Author(s): Hui Xiong, Hui Gao, Jinding Hu, Ying Dai, Hanbo Wang, Min Fu, Taiguo Qi, Lianjun Li, Qinghua Xia, Xunbo Jin, Zilian Cui, Weiting Kang
Software Mentions: 4
Published: over 3 years ago

10.31557/APJCP.2020.21.6.1787

Risk Scoring System based on lncRNA Expression for Predicting Survival in Hepatocellular Carcinoma with Cirrhosis
Cited by: 13
Author(s): Jiaxiang Ye, Haixia Li, Jiazhang Wei, Yue Luo, Hongmei Li, Jinyan Zhang, Xi Luo
Software Mentions: 4
Published: over 4 years ago

10.1186/s12951-020-0576-x

Core–shell nanoparticles suppress metastasis and modify the tumour-supportive activity of cancer-associated fibroblasts
Cited by: 33
Author(s): Dóra Kovács, Nóra Igaz, Annamária Marton, Andrea Rónavári, Péter Bélteky, László Bodai, Gabriella Spengler, László Tiszlavicz, Zsolt Rázga, Péter Hegyi, Csaba Vízler, Imre Boros, Zoltán Kónya, Mónika Kiricsi
Software Mentions: 4
Published: almost 5 years ago

10.7554/eLife.02734

Loss of the multifunctional RNA-binding protein RBM47 as a source of selectable metastatic traits in breast cancer
Cited by: 102
Author(s): Sakari Vanharanta, Christina B. Marney, Weiqun Shu, Manuel Valiente, Yilong Zou, Aldo Mele, Robert B. Darnell, Joan Massagué
Software Mentions: 4
Published: over 10 years ago

10.1038/s41420-021-00462-8

NR5A2 transcriptional activation by BRD4 promotes pancreatic cancer progression by upregulating GDF15
Cited by: 10
Author(s): Feng Guo, Yingke Zhou, Hui Guo, Dianyun Ren, Xin Jin, Heshui Wu
Software Mentions: 4
Published: over 3 years ago

10.3389/fpls.2014.00406

Use of whole genome sequences to develop a molecular phylogenetic framework for Rhodococcus fascians and the Rhodococcus genus
Cited by: 27
Author(s): Allison Creason, Edward W. Davis, M. L. Putnam, Olivier M. Vandeputte, Jeff H. Chang
Software Mentions: 4
Published: over 10 years ago

10.3390/ijms18050922

Transcriptomic Analysis of Calcium Remodeling in Colorectal Cancer
Cited by: 37
Author(s): Enrique Pérez-Riesgo, Lucía Gutiérrez, Daniel Ubierna, Alberto Acedo, Mary Pat Moyer, Lucı́a Núñez, Carlos Alonso
Software Mentions: 4
Published: over 7 years ago

10.1038/s41396-020-0729-9

Transcriptome plasticity underlying plant root colonization and insect invasion by Pseudomonas protegens
Cited by: 35
Author(s): Pilar Vesga, Pascale Flury, Jordan Vacheron, Christoph Keel, Daniel Croll, M. Maurhofer
Software Mentions: 4
Published: about 4 years ago

10.18632/aging.202811

Prognostic analysis of tumor mutation burden and immune infiltration in hepatocellular carcinoma based on TCGA data
Cited by: 6
Author(s): Shaoqing Liu, Qian-Jie Tang, Jianwen Huang, Meixiao Zhan, Wei Zhao, Xiangyu Yang, Li Yong, Lijuan Qiu, Fujun Zhang, Ligong Lu, Xueling He
Software Mentions: 4
Published: over 3 years ago

10.1128/mBio.03348-19

An Advanced Human Intestinal Coculture Model Reveals Compartmentalized Host and Pathogen Strategies during Salmonella Infection
Cited by: 21
Author(s): Leon N. Schulte, Matthias Schweinlin, Alexander J. Westermann, Harshavardhan Janga, Sara Correia Santos, Silke Appenzeller, Heike Walles, Jörg Vogel, Marco Metzger
Software Mentions: 4
Published: over 4 years ago

10.1038/s41368-018-0037-7

Increased virulence of the oral microbiome in oral squamous cell carcinoma revealed by metatranscriptome analyses
Cited by: 74
Author(s): Susan Yost, Philip Stashenko, Yoon-Hee Choi, Maria A. Kukuruzinska, Caroline A. Genco, Andrew Salama, Ellen O. Weinberg, Carolyn D. Kramer, Jorge Frias-Lopez
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-018-29329-2

Determination of system level alterations in host transcriptome due to Zika virus (ZIKV) Infection in retinal pigment epithelium
Cited by: 33
Author(s): Pawan Kumar Singh, Indu Khatri, Alokkumar Jha, Carla D. Pretto, Katherine R. Spindler, Vaithilingaraja Arumugaswami, Shailendra Giri, Ashok Kumar, Manoj Bhasin
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-36984-y

Comparative transcriptome analysis reveals relationship of three major domesticated varieties of Auricularia auricula-judae
Cited by: 15
Author(s): Yuhui Zhao, Liang Wang, Dongshan Zhang, Rong Li, Tianyou Cheng, Yibi Zhang, Liu Xue-ju, Gary Wong, Yuguo Tang, Hui Wang, Shan Gao
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1007133

Genome wide comparison of Ethiopian Leishmania donovani strains reveals differences potentially related to parasite survival
Cited by: 38
Author(s): Arie Zackay, James A. Cotton, Mandy Sanders, Asrat Hailu, Abedelmajeed Nasereddin, Alon Warburg, Charles L. Jaffe
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pgen.1006464

Alternative Splicing within and between Drosophila Species, Sexes, Tissues, and Developmental Stages
Cited by: 52
Author(s): Lauren Gibilisco, Qi Zhou, Shivani Mahajan, Doris Bachtrog
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-020-61569-z

Microbial community structure and functional properties in permanently and seasonally flooded areas in Poyang Lake
Cited by: 11
Author(s): Yang Liu, Ze Ren, Xiaodong Qu, Min Zhang, Yang Yu, Yuhang Zhang, Wenqi Peng
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.22536

Transcriptional networks specifying homeostatic and inflammatory programs of gene expression in human aortic endothelial cells
Cited by: 68
Author(s): Nicholas T Hogan, Michael B. Whalen, Lindsey K Stolze, Nizar K Hadeli, Michael T. Lam, James R. Springstead, Christopher K. Glass, Casey E. Romanoski
Software Mentions: 4
Published: over 7 years ago

10.1016/j.psj.2021.101181

Cecal microbiome profile of Hawaiian feral chickens and pasture-raised broiler (commercial) chickens determined using 16S rRNA amplicon sequencing
Cited by: 12
Author(s): Sudhir Yadav, Kayla D. Caliboso, Jannel E. Nanquil, Jiachao Zhang, Helmut Kae, Kabi R. Neupane, Birendra Mishra
Software Mentions: 4
Published: over 3 years ago

10.1002/2211-5463.12983

Identification of modules and novel prognostic biomarkers in liver cancer through integrated bioinformatics analysis
Cited by: 5
Author(s): Bo Shen, Kun Li, Yuting Zhang
Software Mentions: 4
Published: about 4 years ago

10.3389/fgene.2020.555865

Identification of Tumor Microenvironment-Related Prognostic Biomarkers in Luminal Breast Cancer
Cited by: 15
Author(s): Yanyan Wang, Mingzhi Zhu, Feng Guo, Yi Song, Xunjie Fan, Guijun Qin
Software Mentions: 4
Published: about 4 years ago

10.3390/genes12020203

Characterization of Breed Specific Differences in Spermatozoal Transcriptomes of Sheep in Australia
Cited by: 8
Author(s): Marnie J. Hodge, Sara de las Heras‐Saldana, Sally J. Rindfleish, Cyril Stephen, Sameer D. Pant
Software Mentions: 4
Published: almost 4 years ago

10.3390/genes12010106

Real-Time Culture-Independent Microbial Profiling Onboard the International Space Station Using Nanopore Sequencing
Cited by: 37
Author(s): Sarah Stahl-Rommel, Miten Jain, Hang N. Nguyen, Richard R. Arnold, Serena M. Auñón-Chancellor, Gretta Marie Sharp, C. L. Castro, Kristen K. John, Sissel Juul, Daniel J. Turner, David Stoddart, Benedict Paten, Mark Akeson, Aaron S. Burton, Sarah L. Castro-Wallace
Software Mentions: 4
Published: almost 4 years ago

10.3390/biomedicines8040081

A Protocol for the Multi-Omic Integration of Cervical Microbiota and Urine Metabolomics to Understand Human Papillomavirus (HPV)-Driven Dysbiosis
Cited by: 3
Author(s): Nataliya Chorna, Filipa Godoy-Vitorino
Software Mentions: 4
Published: over 4 years ago

10.3389/fgene.2021.658736

A Prognostic Model Based on the Immune-Related lncRNAs in Colorectal Cancer
Cited by: 16
Author(s): Fen Qin, Houxi Xu, Guoli Wei, Ji Yi, Jialin Yu, Canhong Hu, Chunyi Yuan, Yuzhu Ma, Jun Qian, Lingchang Li, Jiege Huo
Software Mentions: 4
Published: over 3 years ago

10.3390/genes11101219

Genomic Characterization of Methicillin-Resistant Staphylococcus aureus (MRSA) by High-Throughput Sequencing in a Tertiary Care Hospital
Cited by: 8
Author(s): May Sherif Soliman, Noha Salah Soliman, Arwa R Elmanakhly, S. A. El-Banna, Ramy K. Aziz, Amani El-Kholy
Software Mentions: 4
Published: about 4 years ago

10.1016/j.gdata.2016.10.006

Identifying protective host gene expression signatures within the spleen during West Nile virus infection in the collaborative cross model
Cited by: 15
Author(s): Richard Green, Courtney Wilkins, Sunil Thomas, Aimee Sekine, Reneé C. Ireton, Martin T. Ferris, Duncan M. Hendrick, Kathleen Voss, Fernando Pardo-Manuel de Villena, Ralph S. Baric, Mark T. Heise, Michael Gale
Software Mentions: 4
Published: almost 8 years ago

10.1038/s42003-021-01925-5

Inhibiting LXRα phosphorylation in hematopoietic cells reduces inflammation and attenuates atherosclerosis and obesity in mice
Cited by: 2
Author(s): Maud Voisin, Elina Shrestha, Claire Rollet, Cyrus Nikain, Tatjana Josefs, Mélanie Mahé, Tessa Barrett, Hye Rim Chang, Rachel Ruoff, Jeffrey A. Schneider, Michela L. Garabedian, Chris Zoumadakis, Chi Sun Yun, Bara A. Badwan, Emily J. Brown, Adam C. Mar, Robert J. Schneider, Ira J. Goldberg, Inés Pineda-Torra, Edward A. Fisher
Software Mentions: 3
Published: over 3 years ago

10.15252/emmm.201708047

The <scp>GPR</scp> 120 agonist <scp>TUG</scp> ‐891 promotes metabolic health by stimulating mitochondrial respiration in brown fat
Cited by: 75
Author(s): Maaike Schilperoort, Anke Dam, Geerte Hoeke, Irina G. Shabalina, Anthony Okolo, Aylin Hanyaloglu, Lea Dib, Isabel M. Mol, Natarin Caengprasath, Yi‐Wah Chan, Sami Damak, Anne Reifel Miller, Tamer Coşkun, Bharat Shimpukade, Trond Ulven, Sander Kooijman, Patrick C.N. Rensen, Mark Christian
Software Mentions: 3
Published: almost 7 years ago

10.1186/s13148-019-0760-8

The phenotypic variations of multi-locus imprinting disturbances associated with maternal-effect variants of NLRP5 range from overt imprinting disorder to apparently healthy phenotype
Cited by: 19
Author(s): Ángela Sparago, Ankit Verma, Maria Grazia Patricelli, Laura Pignata, Silvia Russo, Luciano Calzari, Naomi De Francesco, Rosita Del Prete, Orazio Palumbo, Massimo Carella, Deborah J G Mackay, Faisal I. Rezwan, Claudia Angelini, Flavia Cerrato, Maria Vittoria Cubellis, Andrea Riccio
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41426-018-0187-x

Filamentation in Candida auris, an emerging fungal pathogen of humans: passage through the mammalian body induces a heritable phenotypic switch
Cited by: 93
Author(s): Huizhen Yue, Bing Jian, Qiushi Zheng, Yulong Zhang, Tianren Hu, Han Du, Hui Wang, Guanghua Huang
Software Mentions: 3
Published: almost 6 years ago

Projects: pypi: heatmap

Papers Mentioning heatmap 285