bioconductor: limma | Projects | Ecosyste.ms: Papers

10.1186/1756-0500-6-428

Parallel deep transcriptome and proteome analysis of zebrafish larvae
Cited by: 15
Author(s): Magnus Palmblad, Christiaan V. Henkel, Ron P. Dirks, Annemarie H. Meijer, André M. Deelder, Herman P. Spaink
Software Mentions: 1
Published: almost 13 years ago

10.1080/0886022X.2016.1244083

Identification of crucial miRNAs and the targets in renal cortex of hypertensive patients by expression profiles
Cited by: 12
Author(s): Guohua Wang, Lan Wu, Zhi Chen, Jinghui Sun
Software Mentions: 1
Published: almost 10 years ago

10.1080/0886022X.2019.1669460

The <i>miR-15a-5p-XIST-CUL3</i> regulatory axis is important for sepsis-induced acute kidney injury
Cited by: 43
Author(s): Guanhua Xu, Lujiao Mo, Channi Wu, Xiaoyuan Shen, Han Dong, Lixin Yu, Ping-Ying Pan, Kanda Pan
Software Mentions: 1
Published: over 7 years ago

10.1186/s12958-015-0010-7

Global gene expression in granulosa cells of growing, plateau and atretic dominant follicles in cattle
Cited by: 49
Author(s): Annie Girard, Isabelle Dufort, Gabriel Douville, Marc‐André Sirard
Software Mentions: 1
Published: over 11 years ago

10.18632/aging.103245

Identification and validation of hub microRNAs dysregulated in esophageal squamous cell carcinoma
Cited by: 16
Author(s): Chen Sang, Ce Chao, Wang Min, Youpu Zhang, Guanghua Luo, Xiaoying Zhang
Software Mentions: 1
Published: over 6 years ago

10.1186/s12958-019-0546-z

Analysis of key genes and their functions in placental tissue of patients with gestational diabetes mellitus
Cited by: 9
Author(s): Yuxia Wang, Haifeng Yu, Fangmei Liu, Xiue Song
Software Mentions: 1
Published: almost 7 years ago

10.18632/aging.202862

Methylation factor MRPL15 identified as a potential biological target in Alzheimer’s disease
Cited by: 2
Author(s): Li Gao, Jianmei Li, Ming Yan, Aili Maimaiti
Software Mentions: 1
Published: over 5 years ago

10.1186/s12958-021-00760-x

TMT-based proteomic and bioinformatic analyses of human granulosa cells from obese and normal-weight female subjects
Cited by: 9
Author(s): Chenchen Si, Nan Wang, Mingjie Wang, Yue Liu, Zhihong Niu, Zhide Ding
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms18122728

Identification of Differentially Expressed miRNAs in Colorado Potato Beetles (Leptinotarsa decemlineata (Say)) Exposed to Imidacloprid
Cited by: 18
Author(s): Mathieu D. Morin, Pierre J. Lyons, Nicolas Crapoulet, Sébastien Boquel, Pier Jr Morin
Software Mentions: 1
Published: over 8 years ago

10.1530/REP-19-0587

Integrated analysis of mRNA and protein expression profiling in tubal endometriosis
Cited by: 5
Author(s): Hang Qi, Huiyu Zhang, Xiujuan Zhao, Ya Qin, Liang Guo, Xiaoqing He, Jian Zhang
Software Mentions: 1
Published: over 6 years ago

10.1530/REP-20-0677

CLDN1 regulates trophoblast apoptosis and proliferation in preeclampsia
Cited by: 9
Author(s): Yuchen Zhang, Xiaoli Qin, Xiaoling Ma, Hui-Qin Mo, Quan Shi, Cheng-Xi Zhang, Xiaowei Wei, Xueqing Liu, Yan Zhang, Fu‐Ju Tian, Yi Lin
Software Mentions: 1
Published: over 5 years ago

10.1186/1756-0500-7-871

miRNome of inflammatory breast cancer
Cited by: 35
Author(s): D. V. Maltseva, Vladimir Galatenko, Timur R. Samatov, Svetlana Zhikrivetskaya, N. A. Khaustova, И. Н. Нечаев, M. Yu. Shkurnikov, A. V. Lebedev, Irina Mityakina, А. Д. Каприн, Udo Schumacher, Alexander G. Tonevitsky
Software Mentions: 1
Published: almost 12 years ago

10.1186/s13104-015-1567-0

Derivation of induced pluripotent stem cells from orangutan skin fibroblasts
Cited by: 22
Author(s): Krishna Ramaswamy, Wing Yan Yik, Xiaoming Wang, Erin N. Oliphant, Wange Lu, Darryl Shibata, Oliver A. Ryder, Joseph G. Hacia
Software Mentions: 1
Published: almost 11 years ago

10.1186/1756-0500-5-40

Factors affecting the yield of microRNAs from laser microdissectates of formalin-fixed tissue sections
Cited by: 6
Author(s): Santosh K. Patnaik, Eric Kannisto, Sai Yendamuri
Software Mentions: 1
Published: over 14 years ago

10.1155/2021/7394344

PP2 Ameliorates Renal Fibrosis by Regulating the NF-κB/COX-2 and PPARγ/UCP2 Pathway in Diabetic Mice
Cited by: 11
Author(s): Jinying Wei, Xia Deng, Li Yang, Runmei Li, Zhaohua Yang, Xiuyuan Li, Shan Song, Yonghong Shi, Huijun Duan, Haijiang Wu
Software Mentions: 1
Published: almost 5 years ago

10.1186/1465-9921-10-2

Transcriptome profiling of primary murine monocytes, lung macrophages and lung dendritic cells reveals a distinct expression of genes involved in cell trafficking
Cited by: 29
Author(s): Zbigniew Zasłona, Jochen Wilhelm, Lidija Cakarova, Leigh M. Marsh, Werner Seeger, Jürgen Lohmeyer, Werner von Wulffen
Software Mentions: 1
Published: over 17 years ago

10.1186/s13104-021-05635-3

Integrated microRNA and mRNA gene expression in peripheral blood mononuclear cells in response to acute psychosocial stress: a repeated-measures within-subject pilot study
Cited by: 1
Author(s): Magdalena Jurkiewicz, Anett Mueller-Alcazar, Dirk Moser, Indralatha Jayatilaka, Anatoly Mikhailik, Jamie Ferri, Nia Fogelman, Turhan Canli
Software Mentions: 1
Published: over 5 years ago

10.18632/aging.102765

Testicular biopsies microarray analysis reveals circRNAs are involved in the pathogenesis of non-obstructive azoospermia
Cited by: 8
Author(s): Hao Bo, Zhizhong Liu, Ruiling Tang, Guanghui Gong, Xingming Wang, Han Zhang, Fang Zhu, Dai Zhou, Wenbing Zhu, Yue‐Qiu Tan, Liqing Fan
Software Mentions: 1
Published: over 6 years ago

10.1186/s12890-017-0472-9

Unsupervised gene expression analyses identify IPF-severity correlated signatures, associated genes and biomarkers
Cited by: 24
Author(s): Yunguan Wang, Jaswanth Yella, Jing Chen, Francis X. McCormack, Satish K. Madala, Anil G. Jegga
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2466-11-39

The asthma candidate gene NPSR1 mediates isoform specific downstream signalling
Cited by: 22
Author(s): Christina Orsmark-Pietras, Johanna Vendelin, Francesca Anedda, Sara Bruce, Mikael Adner, L. Sundman, Ville Pulkkinen, Harri Alenius, Mauro D’Amato, Cilla Söderhäll, Juha Kere
Software Mentions: 1
Published: about 15 years ago

10.1186/s12931-018-0816-x

The therapeutic effect of mesenchymal stem cells on pulmonary myeloid cells following neonatal hyperoxic lung injury in mice
Cited by: 23
Author(s): Ali Al-Rubaie, Andrea F Wise, Foula Sozo, Robert De Matteo, Chrishan S. Samuel, Richard Harding, Sharon D. Ricardo
Software Mentions: 1
Published: over 8 years ago

10.1186/s12931-019-1062-6

Arginase impairs hypoxic pulmonary vasoconstriction in murine endotoxemia
Cited by: 6
Author(s): Bodil Petersen, Cornelius Busch, Grigorij Schleifer, Dominik Schaack, Felix Lasitschka, Kenneth D. Bloch, Donald B. Bloch, Fumito Ichinose
Software Mentions: 1
Published: over 7 years ago

10.1186/s12890-021-01549-9

GPC3 affects the prognosis of lung adenocarcinoma and lung squamous cell carcinoma
Cited by: 6
Author(s): Jing Ning, Shenyi Jiang, Xiaoxi Li, Yang Wang, Xuhong Deng, Zhiqiang Zhang, Lijie He, Daqing Wang, Youyu Jiang
Software Mentions: 1
Published: over 5 years ago

10.1186/s12884-021-03777-7

Differential circular RNA expression profiles in umbilical cord blood exosomes from preeclampsia patients
Cited by: 7
Author(s): Mingtao Cao, Juan Wen, Chaozhi Bu, Chunyan Li, Yongcheng Lin, Hong Zhang, Yanfang Gu, Zhonghua Shi, Yan Zhang, Wei Long, Le Zhang
Software Mentions: 1
Published: over 5 years ago

10.1186/s12931-019-1176-x

Wnt signaling regulates trans-differentiation of stem cell like type 2 alveolar epithelial cells to type 1 epithelial cells
Cited by: 34
Author(s): Elhusseiny Mohamed Mahmud Abdelwahab, Judit Rapp, D. Feller, Veronika Csöngei, Szilárd Pál, Domokos Bartis, David Thickett, Judit E. Pongrácz
Software Mentions: 1
Published: about 7 years ago

10.1007/s00726-015-1956-7

Homocysteine thiolactone and N-homocysteinylated protein induce pro-atherogenic changes in gene expression in human vascular endothelial cells
Cited by: 74
Author(s): Dorota Gurda, Luiza Handschuh, Weronika Kotkowiak, Hieronim Jakubowski
Software Mentions: 1
Published: over 11 years ago

10.1164/rccm.202005-1761OC

Circulating BMP9 Protects the Pulmonary Endothelium during Inflammation-induced Lung Injury in Mice
Cited by: 27
Author(s): Wei Li, Long Lü, Xudong Yang, Zhen Tong, Mark Southwood, Ross King, Paola Caruso, Paul D. Upton, Peiran Yang, Geoffrey A Bocobo, Ivana Nikolić, Angelica Higuera, Richard M. Salmon, He Jiang, Katharine M Lodge, Kim Hoenderdos, Rebecca M. Baron, Paul B. Yu, Alison M. Condliffe, Charlotte Summers, Sussan Nourshargh, Edwin R. Chilvers, Nicholas W. Morrell
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-016-0740-5

Fusarium oxysporum f.sp. radicis-lycopersici induces distinct transcriptome reprogramming in resistant and susceptible isogenic tomato lines
Cited by: 40
Author(s): Daniele Manzo, Francesca Ferriello, Gerardo Puopolo, A. Zoina, Daniela D’Esposito, Luca Tardella, Alberto Ferrarini, Maria Raffaella Ercolano
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2229-14-108

Day and night heat stress trigger different transcriptomic responses in green and ripening grapevine (vitis vinifera) fruit
Cited by: 134
Author(s): Markus Rienth, Laurent Torregrosa, Nathalie Luchaire, Ratthaphon Chatbanyong, David Lecourieux, Mary T. Kelly, Charles Romieu
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2229-11-120

Global transcriptome analysis of two ameiotic1 alleles in maize anthers: defining steps in meiotic entry and progression through prophase I
Cited by: 28
Author(s): Guo-Ling Nan, Arnaud Ronceret, Rachel Wang, John Fernandes, W. Zacheus Cande, Virginia Walbot
Software Mentions: 1
Published: over 15 years ago

10.1186/s12870-020-2317-6

Comparative transcriptome analyses of fruit development among pears, peaches, and strawberries provide new insights into single sigmoid patterns
Cited by: 18
Author(s): Mao-Song Pei, Suhao Cao, Lei Wu, Guo‐Ming Wang, Zhihua Xie, Chao Gu, Shaoling Zhang
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms19072016

Concentrated Conditioned Media from Adipose Tissue Derived Mesenchymal Stem Cells Mitigates Visual Deficits and Retinal Inflammation Following Mild Traumatic Brain Injury
Cited by: 40
Author(s): Kumar Abhiram Jha, Mickey Pentecost, Raji Rajesh Lenin, Lada Klaic, Sally L. Elshaer, Jordy Gentry, J. M. Russell, Alex Beland, Anton Reiner, Veronique Jotterand, Nicolas Sohl, Rajashekhar Gangaraju
Software Mentions: 1
Published: about 8 years ago

10.1186/s12977-018-0409-2

A CRISPR screen for factors regulating SAMHD1 degradation identifies IFITMs as potent inhibitors of lentiviral particle delivery
Cited by: 20
Author(s): Ferdinand Roesch, Molly OhAinle, Michael Emerman
Software Mentions: 1
Published: over 8 years ago

10.1186/1710-1492-10-32

Th17/Treg ratio derived using DNA methylation analysis is associated with the late phase asthmatic response
Cited by: 28
Author(s): Amrit Singh, Masatsugu Yamamoto, Jian Ruan, Jung‐Hye Choi, Gail M. Gauvreau, Sven Olek, Ulrich Hoffmueller, Christopher Carlsten, J. Mark FitzGerald, Louis‐Philippe Boulet, Paul M. O'Byrne, Scott J. Tebbutt
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2229-13-27

Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids
Cited by: 48
Author(s): Hyun Jo Koo, Eric T. McDowell, Xiaoqiang Ma, Kevin Greer, Jeremy Kapteyn, Zhengzhi Xie, Anne Descour, Hye Ran Kim, Yeisoo Yu, David Kudrna, Rod A. Wing, Carol Soderlund, David R. Gang
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2229-11-173

SND2, a NAC transcription factor gene, regulates genes involved in secondary cell wall development in Arabidopsis fibres and increases fibre cell area in Eucalyptus
Cited by: 135
Author(s): Steven G. Hussey, Eshchar Mizrachi, Antanas Spokevicius, Gerd Bossinger, David Kenneth Berger, Alexander Andrew Myburg
Software Mentions: 1
Published: almost 15 years ago

10.1177/2472555220973597

CETSA MS Profiling for a Comparative Assessment of FDA-Approved Antivirals Repurposed for COVID-19 Therapy Identifies TRIP13 as a Remdesivir Off-Target
Cited by: 11
Author(s): Tomas Friman, Alexey Chernobrovkin, Daniel Martinez Molina, Laurence H. Arnold
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2229-10-134

Delineating the structural, functional and evolutionary relationships of sucrose phosphate synthase gene family II in wheat and related grasses
Cited by: 13
Author(s): Shailendra Sharma, Nese Sreenivasulu, Vokkaliga T. Harshavardhan, Christiane Seiler, Shiveta Sharma, Zaynali Nezhad Khalil, Eduard Akhunov, Sunish K. Sehgal, Marion S. Röder
Software Mentions: 1
Published: over 16 years ago

10.1111/all.14016

Blood eosinophil count and airway epithelial transcriptome relationships in COPD versus asthma
Cited by: 31
Author(s): Lauren George, Adam Taylor, Anna Esteve‐Codina, María Soler Artigas, Gian Andri Thun, Stewart Bates, Stelios Pavlidis, Scott Wagers, Anne Boland, Antje Prasse, Pierà Boschetto, David Parr, Adam Nowiński, Imre Barta, Jens M. Hohlfeld, Timm Greulich, Maarten van den Berge, Pieter S. Hiemstra, Wim Timens, Timothy S C Hinks, Sally E. Wenzel, Salman Siddiqui, Matthew Richardson, Per Venge, Simon Heath, Marta Gut, Martin D. Tobin, Lindsay J. Edwards, John Riley, Ratko Djukanović, Charles Auffray, Bertrand DeMeulder, Sven Erik-Dahlen, Ian M. Adcock, Kian Fan Chung, Loems Ziegler-Heitbrock, Peter J. Sterk, Dave Singh, Christopher E. Brightling
Software Mentions: 1
Published: about 7 years ago

10.14336/AD.2020.1112

Prediction of SARS-CoV Interaction with Host Proteins during Lung Aging Reveals a Potential Role for TRIB3 in COVID-19
Cited by: 9
Author(s): Diogo de Moraes, Brunno Vivone Buquete Paiva, Sarah Santiloni Cury, Raissa G. Ludwig, João Pessoa Araújo, Marcelo A. Mori, Robson Francisco Carvalho
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-020-2258-0

Dissecting the control of shoot development in grapevine: genetics and genomics identify potential regulators
Cited by: 9
Author(s): Sabine Guillaumie, Stéphane Decroocq, Nathalie Ollat, Serge Delrot, Éric Gomès, Sarah Jane Cookson
Software Mentions: 1
Published: over 6 years ago

10.1111/acel.13213

SS‐31 and NMN: Two paths to improve metabolism and function in aged hearts
Cited by: 33
Author(s): Jeremy Whitson, Alessandro Bitto, Huiliang Zhang, Mariya T. Sweetwyne, Rene Coig, Saakshi Bhayana, Eric G. Shankland, Lu Wang, Theo K. Bammler, Kathryn F. Mills, Shoichi Imai, Kevin E. Conley, David J. Marcinek, Peter S. Rabinovitch
Software Mentions: 1
Published: about 6 years ago

10.1021/acschemneuro.1c00303

Wide-Ranging Effects on the Brain Proteome in a Transgenic Mouse Model of Alzheimer’s Disease Following Treatment with a Brain-Targeting Somatostatin Peptide
Cited by: 10
Author(s): Fadi Rofo, Friederike Andrea Sandbaumhüter, Aikaterini Chourlia, Nicole G. Metzendorf, Jamie I. Morrison, Stina Syvänen, Per E. Andrén, Erik T. Jansson, Greta Hultqvist
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2229-9-4

Linkage mapping of putative regulator genes of barley grain development characterized by expression profiling
Cited by: 11
Author(s): Christof Pietsch, Nese Sreenivasulu, Ulrich Wobus, Marion S. Röder
Software Mentions: 1
Published: over 17 years ago

10.1186/1472-6793-13-9

Dynamically regulated miRNA-mRNA networks revealed by exercise
Cited by: 99
Author(s): Alexander G. Tonevitsky, D. V. Maltseva, Asghar Abbasi, Timur R. Samatov, D. A. Sakharov, M. Yu. Shkurnikov, A. V. Lebedev, Vladimir Galatenko, Anatoly I. Grigoriev, Hinnak Northoff
Software Mentions: 1
Published: over 13 years ago

10.1186/s12903-021-01827-2

Association between chronic periodontitis and the risk of Alzheimer’s disease: combination of text mining and GEO dataset
Cited by: 8
Author(s): Zhengye Jiang, Yanxi Shi, Wenpeng Zhao, Li-Wei Zhou, Bingchang Zhang, Yuanyuan Xie, Yaya Zhang, Guowei Tan, Zhanxiang Wang
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12886-020-01381-5

Identification of potential molecular targets associated with proliferative diabetic retinopathy
Cited by: 6
Author(s): Dewang Shao, Shang He, Zi Ye, Xuyou Zhu, Wei Sun, Wei Fu, Tianju Ma, Zhaohui Li
Software Mentions: 1
Published: over 6 years ago

10.1186/s12868-016-0333-0

Poly(ADP-ribose) polymerase inhibitors activate the p53 signaling pathway in neural stem/progenitor cells
Cited by: 17
Author(s): Akiko Okuda, Shu Kurokawa, Masanori Takehashi, Aika Maeda, Katsuya Fukuda, Yukari Kubo, Hyuma Nogusa, Tomoka Takatani‐Nakase, Shujiro Okuda, Kunihiro Ueda, Seigo Tanaka
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2202-13-126

High throughput analysis reveals dissociable gene expression profiles in two independent neural systems involved in the regulation of social behavior
Cited by: 22
Author(s): Tyler J. Stevenson, Kirstin Replogle, Jenny Drnevich, David F. Clayton, Gregory F. Ball
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12883-019-1509-x

Low free triiodothyronineis predicts worsen neurological outcome of patients with acute ischemic stroke: a retrospective study with bioinformatics analysis
Cited by: 12
Author(s): Shanchao Zhang, Xia Zhao, Shan Xu, Jing Yuan, Zhihua Si, Yang Yang, Shan Qiao, Xuxu Xu, Aihua Wang
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12882-021-02356-4

Comprehensive analysis of IgA nephropathy expression profiles: identification of potential biomarkers and therapeutic agents
Cited by: 9
Author(s): Alieh Gholaminejad, Yousof Gheisari, Seyed Amir Jalali, Amir Roointan
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2199-13-9

Novel polysome messages and changes in translational activity appear after induction of adipogenesis in 3T3-L1 cells
Cited by: 16
Author(s): Carolin Fromm‐Dornieden, Silvia von der Heyde, Oleksandr Lytovchenko, Gabriela Salinas-Riester, Bertram Brenig, Tim Beißbarth, Bernhard Baumgartner
Software Mentions: 1
Published: over 14 years ago

10.1186/s12867-017-0091-2

Microarray expression profiling in the denervated hippocampus identifies long noncoding RNAs functionally involved in neurogenesis
Cited by: 14
Author(s): Bingying Deng, Xiang Cheng, Haoming Li, Jianbing Qin, Mei Tian, Guohua Jin
Software Mentions: 1
Published: over 9 years ago

10.1186/s12866-017-1137-9

6S RNA plays a role in recovery from nitrogen depletion in Synechocystis sp. PCC 6803
Cited by: 32
Author(s): Beate Heilmann, Kaisa Hakkila, Jens Georg, Taina Tyystjärvi, Wolfgang R. Hess, Ilka M. Axmann, Dennis Dienst
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12866-020-02059-0

The identification of co-expressed gene modules in Streptococcus pneumonia from colonization to infection to predict novel potential virulence genes
Cited by: 0
Author(s): Sadegh Azimzadeh Jamalkandi, Morteza Kouhsar, Jafar Salimian, Ali Ahmadi
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12866-019-1684-3

Temporal analysis of mRNA expression profiles in Orientia infected C3HeB/FeJ mouse
Cited by: 3
Author(s): Chien‐Chung Chao, Ruoting Yang, Zhiwen Zhang, Tatyana Belinskaya, Chye-Teik Chan, Stacy‐Ann Miller, Rasha Hammamieh, Marti Jett, Wei‐Mei Ching
Software Mentions: 1
Published: over 6 years ago

10.1186/s40478-015-0211-5

Identification of targets for rational pharmacological therapy in childhood craniopharyngioma
Cited by: 84
Author(s): Jacob M. Gump, Andrew M. Donson, Diane K. Birks, Vladimir Amani, Karun K. Rao, Andrea Griesinger, B. K. Kleinschmidt-DeMasters, James M. Johnston, Richard C. E. Anderson, Amy Rosenfeld, Michael H. Handler, Lia Gore, Nicholas K. Foreman, Todd C. Hankinson
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2180-12-9

Interleukin-8 is the single most up-regulated gene in whole genome profiling of H. pylori exposed gastric epithelial cells
Cited by: 67
Author(s): Lars Lohne Eftang, Ying Esbensen, Tone Tannæs, Ida Rashida Khan Bukholm, Geir Bukholm
Software Mentions: 1
Published: over 14 years ago

10.1111/acel.12174

Combined administration of testosterone plus an ornithine decarboxylase inhibitor as a selective prostate‐sparing anabolic therapy
Cited by: 13
Author(s): Ravi Jasuja, James C. Costello, Rajan Singh, Vandana Gupta, Catherine S. Spina, Gianluca Toraldo, Hyeran Jang, Hu Li, Carlo Serra, Wen Guo, Pratibha Chauhan, Navjot S. Narula, Tyler Guarneri, Ayla Ergün, Thomas G. Travison, James J. Collins, Shalender Bhasin
Software Mentions: 1
Published: almost 13 years ago

10.1186/1755-8794-4-67

Gene expression during normal and FSHD myogenesis
Cited by: 81
Author(s): Koji Tsumagari, Shao-Chi Chang, Michelle Lacey, Carl Baribault, Sridar V. Chittur, Janet E. Sowden, Rabi Tawil, Gregory E. Crawford, Melanie Ehrlich
Software Mentions: 1
Published: almost 15 years ago

10.1186/s12920-020-0690-5

Amniotic fluid cell-free transcriptome: a glimpse into fetal development and placental cellular dynamics during normal pregnancy
Cited by: 24
Author(s): Adi L. Tarca, Roberto Romero, Roger Piqué-Regi, Percy Pacora, Bogdan Done, Marian Kacerovský, Gaurav Bhatti, Sunil Jaiman, Sonia S. Hassan, Chaur‐Dong Hsu, Nardhy Gómez-López
Software Mentions: 1
Published: over 6 years ago

10.1186/1755-8794-7-35

A systems biology approach to understand the pathophysiological mechanisms of cardiac pathological hypertrophy associated with rosiglitazone
Cited by: 18
Author(s): Lars Verschuren, Peter Y. Wielinga, Thomas Kelder, Marijana Radonjić, Kanita Salic, Robert Kleemann, Ben van Ommen, Teake Kooistra
Software Mentions: 1
Published: about 12 years ago

10.1186/s12920-019-0566-8

Discovery of stroke-related blood biomarkers from gene expression network models
Cited by: 13
Author(s): Konstantinos Theofilatos, Aigli Korfiati, Seferina Mavroudi, Matthew C. Cowperthwaite, Max Shpak
Software Mentions: 1
Published: about 7 years ago

10.1186/s12920-020-00799-6

Comprehensive analysis of angiogenesis-related genes and pathways in early diabetic retinopathy
Cited by: 18
Author(s): Chufeng Gu, Thashi Lhamo, Chen Zou, Chuandi Zhou, Tong Su, Deji Draga, Da Luo, Zhi Zheng, Li Yin, Qinghua Qiu
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12920-020-0657-6

DNA hypermethylation associated with upregulated gene expression in prostate cancer demonstrates the diversity of epigenetic regulation
Cited by: 64
Author(s): Ieva Rauluševičiūtė, Finn Drabløs, Morten Rye
Software Mentions: 1
Published: over 6 years ago

10.1186/s12920-021-01087-7

Integrated bioinformatics analysis of core regulatory elements involved in keloid formation
Cited by: 4
Author(s): Chuying Li, Mei-Tong Jin, Yinli Luo, Zhehu Jin, Long-Quan Pi
Software Mentions: 1
Published: almost 5 years ago

10.1038/srep03372

Hematopoietic Stem and Progenitor Cells Acquire Distinct DNA-Hypermethylation During in vitro Culture
Cited by: 29
Author(s): Carola I. Weidner, Thomas Walenda, Qiong Lin, M Wölfler, Bernd Denecke, Ivan G. Costa, Martin Zenke, Wolfgang Wagner
Software Mentions: 1
Published: almost 13 years ago

10.1038/srep05008

PHF8 and REST/NRSF co-occupy gene promoters to regulate proximal gene expression
Cited by: 13
Author(s): Juan Wang, Xueqiu Lin, Su Wang, Chenfei Wang, Qixuan Wang, Xikun Duan, Peng Lü, Qian Wang, Chengyang Wang, X. Shirley Liu, Jinyan Huang
Software Mentions: 1
Published: over 12 years ago

10.3390/ijms20020446

Analysis of Mucopolysaccharidosis Type VI through Integrative Functional Metabolomics
Cited by: 16
Author(s): Abdellah Tebani, Lénaïg Abily-Donval, Isabelle Schmitz-Afonso, Monique Piraud, Jérôme Ausseil, Farid Zerimech, Carine Pilon, Tony Pereira, Stéphane Marret, Carlos Afonso, Soumeya Bekri
Software Mentions: 1
Published: over 7 years ago

10.1186/s12920-015-0103-3

Integrated genomics has identified a new AT/RT-like yet INI1-positive brain tumor subtype among primary pediatric embryonal tumors
Cited by: 14
Author(s): Donald Ming Tak Ho, Chuan Chi Shih, Muh Lii Liang, Chan Yen Tsai, Tsung Han Hsieh, Chin Han Tsai, Shih Chieh Lin, Ting Chang, Meng En Chao, Hsei Wei Wang, Tai-Tong Wong
Software Mentions: 1
Published: about 11 years ago

10.1038/srep09088

Blood cell transcriptomic-based early biomarkers of adverse programming effects of gestational calorie restriction and their reversibility by leptin supplementation
Cited by: 19
Author(s): Jadwiga Konieczna, Juana Sánchez, Mariona Palou, Catalina Picó, Andreu Taberner Palou
Software Mentions: 1
Published: over 11 years ago

10.1186/1755-8794-6-41

Transcriptome signatures in Helicobacter pylori-infected mucosa identifies acidic mammalian chitinase loss as a corpus atrophy marker
Cited by: 49
Author(s): Intawat Nookaew, Kaisa Thorell, Kuntal Worah, Shugui Wang, Martin L. Hibberd, Henrik Sjövall, Sven Pettersson, Jens Nielsen, Samuel Lundin
Software Mentions: 1
Published: almost 13 years ago

10.1111/acel.12745

Molecular profiling of aged neural progenitors identifies <i>Dbx2</i> as a candidate regulator of age-associated neurogenic decline
Cited by: 27
Author(s): Giuseppe Lupo, Paola S. Nisi, Pilar Esteve, Yu-Lee Paul, Clara Lopes Novo, Ben S. Sidders, Muhammad Amir Khan, Stefano Biagioni, Hai-Kun Liu, Paola Bovolenta, Emanuele Cacci, Peter J. Rugg‐Gunn
Software Mentions: 1
Published: over 8 years ago

10.1038/srep12393

Integrated genomic approaches identify major pathways and upstream regulators in late onset Alzheimer’s disease
Cited by: 102
Author(s): Xinzhong Li, Jintao Long, Taigang He, Robert Belshaw, James A. Scott
Software Mentions: 1
Published: about 11 years ago

10.3390/ijms20030570

Transcriptional Analysis of Immunohistochemically Defined Subgroups of Non-Muscle-Invasive Papillary High-Grade Upper Tract Urothelial Carcinoma
Cited by: 14
Author(s): Min-A Jung, Jeong Hoon Lee, Bohyun Kim, Jeong Hwan Park, Kyung Chul Moon
Software Mentions: 1
Published: over 7 years ago

10.1038/srep13895

Autoantibody Profiling of Glioma Serum Samples to Identify Biomarkers Using Human Proteome Arrays
Cited by: 40
Author(s): Parvez Syed, S. Gupta, Saket Choudhary, Narendra Goud Pandala, Apurva Atak, Annie Richharia, Manubhai Kp, Heng Zhu, Sridhar Epari, Santosh Noronha, Aliasgar Moiyadi, Sanjeeva Srivastava
Software Mentions: 1
Published: about 11 years ago

10.3390/ijms20030513

Expression of Immune Regulatory Genes in the Porcine Internal Genital Tract Is Differentially Triggered by Spermatozoa and Seminal Plasma
Cited by: 50
Author(s): Manuel Álvarez‐Rodríguez, Mohammad Atikuzzaman, Heli Venhoranta, Dominic Wright, Heriberto Rodríguez-Martinez
Software Mentions: 1
Published: over 7 years ago

10.1038/srep15007

Junb controls lymphatic vascular development in zebrafish via miR-182
Cited by: 22
Author(s): Kristin Kiesow, Katrin Bennewitz, Laura Gutierrez-Miranda, Sandra J. Stoll, Bettina Hartenstein, Peter Angel, Jens Krøll, Marina Schorpp-Kistner
Software Mentions: 1
Published: almost 11 years ago

10.1038/srep15214

Expression profiling of lymph nodes in tuberculosis patients reveal inflammatory milieu at site of infection
Cited by: 39
Author(s): Abhijit Maji, Richa Misra, Anupam Mondal, Dhirendra Kumar, Divya Bajaj, Abhinav Singhal, Gunjan Arora, Amit Bhaduri, Andaleeb Sajid, Sugandha Bhatia, Sompal Singh, Harshvardhan Singh, V. Pandu Ranga Rao, Debasis Dash, E. Shalini, Joy Sarojini Michael, Anil Chaudhary, Rajesh S. Gokhale, Yogendra Singh
Software Mentions: 1
Published: almost 11 years ago

10.1186/1755-8794-7-13

Childhood abuse is associated with methylation of multiple loci in adult DNA
Cited by: 147
Author(s): Matthew Suderman, Nada Borghol, Jane J. Pappas, Snehal M Pinto Pereira, Marcus Pembrey, Clyde Hertzman, Chris Power, Moshe Szyf
Software Mentions: 1
Published: over 12 years ago

10.3390/ijms20040864

Serum MicroRNAs as Biomarkers in Hepatitis C: Preliminary Evidence of a MicroRNA Panel for the Diagnosis of Hepatocellular Carcinoma
Cited by: 37
Author(s): Anna Weis, Louise Marquart, Diego A. Calvopina, Berit Genz, Grant A. Ramm, Richard Skoien
Software Mentions: 1
Published: over 7 years ago

10.1038/srep16688

The human decapping scavenger enzyme DcpS modulates microRNA turnover
Cited by: 19
Author(s): Oussama Méziane, Sandra Piquet, Gabriel D. Bossé, Dominic Gagné, Éric R. Paquet, Claude Robert, Michael A. Tones, Martin J. Simard
Software Mentions: 1
Published: almost 11 years ago

10.1038/srep16423

Adaptation to acetaminophen exposure elicits major changes in expression and distribution of the hepatic proteome
Cited by: 34
Author(s): RM Eakins, James Walsh, Laura E. Randle, RE Jenkins, Ina Schuppe-Koistinen, Cliff Rowe, Philip Starkey Lewis, Olga Vasieva, Neus Prats, Nathalie Brillant, Mariona Aulí, M. Bayliss, Steven D. Webb, J A Rees, NR Kitteringham, Goldring Ce, BK Park
Software Mentions: 1
Published: almost 11 years ago

10.1038/srep17518

Glycosylation of Dentin Matrix Protein 1 is critical for osteogenesis
Cited by: 23
Author(s): Ying Sun, Yiming Weng, Chenyang Zhang, Yi Liu, Kang Chen, Zhongshuang Liu, Bo Jing, Qi Zhang, Zuolin Wang
Software Mentions: 1
Published: almost 11 years ago

10.1038/srep17566

Secretome identification of immune cell factors mediating metastatic cell homing
Cited by: 20
Author(s): Brian A. Aguado, Jia Wu, Samira M. Azarin, Dhaval Nanavati, Shreya Rao, Grace G. Bushnell, Chaitanya Medicherla, Lonnie D. Shea
Software Mentions: 1
Published: almost 11 years ago

10.1038/srep17187

Capturing complex tumour biology in vitro: histological and molecular characterisation of precision cut slices
Cited by: 90
Author(s): Emma Davies, Di Meng, Matthias Gutekunst, Katja Närhi, Hanneke J. A. A. van Zoggel, Sami Blom, Ashwini S. Nagaraj, Tauno Metsalu, Eva Oswald, Sigrun Erkens-Schulze, Juan A. Delgado San Martin, Riku Turkki, Stephen R. Wedge, Taija M. af Hällström, Julia Schueler, Wytske M. van Weerden, Emmy W. Verschuren, Simon T. Barry, Heiko van der Kuip, John A. Hickman
Software Mentions: 1
Published: almost 11 years ago

10.1186/1755-8794-6-42

Gene profiling suggests a common evolution of bladder cancer subtypes
Cited by: 8
Author(s): Donna E. Hansel, Zhongfa Zhang, David Petillo, Bin Tean Teh
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12920-020-00744-7

Long non-coding RNA profiling of pediatric Medulloblastoma
Cited by: 14
Author(s): Varun Kesherwani, Mamta Shukla, Donald W. Coulter, John Sharp, Shantaram S. Joshi, Nagendra K. Chaturvedi
Software Mentions: 1
Published: about 6 years ago

10.1186/s12920-021-00918-x

Integrated analysis of lncRNA–miRNA–mRNA ceRNA network and the potential prognosis indicators in sarcomas
Cited by: 15
Author(s): Lu Gao, Yu Zhao, Xuelei Ma, Ling Zhang
Software Mentions: 1
Published: over 5 years ago

10.1186/s12920-020-00795-w

Identification of key genes and functions of circulating tumor cells in multiple cancers through bioinformatic analysis
Cited by: 8
Author(s): Yawen Guan, Fangshi Xu, Yiyuan Wang, Jie Tian, Ziyan Wan, Zhenlong Wang, Tie Chong
Software Mentions: 1
Published: almost 6 years ago

10.1523/ENEURO.0181-17.2017

TU-Tagging: A Method for Identifying Layer-Enriched Neuronal Genes in Developing Mouse Visual Cortex
Cited by: 14
Author(s): Johanna Tomorsky, Leah DeBlander, Clifford Kentros, Chris Q. Doe, Cristopher M. Niell
Software Mentions: 1
Published: about 9 years ago

10.1186/1755-8794-5-46

Defining the genomic signature of the parous breast
Cited by: 63
Author(s): Suraj Peri, Ricardo López de Cicco, Julia Santucci-Pereira, Michael Slifker, Eric A. Ross, Irma H. Russo, Patrícia A. Russo, Alan A. Arslan, Ilana Belitskaya-Lévy, Anne Zeleniuch‐Jacquotte, Pál Bordás, Per Lenner, Janet Åhman, Yelena Afanasyeva, Robert Johansson, Fathima Sheriff, Göran Hallmans, Paolo Toniolo, José Russo
Software Mentions: 1
Published: almost 14 years ago

10.1186/1755-8794-4-86

Early peroxisome proliferator-activated receptor gamma regulated genes involved in expansion of pancreatic beta cell mass
Cited by: 16
Author(s): Yurena Vivas, Cristina Martínez‐García, Alberto Galindo Izquierdo, Francisco García‐García, Sergio Callejas, Ismael Velasco, Mark Campbell, Manuel Ros, Ana Dopazo, Joaquín Dopazo, António Vidal-Puig, Gema Medina-Gómez
Software Mentions: 1
Published: almost 15 years ago

10.1038/srep20864

Selective inhibition of EZH2 by ZLD1039 blocks H3K27methylation and leads to potent anti-tumor activity in breast cancer
Cited by: 45
Author(s): Xian‐Rong Song, Tiantao Gao, Ningyu Wang, Qiang Feng, Xinyu You, Tinghong Ye, Qian Lei, Yiping Zhu, Menghua Xiong, Yong Xia, Fangfang Yang, Yu Shi, Yuquan Wei, Lidan Zhang, Luoting Yu
Software Mentions: 1
Published: over 10 years ago

10.1111/acel.12229

Gene profiling reveals association between altered Wnt signaling and loss of T-cell potential with age in human hematopoietic stem cells
Cited by: 13
Author(s): Melissa Khoo, Stephen M. Carlin, Mark Lutherborrow, Vivek Jayaswal, D. F. David, John J. Moore
Software Mentions: 1
Published: over 12 years ago

10.1186/s12920-015-0100-6

Blood-based identification of non-responders to anti-TNF therapy in rheumatoid arthritis
Cited by: 26
Author(s): Timothy M. Thomson, Reynald Lescarbeau, David A. Drubin, Daphna Laifenfeld, David de Graaf, David A. Fryburg, Bruce H. Littman, Renée Deehan, A. Van Hooser
Software Mentions: 1
Published: over 11 years ago

10.1111/acel.13015

Aging induces cardiac mesenchymal stromal cell senescence and promotes endothelial cell fate of the CD90 + subset
Cited by: 27
Author(s): Hélène Martini, Jason S. Iacovoni, Damien Maggiorani, Marianne Dutaur, Dimitri Marsal, Jérôme Roncalli, Romain Itier, Camille Dambrin, Nathalie Pizzinat, Jeanne Mialet‐Perez, Daniel Cussac, Angelo Parini, Lise Lefèvre, Victorine Douin‐Echinard
Software Mentions: 1
Published: about 7 years ago

10.3390/ijms20071797

Altered Glutamate Receptor Ionotropic Delta Subunit 2 Expression in Stau2-Deficient Cerebellar Purkinje Cells in the Adult Brain
Cited by: 8
Author(s): Helena F. Pernice, Rico Schieweck, Mehrnoosh Jafari, Tobias Straub, Martin Bilban, Michael Kiebler, Bastian Popper
Software Mentions: 1
Published: over 7 years ago

10.1186/s12920-021-00885-3

A novel prognostic prediction model based on seven immune-related RNAs for predicting overall survival of patients in early cervical squamous cell carcinoma
Cited by: 7
Author(s): Rui Qin, Lu Cao, Cong Ye, Junrong Wang, Ziqian Sun
Software Mentions: 1
Published: over 5 years ago

10.1186/s12881-019-0829-4

Assessment of risk based on variant pathways and establishment of an artificial neural network model of thyroid cancer
Cited by: 6
Author(s): Yupei Zhao, Lingzhi Zhao, Tiezhu Mao, Lili Zhong
Software Mentions: 1
Published: over 7 years ago

Projects: bioconductor: limma

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Papers Mentioning limma 7,776