Most cited papers from GeneXplain (Germany)

GeneXplain (Germany)

What are the most cited papers from GeneXplain (Germany)?

The most cited paper from GeneXplain (Germany) is "cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing" (Andrey A. Kechin, Uljana A. Boyarskikh, Alexander E Kel et al., 2017), with 1,480 citations. Next come "GTRD: an integrated view of transcription regulation" (314) and "ROS-dependent activation of JNK converts p53 into an efficient inhibitor of oncogenes leading to robust apoptosis" (234).

Published TypeFieldAccessCitations

Showing 50 of 79 papers. Every paper is listed.

Most cited papers, sortable by citations and release date
#	Paper
1	cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing Andrey A. Kechin, Uljana A. Boyarskikh, Alexander E Kel et al. · Journal of Computational Biology	17 Jul 2017	1,480
2	GTRD: an integrated view of transcription regulation Semyon K. Kolmykov, Ivan Yevshin, Mikhail A. Kulyashov et al. · Nucleic Acids Research Open access	3 Nov 2020	314
3	ROS-dependent activation of JNK converts p53 into an efficient inhibitor of oncogenes leading to robust apoptosis Yao Shi, Fedor Nikulenkov, Joanna E Zawacka-Pankau et al. · Cell Death and Differentiation Open access	10 Jan 2014	234
4	Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis Fedor Nikulenkov, Clemens Spinnler, H. Li et al. · Cell Death and Differentiation Open access	13 Jul 2012	186
5	TFClass: expanding the classification of human transcription factors to their mammalian orthologs Edgar Wingender, Torsten Schoeps, Martin Haubrock et al. · Nucleic Acids Research Open access	12 Oct 2017	157
6	Inhibition of Glycolytic Enzymes Mediated by Pharmacologically Activated p53 Joanna E Zawacka-Pankau, Vera V. Grinkevich, Sabine Hünten et al. · Journal of Biological Chemistry Open access	23 Aug 2011	129
7	Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer Hryhorii Chereda, Annalen Bleckmann, Kerstin Menck et al. · Genome Medicine Open access	11 Mar 2021	121
8	“Upstream Analysis”: An Integrated Promoter-Pathway Analysis Approach to Causal Interpretation of Microarray Data Jeannette Koschmann, Anirban Bhar, Philip Stegmaier et al. · Microarrays Open access	21 May 2015	74
9	Towards a European health research and innovation cloud (HRIC) Frank M. Aarestrup et al. · Genome Medicine Open access	19 Feb 2020	68
10	Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer Alexander E Kel, Ul'yana A. Boyarskikh, Philip Stegmaier et al. · BMC Bioinformatics Open access	Apr 2019	61
11	RNA isolation from precision-cut lung slices (PCLS) from different species Monika Niehof, Tobias Hildebrandt, Olga Danov et al. · BMC Research Notes Open access	8 Mar 2017	58
12	BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data Fedor Kolpakov, Ilya R. Akberdin, Timur A. Kashapov et al. · Nucleic Acids Research Open access	11 May 2019	57
13	Glial responses during epileptogenesis in Mus musculus point to potential therapeutic targets Georgia Kalozoumi, Olga V Kel-Margoulis, Elizabeth Vafiadaki et al. · PLoS ONE Open access	16 Aug 2018	48
14	An integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation Pierre Sabatier et al. · Nature Communications Open access	12 Nov 2021	45
15	Multi-omics “upstream analysis” of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer Alexander E Kel, Philip Stegmaier, Tagir Valeev et al. · EuPA Open Proteomics Open access	16 Sep 2016	44
16	Signaling Pathways Potentially Responsible for Foam Cell Formation: Cholesterol Accumulation or Inflammatory Response—What is First? Alexander Nikolaevich Orekhov, Vasily N. Sukhorukov, Nikita G. Nikiforov et al. · International Journal of Molecular Sciences Open access	14 Apr 2020	42
17	BioUML—towards a universal research platform Fedor Kolpakov, Ilya R. Akberdin, Ilya N. Kiselev et al. · Nucleic Acids Research Open access	14 Apr 2022	39
18	Pathways of aging: comparative analysis of gene signatures in replicative senescence and stress induced premature senescence Kamil Can Kural, Neetu Tandon, Mikhail Y. Skoblov et al. · BMC Genomics Open access	Dec 2016	35
19	Role of Phagocytosis in the Pro-Inflammatory Response in LDL-Induced Foam Cell Formation; a Transcriptome Analysis Alexander Nikolaevich Orekhov, Nikita G. Nikiforov, Vasily N. Sukhorukov et al. · International Journal of Molecular Sciences Open access	27 Jan 2020	34
20	Nucleotide patterns aiding in prediction of eukaryotic promoters Martin Tříska, Victor Solovyev, Ancha V. Baranova et al. · PLoS ONE Open access	15 Nov 2017	31
21	MatrixCatch - a novel tool for the recognition of composite regulatory elements in promoters Igor V. Deyneko, Alexander E Kel, Olga V Kel-Margoulis et al. · BMC Bioinformatics Open access	8 Aug 2013	30
22	DNA Methylation and Gene Expression Profiling Reveal MFAP5 as a Regulatory Driver of Extracellular Matrix Remodeling in Varicose Vein Disease Mariya A. Smetanina, Alexander E Kel, K. S. Sevost’ianova et al. · Epigenomics	Aug 2018	27
23	Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information Marco Masseroli, Barend Mons, Erik Bongcam‐Rudloff et al. · BMC Bioinformatics Open access	2014	25
24	Targeting fibroblast phenotype switching in cardiac remodelling as a promising antifibrotic strategy Alexander E Kel, Thomas Thum, Oksana Kunduzova · European Heart Journal	10 Oct 2024	23
25	Type I IFN and not TNF, is Essential for Cyclic Di-nucleotide-elicited CTL by a Cytosolic Cross-presentation Pathway Darío Lirussi, Thomas Ebensen, Kai Schulze et al. · EBioMedicine Open access	19 Jul 2017	23
26	c-Jun N-terminal kinase 2 promotes enterocyte survival and goblet cell differentiation in the inflamed intestine Ana D. Mandić, Eveline Bennek, Julien Verdier et al. · Mucosal Immunology Open access	18 Jan 2017	23
27	Transcriptome Analysis Reveals Intrinsic Proinflammatory Signaling in Healthy African American Skin Anna Kłopot, Gleb E. Baida, Alexander E Kel et al. · Journal of Investigative Dermatology Open access	29 Oct 2021	21
28	Text mining-based word representations for biomedical data analysis and protein-protein interaction networks in machine learning tasks Halima Alachram, Hryhorii Chereda, Tim Beißbarth et al. · PLoS ONE Open access	15 Oct 2021	20
29	Advanced Computational Biology Methods Identify Molecular Switches for Malignancy in an EGF Mouse Model of Liver Cancer Philip Stegmaier, Nico Voss, Tatiana Meier et al. · PLoS ONE Open access	28 Mar 2011	19
30	Deep insights into the response of human cervical carcinoma cells to a new cyano enone-bearing triterpenoid soloxolone methyl: a transcriptome analysis Andrey V. Markov, Alexander E Kel, Oksana V. Salomatina et al. · Oncotarget Open access	3 Sep 2019	18
31	CRITERIA FOR AN UPDATED CLASSIFICATION OF HUMAN TRANSCRIPTION FACTOR DNA-BINDING DOMAINS Edgar Wingender · Journal of Bioinformatics and Computational Biology	17 Jan 2013	18
32	A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs Philip Stegmaier, Alexander E Kel, Edgar Wingender et al. · PLoS Computational Biology Open access	21 Mar 2013	18
33	Mycoplasma hyorhinis reduces sensitivity of human lung carcinoma cells to Nutlin-3 and promotes their malignant phenotype Uljana A. Boyarskikh, Alexandra S. Shadrina, Mariya A. Smetanina et al. · Journal of Cancer Research and Clinical Oncology Open access	8 May 2018	17
34	Using systems medicine to identify a therapeutic agent with potential for repurposing in inflammatory bowel disease Katie Lloyd, Stamatia Papoutsopoulou, Emily Remington Smith et al. · Disease Models & Mechanisms Open access	21 Sep 2020	16
35	NERO: a biomedical named-entity (recognition) ontology with a large, annotated corpus reveals meaningful associations through text embedding Kanix Wang et al. · npj Systems Biology and Applications Open access	20 Oct 2021	15
36	Computational master-regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI-H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin-3 Ul'yana A. Boyarskikh, Sergey S. Pintus, Nikita Mandrik et al. · BMC Medical Genomics Open access	Feb 2018	15
37	IGFBP2 Is a Potential Master Regulator Driving the Dysregulated Gene Network Responsible for Short Survival in Glioblastoma Multiforme Manasa Kalya Purushothama, Alexander E Kel, Darius Wlochowitz et al. · Frontiers in Genetics Open access	15 Jun 2021	14
38	BRCA-analyzer: Automatic workflow for processing NGS reads of BRCA1 and BRCA2 genes Andrey A. Kechin, Evgeniy A. Khrapov, Uljana A. Boyarskikh et al. · Computational Biology and Chemistry	23 Oct 2018	13
39	Comparative analysis of deeply phenotyped GBM cohorts of ‘short-term’ and ‘long-term’ survivors Archita Biswas et al. · Journal of Neuro-Oncology Open access	26 May 2023	12
40	Detecting reliable non interacting proteins (NIPs) significantly enhancing the computational prediction of protein–protein interactions using machine learning methods Aashish Srivastava, Giovanni Mazzocco, Alexander E Kel et al. · Molecular BioSystems	21 Dec 2015	10
41	geneXplain — eine integrierte Bioinformatik-Plattform Edgar Wingender, Alexander E Kel · BIOspektrum	27 Aug 2012	10
42	Mild mitochondrial uncoupling does not affect mitochondrial biogenesis but downregulates pyruvate carboxylase in adipocytes: role for triglyceride content reduction Aurélia De Pauw, Stéphane Demine, Silvia Tejerina et al. · American Journal of Physiology-Endocrinology and Metabolism Open access	22 Feb 2012	9
43	Complexation of histone deacetylase inhibitor belinostat to Cu(II) prevents premature metabolic inactivation in vitro and demonstrates potent anti-cancer activity in vitro and ex vivo in colon cancer Ellen Finnegan, Wei Ding, Žiga Ude et al. · Cellular Oncology Open access	7 Nov 2023	8
44	Master Transcription Regulators and Transcription Factors Regulate Immune-Associated Differences Between Patients of African and European Ancestry With Colorectal Cancer Parvathi A. Myer, Hyunjin Kim, Anna M. Blümel et al. · Gastro Hep Advances Open access	2022	8
45	Bioelectronic cell-based device provides a strategy for the treatment of the experimental model of multiple sclerosis Emilie Audouard, Fanny Michel, Vanessa Pierroz et al. · Journal of Controlled Release Open access	16 Nov 2022	7
46	Master regulators associated with poor prognosis in glioblastoma multiforme M.P. Kalya, T. Beisbarth, Alexander E Kel · Biomeditsinskaya Khimiya Open access	2021	7
47	Search for Master Regulators in Walking Cancer Pathways Alexander E Kel · Methods in molecular biology Book chapter	2017	7
48	Substantiate a read-across hypothesis by using transcriptome data—A case study on volatile diketones Christina Drake, Matthias M. Wehr, Walter Zobl et al. · Frontiers in Toxicology Open access	3 May 2023	6
49	Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications Eugene Kolker et al. · Big Data	Dec 2013	5
50	Epigenome-Wide Changes in the Cell Layers of the Vein Wall When Exposing the Venous Endothelium to Oscillatory Shear Stress Mariya A. Smetanina, Valeria A. Korolenya, Alexander E Kel et al. · Epigenomes Open access	20 Mar 2023	4

Citations are OpenAlex's own counts, from its 2026-09-23 snapshot, so the ranking can differ from Google Scholar or Web of Science. A paper is listed for an institution when any of its authors gave it as an affiliation; retracted papers and papers whose citation count cannot be traced to citing works are left out, and a preprint and the article it became are shown once. Release dates are OpenAlex's: where a source gave only a month or a year, that is what is shown. How the lists are chosen.