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Tytuł:
xcore: an R package for inference of gene expression regulators.
Autorzy:
Migdał M; Laboratory of Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
Arakawa T; RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
Takizawa S; RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
Furuno M; RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
Suzuki H; RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
Arner E; RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.; GSK, Gunnels Wood Rd, Stevenage, SG1 2NY, UK.
Winata CL; Laboratory of Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland. .
Kaczkowski B; RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan. .; Data Sciences and Quantitative Biology, Discovery Sciences, AstraZeneca R&D, Cambridge, UK. .
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2023 Jan 11; Vol. 24 (1), pp. 14. Date of Electronic Publication: 2023 Jan 11.
Typ publikacji:
Journal Article
MeSH Terms:
Transcription Factors*/genetics
Transcription Factors*/metabolism
Chromatin Immunoprecipitation Sequencing*
Animals ; Chromatin Immunoprecipitation/methods ; Protein Binding ; Gene Expression ; Binding Sites
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Web-MCOT Server for Motif Co-Occurrence Search in ChIP-Seq Data.
Autorzy:
Levitsky VG; Department of System Biology, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia.; Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia.
Mukhin AM; Department of System Biology, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia.
Oshchepkov DY; Department of System Biology, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia.
Zemlyanskaya EV; Department of System Biology, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia.; Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia.
Lashin SA; Department of System Biology, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia.; Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia.
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Źródło:
International journal of molecular sciences [Int J Mol Sci] 2022 Aug 11; Vol. 23 (16). Date of Electronic Publication: 2022 Aug 11.
Typ publikacji:
Journal Article
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*
Transcription Factors*/genetics
Binding Sites ; Chromatin Immunoprecipitation/methods
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome.
Autorzy:
Karimzadeh M; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.; Princess Margaret Cancer Centre, Toronto, ON, Canada.; Vector Institute, Toronto, ON, Canada.
Hoffman MM; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada. .; Princess Margaret Cancer Centre, Toronto, ON, Canada. .; Vector Institute, Toronto, ON, Canada. .; Department of Computer Science, University of Toronto, Toronto, ON, Canada. .
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Źródło:
Genome biology [Genome Biol] 2022 Jun 10; Vol. 23 (1), pp. 126. Date of Electronic Publication: 2022 Jun 10.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*
Transcriptome*
Binding Sites ; Chromatin Immunoprecipitation ; Protein Binding ; Transcription Factors/metabolism
Czasopismo naukowe
Szczegóły
Tytuł:
Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection.
Autorzy:
Eder T; Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria.
Grebien F; Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria. .
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Źródło:
Genome biology [Genome Biol] 2022 May 24; Vol. 23 (1), pp. 119. Date of Electronic Publication: 2022 May 24.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Algorithms*
Chromatin Immunoprecipitation Sequencing*
Chromatin Immunoprecipitation ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Software
Czasopismo naukowe
Szczegóły
Tytuł:
Novel ZNF414 activity characterized by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data.
Autorzy:
Rodriguez-Martinez A; Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland; BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland. Electronic address: .
Vuorinen EM; Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland; BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
Shcherban A; Tays Cancer Center, Tampere University Hospital, Tampere, Finland; BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
Uusi-Mäkelä J; Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland; BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
Rajala NKM; BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
Nykter M; Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland; BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
Kallioniemi A; Tays Cancer Center, Tampere University Hospital, Tampere, Finland; BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Fimlab Laboratories, Tampere, Finland.
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Źródło:
Biochimica et biophysica acta. Gene regulatory mechanisms [Biochim Biophys Acta Gene Regul Mech] 2022 Apr; Vol. 1865 (3), pp. 194811. Date of Electronic Publication: 2022 Mar 19.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Chromatin*/genetics
Chromatin Immunoprecipitation Sequencing*
Chromatin Immunoprecipitation ; DNA ; RNA-Seq
Czasopismo naukowe
Szczegóły
Tytuł:
A cell-sorting-based protocol for cell cycle small-scale ChIP sequencing.
Autorzy:
Whetstine JR; Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.; Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
Van Rechem C; Stanford Medicine Department of Pathology, Stanford, CA 94305, USA.
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Źródło:
STAR protocols [STAR Protoc] 2022 Mar 15; Vol. 3 (2), pp. 101243. Date of Electronic Publication: 2022 Mar 15 (Print Publication: 2022).
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms:
Chromatin*/genetics
Chromatin Immunoprecipitation Sequencing*
Cell Cycle/genetics ; Chromatin Immunoprecipitation/methods ; Histone Code
Czasopismo naukowe
Szczegóły
Tytuł:
ChIP-AP: an integrated analysis pipeline for unbiased ChIP-seq analysis.
Autorzy:
Suryatenggara J; Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
Yong KJ; Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
Tenen DE; Broad Institute of MIT and Harvard, Boston, 02142, USA.
Tenen DG; Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.; Harvard Stem Cell Institute, Boston, 02138, USA.
Bassal MA; Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.; Harvard Stem Cell Institute, Boston, 02138, USA.
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Źródło:
Briefings in bioinformatics [Brief Bioinform] 2022 Jan 17; Vol. 23 (1).
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*
Oligonucleotide Array Sequence Analysis/*methods
Sequence Analysis, DNA/*methods
Algorithms ; Benchmarking ; Cell Line ; Chromatin Immunoprecipitation ; Software ; Transcription Factors
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Statistical estimates of multiple transcription factors binding in the model plant genomes based on ChIP-seq data.
Autorzy:
Dergilev AI; Novosibirsk State University, 630090 Novosibirsk, Russia.; Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
Orlova NG; Financial University under the Government of the Russian Federation, 125993 Moscow, Russia.; Moscow State Technical University of Civil Aviation, 125993 Moscow, Russia.
Dobrovolskaya OB; Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.; Agrarian and Technological Institute, Peoples' Friendship University of Russia, 117198 Moscow, Russia.
Orlov YL; Novosibirsk State University, 630090 Novosibirsk, Russia.; Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.; Agrarian and Technological Institute, Peoples' Friendship University of Russia, 117198 Moscow, Russia.; The Digital Health Institute, I.M.Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia.
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Źródło:
Journal of integrative bioinformatics [J Integr Bioinform] 2021 Dec 21; Vol. 19 (1). Date of Electronic Publication: 2021 Dec 21.
Typ publikacji:
Journal Article
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*
Transcription Factors*/genetics
Transcription Factors*/metabolism
Animals ; Binding Sites/genetics ; Chromatin Immunoprecipitation ; Genome, Plant ; Mammals/genetics ; Mammals/metabolism
Czasopismo naukowe
Szczegóły
Tytuł:
Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Mouse Corneal Epithelial Cells.
Autorzy:
Lu ZJ; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.; Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China.; Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, China.
Ye JG; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
Wang DL; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
Li MK; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
Zhang QK; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
Liu Z; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
Huang YJ; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
Pan CN; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
Lin YH; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
Shi ZX; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
Zheng YF; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.; Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China.; Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, China.
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Źródło:
Investigative ophthalmology & visual science [Invest Ophthalmol Vis Sci] 2023 Mar 01; Vol. 64 (3), pp. 30.
Typ publikacji:
Journal Article
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*
Single-Cell Gene Expression Analysis*
Animals ; Mice ; Chromatin ; Gene Expression Regulation ; Epithelial Cells
Czasopismo naukowe
Szczegóły
Tytuł:
A Unified Deep Learning Framework for Single-Cell ATAC-Seq Analysis Based on ProdDep Transformer Encoder.
Autorzy:
Wang Z; School of Computer Science, Chengdu University of Information Technology, Chengdu 610225, China.
Zhang Y; School of Computer Science, Chengdu University of Information Technology, Chengdu 610225, China.
Yu Y; School of Computer Science, Chengdu University of Information Technology, Chengdu 610225, China.
Zhang J; School of Computer Science, Chengdu University of Information Technology, Chengdu 610225, China.
Liu Y; School of Computer Science, Chengdu University of Information Technology, Chengdu 610225, China.
Zou Q; Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China.
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Źródło:
International journal of molecular sciences [Int J Mol Sci] 2023 Mar 01; Vol. 24 (5). Date of Electronic Publication: 2023 Mar 01.
Typ publikacji:
Journal Article
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*/methods
Deep Learning*
Chromatin ; Gene Expression Regulation ; Transcription Factors/metabolism ; Single-Cell Analysis/methods
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Integrated analysis of ATAC-seq and RNA-seq reveals the transcriptional regulation network in SLE.
Autorzy:
Wu J; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China; Research Unit of Key Technologies of Immune-Related Skin Diseases Diagnosis and Treatment, Chinese Academy of Medical Sciences, Changsha, China.
Li Y; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China; Research Unit of Key Technologies of Immune-Related Skin Diseases Diagnosis and Treatment, Chinese Academy of Medical Sciences, Changsha, China.
Feng D; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China; Research Unit of Key Technologies of Immune-Related Skin Diseases Diagnosis and Treatment, Chinese Academy of Medical Sciences, Changsha, China.
Yu Y; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China; Research Unit of Key Technologies of Immune-Related Skin Diseases Diagnosis and Treatment, Chinese Academy of Medical Sciences, Changsha, China.
Long H; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China; Research Unit of Key Technologies of Immune-Related Skin Diseases Diagnosis and Treatment, Chinese Academy of Medical Sciences, Changsha, China.
Hu Z; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China; Research Unit of Key Technologies of Immune-Related Skin Diseases Diagnosis and Treatment, Chinese Academy of Medical Sciences, Changsha, China.
Lu Q; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China; Research Unit of Key Technologies of Immune-Related Skin Diseases Diagnosis and Treatment, Chinese Academy of Medical Sciences, Changsha, China; Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China.
Zhao M; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China; Research Unit of Key Technologies of Immune-Related Skin Diseases Diagnosis and Treatment, Chinese Academy of Medical Sciences, Changsha, China. Electronic address: .
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Źródło:
International immunopharmacology [Int Immunopharmacol] 2023 Mar; Vol. 116, pp. 109803. Date of Electronic Publication: 2023 Feb 02.
Typ publikacji:
Journal Article
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*
Lupus Erythematosus, Systemic*/metabolism
Humans ; RNA-Seq ; Gene Expression Regulation ; Chromatin ; Membrane Proteins/metabolism ; RNA-Binding Proteins/genetics ; Repressor Proteins/genetics
Czasopismo naukowe
Szczegóły
Tytuł:
Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig.
Autorzy:
Cai S; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, Guangdong, China.; Guangdong Key Laboratory of Animal Breeding and Nutrition, State Key Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China.
Hu B; Guangdong Key Laboratory of Animal Breeding and Nutrition, State Key Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China.
Wang X; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, Guangdong, China.
Liu T; Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
Lin Z; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, Guangdong, China.
Tong X; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, Guangdong, China.
Xu R; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, Guangdong, China.
Chen M; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, Guangdong, China.
Duo T; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, Guangdong, China.
Zhu Q; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, Guangdong, China.
Liang Z; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, Guangdong, China.
Li E; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, Guangdong, China.
Chen Y; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, Guangdong, China.
Li J; Guangdong Key Laboratory of Animal Breeding and Nutrition, State Key Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China. .
Liu X; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, Guangdong, China. .
Mo D; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, Guangdong, China. .
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Źródło:
BMC biology [BMC Biol] 2023 Feb 01; Vol. 21 (1), pp. 19. Date of Electronic Publication: 2023 Feb 01.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*
Single-Cell Gene Expression Analysis*
Animals ; Mice ; Cell Differentiation/genetics ; Chromatin/genetics ; Chromatin/metabolism ; Gene Expression Regulation, Developmental ; Muscle Development/genetics ; Muscle, Skeletal/metabolism ; Single-Cell Analysis ; Swine
Czasopismo naukowe
Szczegóły
Tytuł:
Comprehensive analysis of nonsurrounded nucleolus and surrounded nucleolus oocytes on chromatin accessibility using ATAC-seq.
Autorzy:
Sun X; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
Wang D; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
Li W; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
Gao Q; Laboratory Animal Center, College of Veterinary Medicine, Nanjing Agriculture University, Nanjing, China.
Tao J; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
Liu H; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
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Źródło:
Molecular reproduction and development [Mol Reprod Dev] 2023 Feb; Vol. 90 (2), pp. 87-97. Date of Electronic Publication: 2023 Jan 04.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Chromatin*/metabolism
Chromatin Immunoprecipitation Sequencing*
Animals ; Mice ; Oocytes/metabolism ; Oogenesis/genetics ; Cell Nucleolus/metabolism
Czasopismo naukowe
Szczegóły
Tytuł:
maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.
Autorzy:
Cazares TA; Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America.
Rizvi FW; Systems Biology and Physiology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America.
Iyer B; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.; Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio, United States of America.
Chen X; The Center for Autoimmune Genetics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.
Kotliar M; Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.
Bejjani AT; Molecular and Developmental Biology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America.
Wayman JA; Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.
Donmez O; The Center for Autoimmune Genetics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.
Wronowski B; Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.
Parameswaran S; The Center for Autoimmune Genetics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.
Kottyan LC; The Center for Autoimmune Genetics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America.; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.
Barski A; Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America.; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.
Weirauch MT; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.; The Center for Autoimmune Genetics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America.; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.
Prasath VBS; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.; Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio, United States of America.; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America.
Miraldi ER; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.; Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio, United States of America.; Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America.
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Źródło:
PLoS computational biology [PLoS Comput Biol] 2023 Jan 31; Vol. 19 (1), pp. e1010863. Date of Electronic Publication: 2023 Jan 31 (Print Publication: 2023).
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*
High-Throughput Nucleotide Sequencing*/methods
Nerve Net*
Humans ; Chromatin/genetics ; Deoxyribonucleases/genetics ; Sequence Analysis, DNA/methods
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
peaksat: an R package for ChIP-seq peak saturation analysis.
Autorzy:
Boyd JR; Department of Biomedical and Health Sciences, University of Vermont, 106 Carrigan Drive, 302 Rowell, VT, 04505, Burlington, USA.
Gao C; Department of Biomedical and Health Sciences, University of Vermont, 106 Carrigan Drive, 302 Rowell, VT, 04505, Burlington, USA.
Quinn K; Department of Biomedical and Health Sciences, University of Vermont, 106 Carrigan Drive, 302 Rowell, VT, 04505, Burlington, USA.
Fritz A; Department of Biochemistry, University of Vermont, Burlington, VT, USA.
Stein J; Department of Biochemistry, University of Vermont, Burlington, VT, USA.; University of Vermont Cancer Center, Burlington, VT, USA.
Stein G; Department of Biochemistry, University of Vermont, Burlington, VT, USA.; University of Vermont Cancer Center, Burlington, VT, USA.; Department of Surgery, University of Vermont, Burlington, VT, USA.
Glass K; Department of Biochemistry, University of Vermont, Burlington, VT, USA.; University of Vermont Cancer Center, Burlington, VT, USA.; Department of Pharmacology, University of Vermont, Burlington, VT, USA.
Frietze S; Department of Biomedical and Health Sciences, University of Vermont, 106 Carrigan Drive, 302 Rowell, VT, 04505, Burlington, USA. .; Department of Biochemistry, University of Vermont, Burlington, VT, USA. .; University of Vermont Cancer Center, Burlington, VT, USA. .
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Źródło:
BMC genomics [BMC Genomics] 2023 Jan 25; Vol. 24 (1), pp. 43. Date of Electronic Publication: 2023 Jan 25.
Typ publikacji:
Journal Article
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*/methods
High-Throughput Nucleotide Sequencing*
Sequence Analysis, DNA/methods ; Gene Library
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes.
Autorzy:
Polit L; Institut Cochin, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, 75014, Paris, France.
Kerdivel G; Institut Cochin, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, 75014, Paris, France.
Gregoricchio S; INSERM UMR1170, Equipe Labellisée Ligue Nationale Contre Le Cancer, Gustave Roussy, Paris-Saclay University, 94800, Villejuif, France.
Esposito M; INSERM UMR1170, Equipe Labellisée Ligue Nationale Contre Le Cancer, Gustave Roussy, Paris-Saclay University, 94800, Villejuif, France.
Guillouf C; INSERM UMR1170, Equipe Labellisée Ligue Nationale Contre Le Cancer, Gustave Roussy, Paris-Saclay University, 94800, Villejuif, France.
Boeva V; Institut Cochin, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, 75014, Paris, France. .; Department of Computer Science, Institute for Machine Learning, ETH Zurich, 8092, Zurich, Switzerland. .; Swiss Institute for Bioinformatics (SIB), Zürich, Switzerland. .
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2021 Aug 17; Vol. 22 (1), pp. 407. Date of Electronic Publication: 2021 Aug 17.
Typ publikacji:
Journal Article
MeSH Terms:
Chromatin*
Chromatin Immunoprecipitation Sequencing*
Chromatin Immunoprecipitation ; Protein Binding ; Sequence Analysis, DNA
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicates.
Autorzy:
Newell R; School of Chemistry and Molecular Biosciences, The University of Queensland, Cooper Road, QLD 4072, Australia.
Pienaar R; School of Chemistry and Molecular Biosciences, The University of Queensland, Cooper Road, QLD 4072, Australia.
Balderson B; School of Chemistry and Molecular Biosciences, The University of Queensland, Cooper Road, QLD 4072, Australia.
Piper M; School of Biomedical Science, The University of Queensland, QLD, Australia.
Essebier A; School of Chemistry and Molecular Biosciences, The University of Queensland, Cooper Road, QLD 4072, Australia.
Bodén M; School of Chemistry and Molecular Biosciences, The University of Queensland, Cooper Road, QLD 4072, Australia. Electronic address: .
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Źródło:
Genomics [Genomics] 2021 Jul; Vol. 113 (4), pp. 1855-1866. Date of Electronic Publication: 2021 Apr 18.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Algorithms*
Chromatin Immunoprecipitation Sequencing*
Binding Sites ; Chromatin Immunoprecipitation/methods ; High-Throughput Nucleotide Sequencing/methods ; Reproducibility of Results ; Sequence Analysis, DNA/methods
Czasopismo naukowe
Szczegóły
Tytuł:
UniBind: maps of high-confidence direct TF-DNA interactions across nine species.
Autorzy:
Puig RR; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0349, Oslo, Norway.
Boddie P; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0349, Oslo, Norway.
Khan A; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0349, Oslo, Norway.; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Castro-Mondragon JA; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0349, Oslo, Norway.
Mathelier A; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0349, Oslo, Norway. .; Department of Medical Genetics, Oslo University Hospital, Oslo, 0424, Norway. .
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Źródło:
BMC genomics [BMC Genomics] 2021 Jun 26; Vol. 22 (1), pp. 482. Date of Electronic Publication: 2021 Jun 26.
Typ publikacji:
Journal Article
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*
DNA*/metabolism
Binding Sites ; Chromatin Immunoprecipitation ; Computational Biology ; Protein Binding
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Increased peak detection accuracy in over-dispersed ChIP-seq data with supervised segmentation models.
Autorzy:
Liehrmann A; Institut des Sciences des Plantes de Paris-Saclay (IPS2), Université Paris-Saclay, Université Evry, CNRS, INRAE, 91405, Orsay, France. .; Laboratoire de Mathématiques et Modélisation d'Evry (LAMME), Université Paris-Saclay, Université Evry, CNRS, 91037, Evry, France. .
Rigaill G; Institut des Sciences des Plantes de Paris-Saclay (IPS2), Université Paris-Saclay, Université Evry, CNRS, INRAE, 91405, Orsay, France.; Laboratoire de Mathématiques et Modélisation d'Evry (LAMME), Université Paris-Saclay, Université Evry, CNRS, 91037, Evry, France.
Hocking TD; School of Informatics, Computing, and Cyber Systems (SICCS), Northern Arizona University, 86011, Flagstaff, AZ, USA.
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2021 Jun 14; Vol. 22 (1), pp. 323. Date of Electronic Publication: 2021 Jun 14.
Typ publikacji:
Journal Article
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*
High-Throughput Nucleotide Sequencing*
Algorithms ; Chromatin Immunoprecipitation ; Sequence Analysis, DNA
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Protocol for isolation and ATAC-seq library construction of zebrafish red blood cells.
Autorzy:
Ding Y; State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Institute for Stem Cell and Regeneration, University of Chinese Academy of Sciences, Beijing, China; School of Life Sciences, Shandong University, Qingdao, China.
Liu F; State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Institute for Stem Cell and Regeneration, University of Chinese Academy of Sciences, Beijing, China; School of Life Sciences, Shandong University, Qingdao, China. Electronic address: .
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Źródło:
STAR protocols [STAR Protoc] 2022 Dec 16; Vol. 3 (4), pp. 101889. Date of Electronic Publication: 2022 Nov 23.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Zebrafish*/genetics
Chromatin Immunoprecipitation Sequencing*
Animals ; Sequence Analysis, DNA/methods ; Chromatin ; Erythrocytes
Czasopismo naukowe
Szczegóły
Wyświetlanie 1-20 z 9277

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