Search results for "ChIP-seq"

Hits ?▲	Authors	Title	Venue	Year	Link	Author keywords
58	Bo W. Han, Wei Wang, Phillip D. Zamore, Zhiping Weng	piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing.	Bioinform.	2015	DBLP DOI BibTeX RDF
51	Zhaonan Zou, Tazro Ohta, Fumihito Miura, Shinya Oki	ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data.	Nucleic Acids Res.	2022	DBLP DOI BibTeX RDF
39	George Wu, Jason T. Yustein, Matthew N. McCall, Michael J. Zilliox, Rafael A. Irizarry, Karen Zeller, Chi V. Dang, Hongkai Ji	ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data.	Bioinform.	2013	DBLP DOI BibTeX RDF
39	Xing Tang, Arunima Srivastava, Huayang Liu, Raghu Machiraju, Kun Huang 0001, Gustavo Leone	annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq.	Bioinform.	2018	DBLP DOI BibTeX RDF
39	Xing Tang, Arunima Srivastava, Huayang Liu, Raghu Machiraju, Kun Huang 0001, Gustavo Leone	annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq.	Bioinform.	2017	DBLP DOI BibTeX RDF
38	Lana X. Garmire, Shankar Subramaniam, David G. Garmire, Christopher K. Glass	A Clustering Approach to Identify Intergenic Non-coding RNA in Mouse Macrophages.	BIBE	2010	DBLP DOI BibTeX RDF	ChIP-Seq, RNA polymerase, macrophage, clustering, non-coding RNA
38	Hatice Gulcin Ozer, Doruk Bozdag, Terry Camerlengo, Jiejun Wu, Yi-Wen Huang, Timothy D. R. Hartley, Jeffrey D. Parvin, Tim Hui-Ming Huang, Ümit V. Çatalyürek, Kun Huang 0001	A Comprehensive Analysis Workflow for Genome-Wide Screening Data from ChIP-Sequencing Experiments.	BICoB	2009	DBLP DOI BibTeX RDF	ChIP-seq, short sequence mapping, visualization, parallelization, workflow, normalization
32	George Wu, Hongkai Ji	ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking.	BMC Bioinform.	2013	DBLP DOI BibTeX RDF
32	Jing Qin 0004, Mulin Jun Li, Panwen Wang, Michael Q. Zhang, Junwen Wang	ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor.	Nucleic Acids Res.	2011	DBLP DOI BibTeX RDF
32	Xun Lan, Russell Bonneville, Jeff Apostolos, Wangcheng Wu, Victor X. Jin	W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data.	Bioinform.	2011	DBLP DOI BibTeX RDF
32	Li Chen, George Wu, Hongkai Ji	hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data.	Bioinform.	2011	DBLP DOI BibTeX RDF
32	Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson, Hervé Pagès, Simon M. Lin, David S. Lapointe, Michael R. Green	ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data.	BMC Bioinform.	2010	DBLP DOI BibTeX RDF
32	Frank Johannes, René Wardenaar, Maria Colomé-Tatché, Florence Mousson, Petra de Graaf, Michal Mokry, Victor Guryev, H. Th. Marc Timmers, Edwin Cuppen, Ritsert C. Jansen	Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq.	Bioinform.	2010	DBLP DOI BibTeX RDF
32	Hyungwon Choi, Alexey I. Nesvizhskii, Debashis Ghosh, Zhaohui S. Qin	Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data.	Bioinform.	2009	DBLP DOI BibTeX RDF
32	Ana B. Romero-Losada, Christina Arvanitidou, Pedro de los Reyes, Mercedes García-González, Francisco José Romero-Campero	ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS.	BMC Bioinform.	2022	DBLP DOI BibTeX RDF
32	Joshua D. Fortriede, Troy J. Pells, Stanley Chu, Praneet Chaturvedi, Dong Zhou Wang, Malcolm E. Fisher, Christina James-Zorn, Ying Wang, Mardi J. Nenni, Kevin A. Burns, Vaneet Lotay, Virgilio G. Ponferrada, Kamran Karimi, Aaron M. Zorn, Peter D. Vize	Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database.	Nucleic Acids Res.	2020	DBLP DOI BibTeX RDF
32	Xi Chen 0056, Jinghua Gu, Xiao Wang 0031, Jin-Gyoung Jung, Tian-Li Wang, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan	CRNET: an efficient sampling approach to infer functional regulatory networks by integrating large-scale ChIP-seq and time-course RNA-seq data.	Bioinform.	2018	DBLP DOI BibTeX RDF
32	Qian Qin, Shenglin Mei, Qiu Wu, Hanfei Sun, Lewyn Li, Len Taing, Sujun Chen, Fugen Li, Tao Liu 0022, Chongzhi Zang, Han Xu, Yiwen Chen, Clifford A. Meyer, Yong Zhang 0006, Myles Brown, Henry Long	ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.	BMC Bioinform.	2016	DBLP DOI BibTeX RDF
32	Bohdan B. Khomtchouk, James R. Hennessy, Claes Wahlestedt	MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps.	BMC Bioinform.	2016	DBLP DOI BibTeX RDF
32	Hanfei Sun, Bo Qin, Tao Liu 0022, Qixuan Wang, Jing Liu, Juan Wang, Xueqiu Lin, Yulin Yang, Len Taing, Prakash K. Rao, Myles Brown, Yong Zhang 0006, Henry Long, Xiaole Shirley Liu	CistromeFinder for ChIP-seq and DNase-seq data reuse.	Bioinform.	2013	DBLP DOI BibTeX RDF
32	Bo Qin, Meng Zhou, Ying Ge, Len Taing, Tao Liu 0022, Qian Wang, Su Wang, Junsheng Chen, Lingling Shen, Xikun Duan, Sheng'en Hu, Wei Li 0036, Henry Long, Yong Zhang 0006, Xiaole Shirley Liu	CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human.	Bioinform.	2012	DBLP DOI BibTeX RDF
27	Rami Jaschek, Amos Tanay	Spatial Clustering of Multivariate Genomic and Epigenomic Information.	RECOMB	2009	DBLP DOI BibTeX RDF
26	Jeremiah Suryatenggara, Kol Jia Yong, Danielle E. Tenen, Daniel G. Tenen, Mahmoud A. Bassal	ChIP-AP: an integrated analysis pipeline for unbiased ChIP-seq analysis.	Briefings Bioinform.	2022	DBLP DOI BibTeX RDF
26	Tong Liu, Zheng Wang 0049	ST-ChIP: Accurate prediction of spatiotemporal ChIP-seq data with recurrent neural networks.	BIBM	2022	DBLP DOI BibTeX RDF
26	Laura Puente-Santamaria, Wyeth W. Wasserman, Luis del Peso	TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets.	Bioinform.	2019	DBLP DOI BibTeX RDF
26	Peter Hansen	Robust algorithms for improved reproducible ChIP-seq and ChIP-nexus peak calling (Robuste Algorithmen für eine verbesserte reproduzierbare Vorhersage von Proteinbindungstellen)		2019	RDF
26	Lin Zhu 0008, Wei-Li Guo, Suping Deng, De-Shuang Huang	ChIP-PIT: Enhancing the Analysis of ChIP-Seq Data Using Convex-Relaxed Pair-Wise Interaction Tensor Decomposition.	IEEE ACM Trans. Comput. Biol. Bioinform.	2016	DBLP DOI BibTeX RDF
19	P. Theepalakshmi, U. Srinivasulu Reddy 0001	A new efficient quorum planted (ℓ, d) motif search on ChIP-seq dataset using segmentation to filtration and freezing firefly algorithms.	Soft Comput.	2024	DBLP DOI BibTeX RDF
19	Lijun Quan, Xiaomin Chu, Xiaoyu Sun 0006, Tingfang Wu, Qiang Lyu	How Deepbics Quantifies Intensities of Transcription Factor-DNA Binding and Facilitates Prediction of Single Nucleotide Variant Pathogenicity With a Deep Learning Model Trained On ChIP-Seq Data Sets.	IEEE ACM Trans. Comput. Biol. Bioinform.	2023	DBLP DOI BibTeX RDF
19	Vivian Hecht, Kevin Dong, Sreshtaa Rajesh, Polina Shpilker, Siddarth Wekhande, Noam Shoresh	Analyzing histone ChIP-seq data with a bin-based probability of being signal.	PLoS Comput. Biol.	2023	DBLP DOI BibTeX RDF
19	Tong Liu, Zheng Wang 0049	DeepChIA-PET: Accurately predicting ChIA-PET from Hi-C and ChIP-seq with deep dilated networks.	PLoS Comput. Biol.	2023	DBLP DOI BibTeX RDF
19	Sajad Amouei Sheshkal, Michael Alexander Riegler, Hugo Lewi Hammer	ML-Peaks: CHIP-Seq Peak Detection Pipeline using Machine Learning Techniques.	CBMS	2023	DBLP DOI BibTeX RDF
19	Lijun Quan, Xiaoyu Sun 0006, Jian Wu, Jie Mei, Liqun Huang, Ruji He, Liangpeng Nie, Yu Chen 0064, Qiang Lyu	Learning Useful Representations of DNA Sequences From ChIP-Seq Datasets for Exploring Transcription Factor Binding Specificities.	IEEE ACM Trans. Comput. Biol. Bioinform.	2022	DBLP DOI BibTeX RDF
19	Musab Naik, Luis Rueda 0001, Akram Vasighizaker	Identification of Enriched Regions in ChIP-Seq Data via a Linear-Time Multi-Level Thresholding Algorithm.	IEEE ACM Trans. Comput. Biol. Bioinform.	2022	DBLP DOI BibTeX RDF
19	Zhaonan Zou, Michio Iwata, Yoshihiro Yamanishi, Shinya Oki	Epigenetic landscape of drug responses revealed through large-scale ChIP-seq data analyses.	BMC Bioinform.	2022	DBLP DOI BibTeX RDF
19	Arthur I. Dergilev, Nina Orlova, Oxana B. Dobrovolskaya, Yuriy L. Orlov	Statistical estimates of multiple transcription factors binding in the model plant genomes based on ChIP-seq data.	J. Integr. Bioinform.	2022	DBLP DOI BibTeX RDF
19	Ashwath Kumar	Quantitative analysis of ChIP-seq signals and transcriptomes.		2022	RDF
19	Qinhu Zhang, Dailun Wang, Kyungsook Han, De-Shuang Huang	Predicting TF-DNA Binding Motifs from ChIP-seq Datasets Using the Bag-Based Classifier Combined With a Multi-Fold Learning Scheme.	IEEE ACM Trans. Comput. Biol. Bioinform.	2021	DBLP DOI BibTeX RDF
19	Arnaud Liehrmann, Guillem Rigaill, Toby Dylan Hocking	Increased peak detection accuracy in over-dispersed ChIP-seq data with supervised segmentation models.	BMC Bioinform.	2021	DBLP DOI BibTeX RDF
19	Aseel Awdeh, Marcel Turcotte, Theodore J. Perkins	WACS: improving ChIP-seq peak calling by optimally weighting controls.	BMC Bioinform.	2021	DBLP DOI BibTeX RDF
19	Lélia Polit, Gwenneg Kerdivel, Sebastian Gregoricchio, Michela Esposito, Christel Guillouf, Valentina Boeva	CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes.	BMC Bioinform.	2021	DBLP DOI BibTeX RDF
19	Tatiana Subkhankulova, Fedor Naumenko, Oleg E. Tolmachov, Yuriy L. Orlov	Novel ChIP-seq simulating program with superior versatility: isChIP.	Briefings Bioinform.	2021	DBLP DOI BibTeX RDF
19	Michael Menzel, Sabine Hurka, Stefan Glasenhardt, Andreas Gogol-Döring	NoPeak: k-mer-based motif discovery in ChIP-Seq data without peak calling.	Bioinform.	2021	DBLP DOI BibTeX RDF
19	Mohammad Hallal, Mariette Awad, Pierre H. Khoueiry	TempoMAGE: a deep learning framework that exploits the causal dependency between time-series data to predict histone marks in open chromatin regions at time-points with missing ChIP-seq datasets.	Bioinform.	2021	DBLP DOI BibTeX RDF
19	Cerag Oguztuzun, Pelin Yasar, Kerim Yavuz, Mesut Muyan, Tolga Can	MotifGenie: a Python application for searching transcription factor binding sequences using ChIP-Seq datasets.	Bioinform.	2021	DBLP DOI BibTeX RDF
19	Rongbin Zheng, Xin Dong, Changxin Wan, Xiaoying Shi, Xiaoyan Zhang, Clifford A. Meyer	Cistrome Data Browser and Toolkit: analyzing human and mouse genomic data using compendia of ChIP-seq and chromatin accessibility data.	Quant. Biol.	2020	DBLP DOI BibTeX RDF
19	Chongzhi Zang, Yiren Wang, Weiqun Peng	RECOGNICER: A coarse-graining approach for identifying broad domains from ChIP-seq data.	Quant. Biol.	2020	DBLP DOI BibTeX RDF
19	Hayato Anzawa, Hitoshi Yamagata, Kengo Kinoshita	Theoretical characterisation of strand cross-correlation in ChIP-seq.	BMC Bioinform.	2020	DBLP DOI BibTeX RDF
19	Erik Czipa, Mátyás Schiller, Tibor Nagy, Levente Kontra, László Steiner, Júlia Koller, Orsolya Pálné-Szén, Endre Barta	ChIPSummitDB: a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them.	Database J. Biol. Databases Curation	2020	DBLP DOI BibTeX RDF
19	Moli Huang, Yunpeng Wang, Manqiu Yang, Jun Yan, Henry Yang, Wenzhuo Zhuang, Ying Xu, H. Phillip Koeffler, De-Chen Lin, Xi Chen 0039	dbInDel: a database of enhancer-associated insertion and deletion variants by analysis of H3K27ac ChIP-Seq.	Bioinform.	2020	DBLP DOI BibTeX RDF
19	Guodong Yang, Aiqun Ma, Zhaohui S. Qin, Li Chen	Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent transcriptional regulatory modules.	Bioinform.	2020	DBLP DOI BibTeX RDF
19	Hongjian Jin, Lawryn H. Kasper, Jon D. Larson, Gang Wu, Suzanne J. Baker, Jinghui Zhang, Yiping Fan	ChIPseqSpikeInFree: a ChIP-seq normalization approach to reveal global changes in histone modifications without spike-in.	Bioinform.	2020	DBLP DOI BibTeX RDF
19	Charles E. Wimberley, Steffen Heber	PeakPass: Automating ChIP-Seq Blacklist Creation.	J. Comput. Biol.	2020	DBLP DOI BibTeX RDF
19	Ruben Esse	ChIPdig: a comprehensive user-friendly tool for mining multi-sample ChIP-seq data.	F1000Research	2019	DBLP DOI BibTeX RDF
19	Alejandro Saettone, Marcelo Ponce, Syed Nabeel-Shah, Jeffrey Fillingham	RACS: rapid analysis of ChIP-Seq data for contig based genomes.	BMC Bioinform.	2019	DBLP DOI BibTeX RDF
19	Min Li 0007, Li Tang, Fang-Xiang Wu, Yi Pan 0001, Jianxin Wang 0001	CSA: a web service for the complete process of ChIP-Seq analysis.	BMC Bioinform.	2019	DBLP DOI BibTeX RDF
19	Shaojuan Li, Changxin Wan, Rongbin Zheng, Jingyu Fan, Xin Dong, Clifford A. Meyer, Xiaole Shirley Liu	Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks.	Nucleic Acids Res.	2019	DBLP DOI BibTeX RDF
19	Chi-Nga Chow, Tzong-Yi Lee, Yu-Cheng Hung, Guan-Zhen Li, Kuan-Chieh Tseng, Ya-Hsin Liu, Po-Li Kuo, Han-Qin Zheng, Wen-Chi Chang	PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants.	Nucleic Acids Res.	2019	DBLP DOI BibTeX RDF
19	Jihed Chouaref, Mattijs Bliek, Marc Galland	A reproducible Snakemake pipeline to analyse Illumina paired-end data from ChiP-Seq experiments.	J. Open Source Softw.	2019	DBLP DOI BibTeX RDF
19	Yang Li 0089, Pengyu Ni, Shaoqiang Zhang, Guojun Li, Zhengchang Su	ProSampler: an ultrafast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery.	Bioinform.	2019	DBLP DOI BibTeX RDF
19	Endre Bakken Stovner, Pål Sætrom	epic2 efficiently finds diffuse domains in ChIP-seq data.	Bioinform.	2019	DBLP DOI BibTeX RDF
19	Justin G. Chitpin, Aseel Awdeh, Theodore J. Perkins	RECAP reveals the true statistical significance of ChIP-seq peak calls.	Bioinform.	2019	DBLP DOI BibTeX RDF
19	Chun-xiao Sun, Yu Yang, Hua Wang 0003, Wen-hu Wang	A Clustering Approach for Motif Discovery in ChIP-Seq Dataset.	Entropy	2019	DBLP DOI BibTeX RDF
19	Vishaka Datta, Sridhar Hannenhalli, Rahul Siddharthan	ChIPulate: A comprehensive ChIP-seq simulation pipeline.	PLoS Comput. Biol.	2019	DBLP DOI BibTeX RDF
19	Ivar Grytten, Knut D. Rand, Alexander Johan Nederbragt, Geir Storvik, Ingrid Kristine Glad, Geir Kjetil Sandve	Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes.	PLoS Comput. Biol.	2019	DBLP DOI BibTeX RDF
19	Shankara Anand, Laurynas Kalesinskas, Craig Smail, Yosuke Tanigawa	SNPs2ChIP: Latent Factors of ChIP-seq to infer functions of non-coding SNPs.	PSB	2019	DBLP BibTeX RDF
19	Hasnaa Imad Al-Shaikhli, Elise de Doncker	qSMF: an Approximate Algorithm for Quotum Planted Motif Search on ChIP-Seq Data.	EIT	2019	DBLP DOI BibTeX RDF
19	Emilian Jungwirth, Katrin Panzitt, Hanns-Ulrich Marschall, Martin Wagner, Gerhard G. Thallinger	A Comprehensive FXR Signaling Atlas Derived from Pooled ChIP-seq Data.	dHealth	2019	DBLP DOI BibTeX RDF
19	Charles E. Wimberley, Steffen Heber	PeakPass: Automating ChIP-Seq Blacklist Creation.	ISBRA	2019	DBLP DOI BibTeX RDF
19	Eirini Stamoulakatou, Carlo Piccardi, Marco Masseroli	Analysis of Gene Regulatory Networks Inferred from ChIP-seq Data.	IWBBIO (1)	2019	DBLP DOI BibTeX RDF
19	Avantika R. Diwadkar, Mengyuan Kan, Blanca E. Himes	Facilitating Analysis of Publicly Available ChIP-Seq Data for Integrative Studies.	AMIA	2019	DBLP BibTeX RDF
19	Dejian Zhao, Deyou Zheng	SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis.	BMC Bioinform.	2018	DBLP DOI BibTeX RDF
19	Bingqiang Liu, Jinyu Yang, Yang Li 0089, Adam McDermaid, Qin Ma 0003	An algorithmic perspective of de novo cis-regulatory motif finding based on ChIP-seq data.	Briefings Bioinform.	2018	DBLP DOI BibTeX RDF
19	René Dreos, Giovanna Ambrosini, Romain Groux, Rouaïda Cavin Périer, Philipp Bucher	MGA repository: a curated data resource for ChIP-seq and other genome annotated data.	Nucleic Acids Res.	2018	DBLP DOI BibTeX RDF
19	Moli Huang, Ye Chen, Manqiu Yang, Anyuan Guo, Ying Xu, Liang Xu 0006, H. Phillip Koeffler	dbCoRC: a database of core transcriptional regulatory circuitries modeled by H3K27ac ChIP-seq signals.	Nucleic Acids Res.	2018	DBLP DOI BibTeX RDF
19	Ivan V. Kulakovskiy, Ilya E. Vorontsov, Ivan S. Yevshin, Ruslan N. Sharipov, Alla D. Fedorova, Eugene I. Rumynskiy, Yulia A. Medvedeva, Arturo Magana-Mora, Vladimir B. Bajic, Dmitri A. Papatsenko, Fedor A. Kolpakov, Vsevolod J. Makeev	HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis.	Nucleic Acids Res.	2018	DBLP DOI BibTeX RDF
19	Jeanne Chèneby, Marius Gheorghe, Marie Artufel, Anthony Mathelier, Benoît Ballester	ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments.	Nucleic Acids Res.	2018	DBLP DOI BibTeX RDF
19	Ryuichiro Nakato, Katsuhiko Shirahige	Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile.	Bioinform.	2018	DBLP DOI BibTeX RDF
19	Vahid Jalili, Matteo Matteucci, Marco Masseroli, Marco J. Morelli	Using combined evidence from replicates to evaluate ChIP-seq peaks.	Bioinform.	2018	DBLP DOI BibTeX RDF
19	Vida Ravanmehr, Minji Kim 0007, Zhiying Wang 0001, Olgica Milenkovic	ChIPWig: a random access-enabling lossless and lossy compression method for ChIP-seq data.	Bioinform.	2018	DBLP DOI BibTeX RDF
19	Shiqi Tu, Zhen Shao	An introduction to computational tools for differential binding analysis with ChIP-seq data.	Quant. Biol.	2017	DBLP DOI BibTeX RDF
19	Ryuichiro Nakato, Katsuhiko Shirahige	Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation.	Briefings Bioinform.	2017	DBLP DOI BibTeX RDF
19	Reuben Thomas, Sean Thomas, Alisha K. Holloway, Katherine S. Pollard	Features that define the best ChIP-seq peak calling algorithms.	Briefings Bioinform.	2017	DBLP DOI BibTeX RDF
19	Shenglin Mei, Qian Qin, Qiu Wu, Hanfei Sun, Rongbin Zheng, Chongzhi Zang, Muyuan Zhu, Jiaxin Wu, Xiaohui Shi, Len Taing, Tao Liu 0022, Myles Brown, Clifford A. Meyer, Xiaole Shirley Liu	Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse.	Nucleic Acids Res.	2017	DBLP DOI BibTeX RDF
19	Ivan S. Yevshin, Ruslan N. Sharipov, Tagir F. Valeev, Alexander E. Kel, Fedor A. Kolpakov	GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments.	Nucleic Acids Res.	2017	DBLP DOI BibTeX RDF
19	Keren Zhou 0002, Shun Liu, Wen-Ju Sun, Ling-Ling Zheng, Hui Zhou 0006, Jian-Hua Yang, Liang-Hu Qu	ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data.	Nucleic Acids Res.	2017	DBLP DOI BibTeX RDF
19	Georg Stricker, Alexander Engelhardt, Daniel Schulz, Matthias Schmid, Achim Tresch, Julien Gagneur	GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis.	Bioinform.	2017	DBLP DOI BibTeX RDF
19	Pang Wei Koh, Emma Pierson, Anshul Kundaje	Denoising genome-wide histone ChIP-seq with convolutional neural networks.	Bioinform.	2017	DBLP DOI BibTeX RDF
19	Toby Dylan Hocking, Patricia Goerner-Potvin, Andreanne Morin, Xiaojian Shao, Tomi Pastinen, Guillaume Bourque	Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning.	Bioinform.	2017	DBLP DOI BibTeX RDF
19	Alice C. L. Parodi, Laura M. Sangalli, Simone Vantini, Bruno Amati, Piercesare Secchi, Marco J. Morelli	FunChIP: an R/Bioconductor package for functional classification of ChIP-seq shapes.	Bioinform.	2017	DBLP DOI BibTeX RDF
19	Chandler Zuo, Kailei Chen, Sündüz Keles	A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets.	J. Comput. Biol.	2017	DBLP DOI BibTeX RDF
19	Hongbo Zhang, De-Shuang Huang	Soft-bag based motif discovery for ChIP-seq datasets.	BIBM	2017	DBLP DOI BibTeX RDF
19	Nawanol Theera-Ampornpunt, Somali Chaterji	Prediction of enhancer RNA activity levels from ChIP-seq-derived histone modification combinatorial codes.	BIBM	2017	DBLP DOI BibTeX RDF
19	Aseel Awdeh, Theodore J. Perkins	Analysis of Controls in ChIP-seq.	BCB	2017	DBLP DOI BibTeX RDF
19	Miklos Laczik	Improvement of the ChIP-seq technique for histone posttranslational modifications through enhanced laboratory protocols and data processing methods.		2017	RDF
19	Haitham Ashoor	Computational Methods for ChIP-seq Data Analysis and Applications.		2017	RDF
19	Nathan Cormier, Tyler Kolisnik, Mark Bieda	Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis.	BMC Bioinform.	2016	DBLP DOI BibTeX RDF
19	Marcin Piechota, Michal Korostynski, Joanna Ficek, Andrzej Tomski, Ryszard Przewlocki	Seqinspector: position-based navigation through the ChIP-seq data landscape to identify gene expression regulators.	BMC Bioinform.	2016	DBLP DOI BibTeX RDF
19	Joshua D. Starmer, Terry Magnuson	Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains.	BMC Bioinform.	2016	DBLP DOI BibTeX RDF
19	Qi Zhang, Xin Zeng, Samuel G. Younkin, Trupti Kawli, Michael P. Snyder, Sündüz Keles	Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection.	BMC Bioinform.	2016	DBLP DOI BibTeX RDF