Sparse partial least squares regression for simultaneous dimension reduction and variable selection von Chun, Hyonho, Keleş, Sündüz

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Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding von Myers, Kevin S, Yan, Huihuang, Ong, Irene M, Chung, Dongjun, Liang, Kun, Tran, Frances, Keleş, Sündüz, Landick, Robert, Kiley, Patricia J

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A Statistical Framework for the Analysis of ChIP-Seq Data von Kuan, Pei Fen, Chung, Dongjun, Pan, Guangjin, Thomson, James A., Stewart, Ron, Keleş, Sündüz

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O₂ availability impacts iron homeostasis in Escherichia coli von Beauchene, Nicole A., Mettert, Erin L., Moore, Laura J., Keleş, Sündüz, Willey, Emily R., Kiley, Patricia J.

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Epstein-Barr Virus Infection Promotes Epithelial Cell Growth by Attenuating Differentiation-Dependent Exit from the Cell Cycle von Eichelberg, Mark R, Welch, Rene, Guidry, J Tod, Ali, Ahmed, Ohashi, Makoto, Makielski, Kathleen R, McChesney, Kyle, Van Sciver, Nicholas, Lambert, Paul F, Keleș, Sündüz, Kenney, Shannon C, Scott, Rona S, Johannsen, Eric

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Normalization of ChIP-seq data with control von Liang, Kun, Keleş, Sündüz

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GEEES: inferring cell-specific gene-enhancer interactions from multi-modal single-cell data von Chen, Shuyang, Keleş, Sündüz

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FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation von Zheng, Ye, Keleş, Sündüz

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Normalization and de-noising of single-cell Hi-C data with BandNorm and scVI-3D von Zheng, Ye, Shen, Siqi, Keleş, Sündüz

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Joint Tensor Modeling of Single Cell 3D Genome and Epigenetic Data with Muscle von Park, Kwangmoon, Keleş, Sündüz

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Chemical-genomic dissection of the CTD code von Akhtar, Md Sohail, Zhang, David W, Rodríguez-Molina, Juan B, Tietjen, Joshua R, Ansari, Aseem Z, Heidemann, Martin, Eick, Dirk, Li, Xin, Chapman, Rob D, Shokat, Kevan, White, Brent E, Keles, Sündüz

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Transcription of histone gene cluster by differential core-promoter factors von Isogai, Yoh, Keles, Sündüz, Prestel, Matthias, Hochheimer, Andreas, Tjian, Robert

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dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data von Chung, Dongjun, Park, Dan, Myers, Kevin, Grass, Jeffrey, Kiley, Patricia, Landick, Robert, Keleş, Sündüz

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Fungal Morphology, Iron Homeostasis, and Lipid Metabolism Regulated by a GATA Transcription Factor in Blastomyces dermatitidis von Marty, Amber J, Broman, Aimee T, Zarnowski, Robert, Dwyer, Teigan G, Bond, Laura M, Lounes-Hadj Sahraoui, Anissa, Fontaine, Joël, Ntambi, James M, Keleş, Sündüz, Kendziorski, Christina, Gauthier, Gregory M

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Detecting differential binding of transcription factors with ChIP-seq von Liang, Kun, Kele, Sündüz

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SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins von Chen, Fan, Keles, Sunduz

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scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data von Shen, Siqi, Zheng, Ye, Keleş, Sündüz

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atSNP: transcription factor binding affinity testing for regulatory SNP detection von Zuo, Chandler, Shin, Sunyoung, Keleş, Sündüz

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GLANET: genomic loci annotation and enrichment tool von Otlu, Burçak, Firtina, Can, Keles, Sündüz, Tastan, Oznur

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Gene by environment interaction mouse model reveals a functional role for 5-hydroxymethylcytosine in neurodevelopmental disorders von Papale, Ligia A, Madrid, Andy, Zhang, Qi, Chen, Kailei, Sak, Lara, Keleş, Sündüz, Alisch, Reid S

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