GEEES: inferring cell-specific gene-enhancer interactions from multi-modal single-cell data von Chen, Shuyang, 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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FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation von Zheng, Ye, Keleş, Sündüz

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Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies von Zheng, Ye, Ay, Ferhat, 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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Detecting differential binding of transcription factors with ChIP-seq von Liang, Kun, Kele, Sündüz

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Integrative annotation scores of variants for impact on RNA binding protein activities von Duan, Jingqi, Gasch, Audrey P, 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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FreeHi-C spike-in simulations for benchmarking differential chromatin interaction detection von Zheng, Ye, Zhou, Peigen, Keleş, Sündüz

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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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Unbiased screen of RNA tailing activities reveals a poly(UG) polymerase von Preston, Melanie A., Porter, Douglas F., Chen, Fan, Buter, Natascha, Lapointe, Christopher P., Keles, Sunduz, Kimble, Judith, Wickens, Marvin

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Mechanisms of erythrocyte development and regeneration: implications for regenerative medicine and beyond von Bresnick, Emery H, Hewitt, Kyle J, Mehta, Charu, Keles, Sunduz, Paulson, Robert F, Johnson, Kirby D

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Sparse Partial Least Squares Classification for High Dimensional Data von Chung, Dongjun, Keles, Sunduz

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PKM2‐TMEM33 axis regulates lipid homeostasis in cancer cells by controlling SCAP stability von Liu, Fabao, Ma, Min, Gao, Ang, Ma, Fengfei, Ma, Gui, Liu, Peng, Jia, Chenxi, Wang, Yidan, Donahue, Kristine, Zhang, Shengjie, Ong, Irene M, Keles, Sunduz, Li, Lingjun, Xu, Wei

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An empirical Bayes test for allelic-imbalance detection in ChIP-seq von Zhang, Qi, Keleş, Sündüz

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atSNP Search: a web resource for statistically evaluating influence of human genetic variation on transcription factor binding von Shin, Sunyoung, Hudson, Rebecca, Harrison, Christopher, Craven, Mark, Keleş, Sündüz

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MuDCoD: multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing von Şapcı, Ali Osman Berk, Lu, Shan, Yan, Shuchen, Ay, Ferhat, Tastan, Oznur, Keleş, Sündüz

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PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments von Liu, Peng, Soukup, Alexandra A, Bresnick, Emery H, Dewey, Colin N, Keleş, Sündüz

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Discovering Hematopoietic Mechanisms through Genome-wide Analysis of GATA Factor Chromatin Occupancy von Fujiwara, Tohru, O'Geen, Henriette, Keles, Sunduz, Blahnik, Kimberly, Linnemann, Amelia K., Kang, Yoon-A., Choi, Kyunghee, Farnham, Peggy J., Bresnick, Emery H.

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Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments von Welch, Rene, Chung, Dongjun, Grass, Jeffrey, Landick, Robert, Keles, Sündüz

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