Protocol for development and use of spike-in control for chromatin immunoprecipitation of chromatin-binding proteins in Schizosaccharomyces pombe by Jasbeer S. Khanduja, Mo Motamedi

Subjects: “…ChIP-seq…”
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Protocol to investigate bivalent histone modification dynamics via chromatin immunoprecipitation followed by re-chromatin immunoprecipitation by Zhengyao Shao, Hong Qiao

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Protease‐resistant streptavidin for interaction proteomics by Mahmoud‐Reza Rafiee, Gianluca Sigismondo, Mathias Kalxdorf, Laura Förster, Britta Brügger, Julien Béthune, Jeroen Krijgsveld

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AlleleSeq: analysis of allele‐specific expression and binding in a network framework by Joel Rozowsky, Alexej Abyzov, Jing Wang, Pedro Alves, Debasish Raha, Arif Harmanci, Jing Leng, Robert Bjornson, Yong Kong, Naoki Kitabayashi, Nitin Bhardwaj, Mark Rubin, Michael Snyder, Mark Gerstein

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Chromatin endogenous cleavage provides a global view of yeast RNA polymerase II transcription kinetics by Jake VanBelzen, Bennet Sakelaris, Donna G Brickner, Nikita Marcou, Hermann Riecke, Niall M Mangan, Jason H Brickner

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Genome-wide identification of the H3K27ac signals reveals key thermogenic cis-regulatory elements of brown adipose tissues in Oryctolagus cuniculus by Kun Du, Qian Wu, Yu-Xuan Gan, Xin-Yue Tang, Jia-Xin Zan, Wen-Qiang Sun, Gang Luo, Xi-Wen Chen, Dai-Hua Wang

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Annotation of cis-regulatory-associated histone modifications in the genomes of two Thoroughbred stallions by Alexa M. Barber, Alexa M. Barber, Nicole B. Kingsley, Nicole B. Kingsley, Sichong Peng, Elena Giulotto, Rebecca R. Bellone, Rebecca R. Bellone, Carrie J. Finno, Ted Kalbfleisch, Jessica L. Petersen

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Study on the regulatory mechanism of NsdAsr on rimocidin biosynthesis in Streptomyces rimosus M527 by Yawen Xie, Yujie Jiang, Yongyong Zhang, Andreas Bechthold, Xiaoping Yu, Zheng Ma

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GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome by Matthew D Sekedat, David Fenyö, Richard S Rogers, Alan J Tackett, John D Aitchison, Brian T Chait

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Prevalence of transcription promoters within archaeal operons and coding sequences by Tie Koide, David J Reiss, J Christopher Bare, Wyming Lee Pang, Marc T Facciotti, Amy K Schmid, Min Pan, Bruz Marzolf, Phu T Van, Fang‐Yin Lo, Abhishek Pratap, Eric W Deutsch, Amelia Peterson, Dan Martin, Nitin S Baliga

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Loop Catalog: a comprehensive HiChIP database of human and mouse samples by Joaquin Reyna, Kyra Fetter, Romeo Ignacio, Cemil Can Ali Marandi, Astoria Ma, Nikhil Rao, Zichen Jiang, Daniela Salgado Figueroa, Sourya Bhattacharyya, Ferhat Ay

Subjects: “…HiChIP…”
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A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability by Amy K Schmid, David J Reiss, Min Pan, Tie Koide, Nitin S Baliga

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Genome-wide characterization of the GmLUX binding preferences and its epigenic features in the soybean genome by Lv Tianxiao, Hong Xiao, Jingxing Wang, Ling Zhang, Tian Fan, Mingkun Huang, Chang-En Tian, Hua Yang, Yufang Hu

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A high‐throughput ChIP‐Seq for large‐scale chromatin studies by Christophe D Chabbert, Sophie H Adjalley, Bernd Klaus, Emilie S Fritsch, Ishaan Gupta, Vicent Pelechano, Lars M Steinmetz

Subjects: “…ChIP‐Seq…”
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CHIRP-Seq: FOXP2 transcriptional targets in zebra finch brain include numerous speech and language-related genes by Gregory L. Gedman, Todd H. Kimball, Lee L. Atkinson, Daniella Factor, Gabriela Vojtova, Madza Farias-Virgens, Timothy F. Wright, Stephanie A. White

Subjects: “…ChIP-Seq…”
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Cooperation of LIM domain‐binding 2 (LDB2) with EGR in the pathogenesis of schizophrenia by Tetsuo Ohnishi, Yuji Kiyama, Fumiko Arima‐Yoshida, Mitsutaka Kadota, Tomoe Ichikawa, Kazuyuki Yamada, Akiko Watanabe, Hisako Ohba, Kaori Tanaka, Akihiro Nakaya, Yasue Horiuchi, Yoshimi Iwayama, Manabu Toyoshima, Itone Ogawa, Chie Shimamoto‐Mitsuyama, Motoko Maekawa, Shabeesh Balan, Makoto Arai, Mitsuhiro Miyashita, Kazuya Toriumi, Yayoi Nozaki, Rumi Kurokawa, Kazuhiro Suzuki, Akane Yoshikawa, Tomoko Toyota, Toshihiko Hosoya, Hiroyuki Okuno, Haruhiko Bito, Masanari Itokawa, Shigehiro Kuraku, Toshiya Manabe, Takeo Yoshikawa

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ChIPbinner: an R package for analyzing broad histone marks binned in uniform windows from ChIP-Seq or CUT&RUN/TAG data by Reinnier Padilla, Eric Bareke, Bo Hu, Jacek Majewski

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H3K4me3 changes occur in cell wall genes during the development of Fagopyrum tataricum morphogenic and non-morphogenic calli by Alicja Tomasiak, Artur Piński, Anna Milewska-Hendel, Ignasi Andreu Godall, Natalia Borowska-Żuchowska, Joanna Morończyk, Jordi Moreno-Romero, Alexander Betekhtin

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A transcription network underlies the dual genomic coordination of mitochondrial biogenesis by Fan Zhang, Annie Lee, Anna V Freitas, Jake T Herb, Zong-Heng Wang, Snigdha Gupta, Zhe Chen, Hong Xu

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CacPred: a cascaded convolutional neural network for TF-DNA binding prediction by Shuangquan Zhang, Anjun Ma, Xuping Xie, Zhichao Lian, Yan Wang

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