Citation And Reference

Citation And Reference

1

Hanqing Liu, Jingtian Zhou, Wei Tian, Chongyuan Luo, Anna Bartlett, Andrew Aldridge, Jacinta Lucero, Julia K Osteen, Joseph R Nery, Huaming Chen, Angeline Rivkin, Rosa G Castanon, Ben Clock, Yang Eric Li, Xiaomeng Hou, Olivier B Poirion, Sebastian Preissl, Antonio Pinto-Duarte, Carolyn O'Connor, Lara Boggeman, Conor Fitzpatrick, Michael Nunn, Eran A Mukamel, Zhuzhu Zhang, Edward M Callaway, Bing Ren, Jesse R Dixon, M Margarita Behrens, and Joseph R Ecker. DNA methylation atlas of the mouse brain at single-cell resolution. Nature, 598(7879):120–128, October 2021.

2

Heng Li. Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics, 27(5):718–719, March 2011.

3

Frederique Ruf-Zamojski, Zidong Zhang, Michel Zamojski, Gregory R Smith, Natalia Mendelev, Hanqing Liu, German Nudelman, Mika Moriwaki, Hanna Pincas, Rosa Gomez Castanon, Venugopalan D Nair, Nitish Seenarine, Mary Anne S Amper, Xiang Zhou, Luisina Ongaro, Chirine Toufaily, Gauthier Schang, Joseph R Nery, Anna Bartlett, Andrew Aldridge, Nimisha Jain, Gwen V Childs, Olga G Troyanskaya, Joseph R Ecker, Judith L Turgeon, Corrine K Welt, Daniel J Bernard, and Stuart C Sealfon. Single nucleus multi-omics regulatory landscape of the murine pituitary. Nat. Commun., 12(1):2677, May 2021.

4

Samuel L Wolock, Romain Lopez, and Allon M Klein. Scrublet: computational identification of cell doublets in Single-Cell transcriptomic data. Cell Syst, 8(4):281–291.e9, April 2019.

5

Matthew D Schultz, Yupeng He, John W Whitaker, Manoj Hariharan, Eran A Mukamel, Danny Leung, Nisha Rajagopal, Joseph R Nery, Mark A Urich, Huaming Chen, Shin Lin, Yiing Lin, Inkyung Jung, Anthony D Schmitt, Siddarth Selvaraj, Bing Ren, Terrence J Sejnowski, Wei Wang, and Joseph R Ecker. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature, 523(7559):212–216, July 2015.

6

Yupeng He, Manoj Hariharan, David U Gorkin, Diane E Dickel, Chongyuan Luo, Rosa G Castanon, Joseph R Nery, Ah Young Lee, Yuan Zhao, Hui Huang, Brian A Williams, Diane Trout, Henry Amrhein, Rongxin Fang, Huaming Chen, Bin Li, Axel Visel, Len A Pennacchio, Bing Ren, and Joseph R Ecker. Spatiotemporal DNA methylome dynamics of the developing mouse fetus. Nature, 583(7818):752–759, July 2020.

7

Aziz Khan, Oriol Fornes, Arnaud Stigliani, Marius Gheorghe, Jaime A Castro-Mondragon, Robin van der Lee, Adrien Bessy, Jeanne Chèneby, Shubhada R Kulkarni, Ge Tan, Damir Baranasic, David J Arenillas, Albin Sandelin, Klaas Vandepoele, Boris Lenhard, Benoît Ballester, Wyeth W Wasserman, François Parcy, and Anthony Mathelier. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res., 46(D1):D260–D266, January 2018.

8

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, Dmitry A Papatsenko, Fedor A Kolpakov, and 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., 46(D1):D252–D259, January 2018.

9

Arttu Jolma, Jian Yan, Thomas Whitington, Jarkko Toivonen, Kazuhiro R Nitta, Pasi Rastas, Ekaterina Morgunova, Martin Enge, Mikko Taipale, Gonghong Wei, Kimmo Palin, Juan M Vaquerizas, Renaud Vincentelli, Nicholas M Luscombe, Timothy R Hughes, Patrick Lemaire, Esko Ukkonen, Teemu Kivioja, and Jussi Taipale. DNA-binding specificities of human transcription factors. Cell, 152(1-2):327–339, January 2013.

10

Jeff Vierstra, John Lazar, Richard Sandstrom, Jessica Halow, Kristen Lee, Daniel Bates, Morgan Diegel, Douglas Dunn, Fidencio Neri, Eric Haugen, Eric Rynes, Alex Reynolds, Jemma Nelson, Audra Johnson, Mark Frerker, Michael Buckley, Rajinder Kaul, Wouter Meuleman, and John A Stamatoyannopoulos. Global reference mapping of human transcription factor footprints. Nature, 583(7818):729–736, July 2020.

11

Pavlin G Poličar, Martin Stražar, and Blaž Zupan. openTSNE: a modular python library for t-SNE dimensionality reduction and embedding. bioRxiv, pages 731877, August 2019.

12

Dmitry Kobak and Philipp Berens. The art of using t-SNE for single-cell transcriptomics. Nat. Commun., 10(1):5416, November 2019.

13

Amit Zeisel, Hannah Hochgerner, Peter Lönnerberg, Anna Johnsson, Fatima Memic, Job van der Zwan, Martin Häring, Emelie Braun, Lars E Borm, Gioele La Manno, Simone Codeluppi, Alessandro Furlan, Kawai Lee, Nathan Skene, Kenneth D Harris, Jens Hjerling-Leffler, Ernest Arenas, Patrik Ernfors, Ulrika Marklund, and Sten Linnarsson. Molecular architecture of the mouse nervous system. Cell, 174(4):999–1014.e22, August 2018.

14

Gioele La Manno, Kimberly Siletti, Alessandro Furlan, Daniel Gyllborg, Elin Vinsland, Alejandro Mossi Albiach, Christoffer Mattsson Langseth, Irina Khven, Alex R Lederer, Lisa M Dratva, Anna Johnsson, Mats Nilsson, Peter Lönnerberg, and Sten Linnarsson. Molecular architecture of the developing mouse brain. Nature, July 2021.