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1

The changing mouse embryo transcriptome at whole tissue and single-cell resolution

He, Peng, Williams, Brian A., Trout, Diane, Marinov, Georgi K., Amrhein, Henry, Berghella, Libera, Goh, Say-Tar, Plajzer-Frick, Ingrid, Afzal, Veena, Pennacchio, Len A., Dickel, Diane E., Visel, Axel,

Journal:

Year:

2020

File:

PDF, 113.10 MB

2020

2

ChIP-seq accurately predicts tissue-specific activity of enhancers

Visel, Axel, Blow, Matthew J., Li, Zirong, Zhang, Tao, Akiyama, Jennifer A., Holt, Amy, Plajzer-Frick, Ingrid, Shoukry, Malak, Wright, Crystal, Chen, Feng

Journal:

Year:

2009

Language:

english

File:

PDF, 538 KB

english, 2009

3

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

Rubin, Edward M, Pennacchio, Len A, Visel, Axel, Prabhakar, Shyam, Akiyama, Jennifer A, Shoukry, Malak, Lewis, Keith D, Holt, Amy, Plajzer-Frick, Ingrid, Afzal, Veena

Journal:

Nature Genetics

Year:

2008

Language:

english

File:

PDF, 252 KB

english, 2008

4

A High-Resolution Enhancer Atlas of the Developing Telencephalon

Visel, Axel, Taher, Leila, Girgis, Hani, May, Dalit, Golonzhka, Olga, Hoch, Renee V., McKinsey, Gabriel L., Pattabiraman, Kartik, Silberberg, Shanni N., Blow, Matthew J., Hansen, David V., Nord, Alex

Journal:

Year:

2013

Language:

english

File:

PDF, 4.02 MB

english, 2013

5

The Ties That Bind: Mapping the Dynamic Enhancer-Promoter Interactome

Spurrell, Cailyn H., Dickel, Diane E., Visel, Axel

Journal:

Year:

2016

Language:

english

File:

PDF, 554 KB

english, 2016

6

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation

Preissl, Sebastian, Fang, Rongxin, Huang, Hui, Zhao, Yuan, Raviram, Ramya, Gorkin, David U., Zhang, Yanxiao, Sos, Brandon C., Afzal, Veena, Dickel, Diane E., Kuan, Samantha, Visel, Axel, Pennacchio, L

Journal:

Nature Neuroscience

Year:

2018

Language:

english

File:

PDF, 4.12 MB

english, 2018

7

Comprehensive analysis of the expression patterns of the adenylate cyclase gene family in the developing and adult mouse brain

Axel Visel, Gonzalo Alvarez-Bolado, Christina Thaller, Gregor Eichele

Journal:

The Journal of Comparative Neurology

Year:

2006

Language:

english

File:

PDF, 2.80 MB

english, 2006

8

Comprehensive expression atlas of fibroblast growth factors and their receptors generated by a novel robotic in situ hybridization platform

Murat Burak Yaylaoglu, Andrew Titmus, Axel Visel, Gonzalo Alvarez-Bolado, Christina Thaller, Gregor Eichele

Journal:

Developmental Dynamics

Year:

2005

Language:

english

File:

PDF, 433 KB

english, 2005

9

Transcriptional control of axonal guidance and sorting in dorsal interneurons by the Lim-HD proteins Lhx9 and Lhx1

Oshri Avraham, Yoav Hadas, Lilach Vald, Sophie Zisman, Adi Schejter, Axel Visel, Avihu Klar

Journal:

Neural Development

Year:

2009

Language:

english

File:

PDF, 5.26 MB

english, 2009

10

Genomic views of distant-acting enhancers

Visel, Axel, Rubin, Edward M., Pennacchio, Len A.

Journal:

Year:

2009

Language:

english

File:

PDF, 1.95 MB

english, 2009

11

Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice

Visel, Axel, Zhu, Yiwen, May, Dalit, Afzal, Veena, Gong, Elaine, Attanasio, Catia, Blow, Matthew J., Cohen, Jonathan C., Rubin, Edward M., Pennacchio, Len A.

Journal:

Year:

2010

Language:

english

File:

PDF, 433 KB

english, 2010

12

Disruption of an AP-2α binding site in an IRF6 enhancer is associated with cleft lip

Rahimov, Fedik, Marazita, Mary L, Visel, Axel, Cooper, Margaret E, Hitchler, Michael J, Rubini, Michele, Domann, Frederick E, Govil, Manika, Christensen, Kaare, Bille, Camille

Journal:

Nature Genetics

Year:

2008

Language:

english

File:

PDF, 647 KB

english, 2008

13

Limits of sequence and functional conservation

Pennacchio, Len A, Visel, Axel

Journal:

Nature Genetics

Year:

2010

Language:

english

File:

PDF, 815 KB

english, 2010

14

Scaffolding by ERK3 regulates MK5 in development

Schumacher, Stefanie, Laaß, Kathrin, Kant, Shashi, Shi, Yu, Visel, Axel, Gruber, Achim D, Kotlyarov, Alexey, Gaestel, Matthias

Journal:

The EMBO Journal

Year:

2004

Language:

english

File:

PDF, 313 KB

english, 2004

15

Expression of the winged helix/forkhead gene, foxn4, during zebrafish development

Nadia Danilova, Axel Visel, Catherine E. Willett, Lisa A. Steiner

Journal:

Developmental Brain Research

Year:

2004

Language:

english

File:

PDF, 480 KB

english, 2004

16

Combinatorial Regulation of Endothelial Gene Expression by Ets and Forkhead Transcription Factors

Sarah De Val, Neil C. Chi, Stryder M. Meadows, Simon Minovitsky, Joshua P. Anderson, Ian S. Harris, Melissa L. Ehlers, Pooja Agarwal, Axel Visel, Shan-Mei Xu, Len A. Pennacchio, Inna Dubchak, Paul A.

Journal:

Year:

2008

Language:

english

File:

PDF, 1.95 MB

english, 2008

17

Enhancer identification through comparative genomics

Axel Visel, James Bristow, Len A. Pennacchio

Journal:

Seminars in Cell & Developmental Biology

Year:

2007

Language:

english

File:

PDF, 1.29 MB

english, 2007

18

Adenylate Cyclase 1 dependent refinement of retinotopic maps in the mouse

Daniel T. Plas, Axel Visel, Ernesto Gonzalez, Wei-Chi She, Michael C. Crair

Journal:

Vision Research

Year:

2004

Language:

english

File:

PDF, 451 KB

english, 2004

19

Identification and characterization of novel Fgf17 enhancers active in the rostral forebrain signaling center

Renee V. Hoch, Axel Visel, Len A. Pennacchio, John L.R. Rubenstein

Journal:

Developmental Biology

Year:

2008

Language:

english

File:

PDF, 84 KB

english, 2008

20

Functional autonomy of distant-acting human enhancers

Axel Visel, Jennifer A. Akiyama, Malak Shoukry, Veena Afzal, Edward M. Rubin, Len A. Pennacchio

Journal:

Year:

2009

Language:

english

File:

PDF, 681 KB

english, 2009

21

Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression

Ariza-Cosano, Ana, Visel, Axel, Pennacchio, Len A, Fraser, Hunter B, Gómez-Skarmeta, José, Irimia, Manuel, Bessa, José

Journal:

Year:

2012

Language:

english

File:

PDF, 1.16 MB

english, 2012

22

De novotranscriptome assembly of drought tolerant CAM plants,Agave desertiandAgave tequilana

Gross, Stephen M, Martin, Jeffrey A, Simpson, June, Abraham-Juarez, María, Wang, Zhong, Visel, Axel

Journal:

Year:

2013

Language:

english

File:

PDF, 1.28 MB

english, 2013

23

Function-based identification of mammalian enhancers using site-specific integration

Dickel, Diane E, Zhu, Yiwen, Nord, Alex S, Wylie, John N, Akiyama, Jennifer A, Afzal, Veena, Plajzer-Frick, Ingrid, Kirkpatrick, Aileen, Göttgens, Berthold, Bruneau, Benoit G, Visel, Axel, Pennacchio,

Journal:

Year:

2014

Language:

english

File:

PDF, 793 KB

english, 2014

24

Fuzzy GIS-based multi-criteria evaluation for US Agave production as a bioenergy feedstock

Lewis, Sarah M., Gross, Stephen, Visel, Axel, Kelly, Maggi, Morrow, William

Journal:

Year:

2015

Language:

english

File:

PDF, 596 KB

english, 2015

25

Dlx1&2-Dependent Expression of Zfhx1b (Sip1, Zeb2) Regulates the Fate Switch between Cortical and Striatal Interneurons

McKinsey, Gabriel L., Lindtner, Susan, Trzcinski, Brett, Visel, Axel, Pennacchio, Len A., Huylebroeck, Danny, Higashi, Yujiro, Rubenstein, John L.R.

Journal:

Year:

2013

Language:

english

File:

PDF, 3.42 MB

english, 2013

26

Dynamic GATA4 enhancers shape the chromatin landscape central to heart development and disease

He, Aibin, Gu, Fei, Hu, Yong, Ma, Qing, Yi Ye, Lillian, Akiyama, Jennifer A., Visel, Axel, Pennacchio, Len A., Pu, William T.

Journal:

Nature Communications

Year:

2014

Language:

english

File:

PDF, 1.77 MB

english, 2014

27

HAND2 Targets Define a Network of Transcriptional Regulators that Compartmentalize the Early Limb Bud Mesenchyme

Osterwalder, Marco, Speziale, Dario, Shoukry, Malak, Mohan, Rajiv, Ivanek, Robert, Kohler, Manuel, Beisel, Christian, Wen, Xiaohui, Scales, Suzie J., Christoffels, Vincent M., Visel, Axel, Lopez-Rios,

Journal:

Developmental Cell

Year:

2014

Language:

english

File:

PDF, 4.93 MB

english, 2014

28

Genomic Perspectives of Transcriptional Regulation in Forebrain Development

Nord, Alex S., Pattabiraman, Kartik, Visel, Axel, Rubenstein, John L.R.

Journal:

Year:

2015

Language:

english

File:

PDF, 4.67 MB

english, 2015

29

Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility

Dogan, Nergiz, Wu, Weisheng, Morrissey, Christapher S, Chen, Kuan-Bei, Stonestrom, Aaron, Long, Maria, Keller, Cheryl A, Cheng, Yong, Jain, Deepti, Visel, Axel, Pennacchio, Len A, Weiss, Mitchell J, B

Journal:

Epigenetics & Chromatin

Year:

2015

Language:

english

File:

PDF, 2.76 MB

english, 2015

30

The Joint Genome Institute's synthetic biology internal review process

Simirenko, Lisa, Harmon-Smith, Miranda, Visel, Axel, Rubin, Edward M., Hillson, Nathan J.

Journal:

Journal of Responsible Innovation

Year:

2015

Language:

english

File:

PDF, 236 KB

english, 2015

31

Regulatory Pathway Analysis by High-Throughput In Situ Hybridization

Visel, Axel, Carson, James, Oldekamp, Judit, Warnecke, Marei, Jakubcakova, Vladimira, Zhou, Xunlei, Shaw, Chad A., Alvarez-Bolado, Gonzalo, Eichele, Gregor

Journal:

Year:

2007

Language:

english

File:

PDF, 2.50 MB

english, 2007

32

Tissue-Specific RNA Expression Marks Distant-Acting Developmental Enhancers

Wu, Han, Nord, Alex S., Akiyama, Jennifer A., Shoukry, Malak, Afzal, Veena, Rubin, Edward M., Pennacchio, Len A., Visel, Axel, Barsh, Gregory S.

Journal:

Year:

2014

Language:

english

File:

PDF, 2.65 MB

english, 2014

33

Deletion of Ultraconserved Elements Yields Viable Mice

Ahituv, Nadav, Zhu, Yiwen, Visel, Axel, Holt, Amy, Afzal, Veena, Pennacchio, Len A., Rubin, Edward M.

Journal:

Year:

2007

Language:

english

File:

PDF, 314 KB

english, 2007

34

Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species

Coleman-Derr, Devin, Desgarennes, Damaris, Fonseca-Garcia, Citlali, Gross, Stephen, Clingenpeel, Scott, Woyke, Tanja, North, Gretchen, Visel, Axel, Partida-Martinez, Laila P., Tringe, Susannah G.

Journal:

New Phytologist

Year:

2015

Language:

english

File:

PDF, 1.59 MB

english, 2015

35

Pbx Regulates Patterning of the Cerebral Cortex in Progenitors and Postmitotic Neurons

Golonzhka, Olga, Nord, Alex, Tang, Paul L.F., Lindtner, Susan, Ypsilanti, Athena R., Ferretti, Elisabetta, Visel, Axel, Selleri, Licia, Rubenstein, John L.R.

Journal:

Year:

2015

Language:

english

File:

PDF, 5.30 MB

english, 2015

36

A distal 594bp ECR specifies Hmx1 expression in pinna and lateral facial morphogenesis and is regulated by Hox-Pbx-Meis

Rosin, Jessica M., Li, Wenjie, Cox, Liza L., Rolfe, Sara M., Latorre, Victor, Akiyama, Jennifer A., Visel, Axel, Kuramoto, Takashi, Bobola, Nicoletta, Turner, Eric E., Cox, Timothy C.

Journal:

Development (The Company of Biologists)

Year:

2016

Language:

english

File:

PDF, 2.29 MB

english, 2016

37

Distal Limb Patterning Requires Modulation of cis -Regulatory Activities by HOX13

Sheth, Rushikesh, Barozzi, Iros, Langlais, David, Osterwalder, Marco, Nemec, Stephen, Carlson, Hanqian L., Stadler, H. Scott, Visel, Axel, Drouin, Jacques, Kmita, Marie

Journal:

Year:

2016

Language:

english

File:

PDF, 4.92 MB

english, 2016

38

Improved regulatory element prediction based on tissue-specific local epigenomic signatures

He, Yupeng, Gorkin, David U., Dickel, Diane E., Nery, Joseph R., Castanon, Rosa G., Lee, Ah Young, Shen, Yin, Visel, Axel, Pennacchio, Len A., Ren, Bing, Ecker, Joseph R.

Journal:

Proceedings of the National Academy of Sciences

Year:

2017

Language:

english

File:

PDF, 934 KB

english, 2017

39

HAND2 Target Gene Regulatory Networks Control Atrioventricular Canal and Cardiac Valve Development

Laurent, Frédéric, Girdziusaite, Ausra, Gamart, Julie, Barozzi, Iros, Osterwalder, Marco, Akiyama, Jennifer A., Lincoln, Joy, Lopez-Rios, Javier, Visel, Axel, Zuniga, Aimée, Zeller, Rolf

Journal:

Year:

2017

Language:

english

File:

PDF, 5.33 MB

english, 2017

40

Dlx1 and Dlx2 Promote Interneuron GABA Synthesis, Synaptogenesis, and Dendritogenesis

Pla, Ramon, Stanco, Amelia, Howard, MacKenzie A, Rubin, Anna N, Vogt, Daniel, Mortimer, Niall, Cobos, Inma, Potter, Gregory Brian, Lindtner, Susan, Price, James D, Nord, Alex S, Visel, Axel, Schreiner

Journal:

Cerebral Cortex

Year:

2017

Language:

english

File:

PDF, 1.84 MB

english, 2017

41

Composition and dosage of a multipartite enhancer cluster control developmental expression of Ihh (Indian hedgehog)

Will, Anja J, Cova, Giulia, Osterwalder, Marco, Chan, Wing-Lee, Wittler, Lars, Brieske, Norbert, Heinrich, Verena, de Villartay, Jean-Pierre, Vingron, Martin, Klopocki, Eva, Visel, Axel, Lupiáñez, Dar

Journal:

Nature Genetics

Year:

2017

Language:

english

File:

PDF, 3.85 MB

english, 2017

42

Author Correction: Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation

Preissl, Sebastian, Fang, Rongxin, Huang, Hui, Zhao, Yuan, Raviram, Ramya, Gorkin, David U., Zhang, Yanxiao, Sos, Brandon C., Afzal, Veena, Dickel, Diane E., Kuan, Samantha, Visel, Axel, Pennacchio, L

Journal:

Nature Neuroscience

Year:

2018

File:

PDF, 546 KB

2018

43

Use of “MGE Enhancers” for Labeling and Selection of Embryonic Stem Cell-Derived Medial Ganglionic Eminence (MGE) Progenitors and Neurons

Chen, Ying-Jiun J., Vogt, Daniel, Wang, Yanling, Visel, Axel, Silberberg, Shanni N., Nicholas, Cory R., Danjo, Teruko, Pollack, Joshua L., Pennacchio, Len A., Anderson, Stewart, Sasai, Yoshiki, Baraba

Journal:

Year:

2013

Language:

english

File:

PDF, 15.05 MB

english, 2013

44

The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity

Fonseca-García, Citlali, Coleman-Derr, Devin, Garrido, Etzel, Visel, Axel, Tringe, Susannah G., Partida-Martínez, Laila P.

Journal:

Frontiers in Microbiology

Year:

2016

Language:

english

File:

PDF, 5.57 MB

english, 2016

45

Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers

Hashimoto, Hisayuki, Wang, Zhaoning, Garry, Glynnis A., Malladi, Venkat S., Botten, Giovanni A., Ye, Wenduo, Zhou, Huanyu, Osterwalder, Marco, Dickel, Diane E., Visel, Axel, Liu, Ning, Bassel-Duby, Rh

Journal:

Year:

2019

Language:

english

File:

PDF, 9.44 MB

english, 2019

46

Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers

Hashimoto, Hisayuki, Wang, Zhaoning, Garry, Glynnis A., Malladi, Venkat S., Botten, Giovanni A., Ye, Wenduo, Zhou, Huanyu, Osterwalder, Marco, Dickel, Diane E., Visel, Axel, Liu, Ning, Bassel-Duby, Rh

Journal:

Year:

2019

File:

PDF, 9.44 MB

2019

47

Stable enhancers are active in development, and fragile enhancers are associated with evolutionary adaptation

Li, Shan, Kvon, Evgeny Z., Visel, Axel, Pennacchio, Len A., Ovcharenko, Ivan

Journal:

Year:

2019

Language:

english

File:

PDF, 3.15 MB

english, 2019

48

Stable enhancers are active in development, and fragile enhancers are associated with evolutionary adaptation

Li, Shan, Kvon, Evgeny Z., Visel, Axel, Pennacchio, Len A., Ovcharenko, Ivan

Journal:

Year:

2019

File:

PDF, 3.15 MB

2019

49

“Interrogating the grainyhead-like 2 (Grhl2) genomic locus identifies an enhancer element that regulates palatogenesis in mouse”

de Vries, Michael, Carpinelli, Marina, Rutland, Emilie, Hatzipantelis, Aaron, Partridge, Darren, Auden, Alana, Anderson, Peter J., De Groef, Bert, Wu, Han, Osterwalder, Marco, Visel, Axel, Jane, Steph

Journal:

Developmental Biology

Year:

2019

Language:

english

File:

PDF, 2.15 MB

english, 2019

50

“Interrogating the grainyhead-like 2 (Grhl2) genomic locus identifies an enhancer element that regulates palatogenesis in mouse”

de Vries, Michael, Carpinelli, Marina, Rutland, Emilie, Hatzipantelis, Aaron, Partridge, Darren, Auden, Alana, Anderson, Peter J., De Groef, Bert, Wu, Han, Osterwalder, Marco, Visel, Axel, Jane, Steph

Journal:

Developmental Biology

Year:

2019

File:

PDF, 2.15 MB

2019