A comparative encyclopedia of DNA elements in the mouse genome

Feng Yue; Yong Cheng; Alessandra Breschi; Jeff Vierstra; Weisheng Wu; Tyrone Ryba; Richard Sandstrom; Zhihai Ma; Carrie Davis; Benjamin D. Pope; Yin Shen; Dmitri D. Pervouchine; Sarah Djebali; Robert E. Thurman; Rajinder Kaul; Eric Rynes; Anthony Kirilusha; Georgi K. Marinov; Brian A. Williams; Diane Trout; Henry Amrhein; Katherine Fisher-Aylor; Igor Antoshechkin; Gilberto DeSalvo; Lei Hoon See; Meagan Fastuca; Jorg Drenkow; Chris Zaleski; Alex Dobin; Pablo Prieto; Julien Lagarde; Giovanni Bussotti; Andrea Tanzer; Olgert Denas; Kanwei Li; M. A. Bender; Miaohua Zhang; Rachel Byron; Mark T. Groudine; David McCleary; Long Pham; Zhen Ye; Samantha Kuan; Lee Edsall; Yi Chieh Wu; Matthew D. Rasmussen; Mukul S. Bansal; Manolis Kellis; Cheryl A. Keller; Christapher S. Morrissey; Tejaswini Mishra; Deepti Jain; Nergiz Dogan; Robert S. Harris; Philip Cayting; Trupti Kawli; Alan P. Boyle; Ghia Euskirchen; Anshul Kundaje; Shin Lin; Yiing Lin; Camden Jansen; Venkat S. Malladi; Melissa S. Cline; Drew T. Erickson; Vanessa M. Kirkup; Katrina Learned; Cricket A. Sloan; Kate R. Rosenbloom; Beatriz Lacerda De Sousa; Kathryn Beal; Miguel Pignatelli; Paul Flicek; Jin Lian; Tamer Kahveci; Dongwon Lee; W. James Kent; Miguel Ramalho Santos; Javier Herrero; Cedric Notredame; Audra Johnson; Shinny Vong; Kristen Lee; Daniel Bates; Fidencio Neri; Morgan Diegel; Theresa Canfield; Peter J. Sabo; Matthew S. Wilken; Thomas A. Reh; Erika Giste; Anthony Shafer; Tanya Kutyavin; Eric Haugen; Douglas Dunn; Alex P. Reynolds; Shane Neph; Richard Humbert; R. Scott Hansen; Marella De Bruijn; Licia Selleri; Alexander Rudensky; Steven Josefowicz; Robert Samstein; Evan E. Eichler; Stuart H. Orkin; Dana Levasseur; Thalia Papayannopoulou; Kai Hsin Chang; Arthur Skoultchi; Srikanta Gosh; Christine Disteche; Piper Treuting; Yanli Wang; Mitchell J. Weiss; Gerd A. Blobel; Xiaoyi Cao; Sheng Zhong; Ting Wang; Peter J. Good; Rebecca F. Lowdon; Leslie B. Adams; Xiao Qiao Zhou; Michael J. Pazin; Elise A. Feingold; Barbara Wold; James Taylor; Ali Mortazavi; Sherman M. Weissman; John A. Stamatoyannopoulos; Michael P. Snyder; Roderic Guigo; Thomas R. Gingeras; David M. Gilbert; Ross C. Hardison; Michael A. Beer; Bing Ren

doi:10.1038/nature13992

A comparative encyclopedia of DNA elements in the mouse genome

Feng Yue, Yong Cheng, Alessandra Breschi, Jeff Vierstra, Weisheng Wu, Tyrone Ryba, Richard Sandstrom, Zhihai Ma, Carrie Davis, Benjamin D. Pope, Yin Shen, Dmitri D. Pervouchine, Sarah Djebali, Robert E. Thurman, Rajinder Kaul, Eric Rynes, Anthony Kirilusha, Georgi K. Marinov, Brian A. Williams, Diane TroutHenry Amrhein, Katherine Fisher-Aylor, Igor Antoshechkin, Gilberto DeSalvo, Lei Hoon See, Meagan Fastuca, Jorg Drenkow, Chris Zaleski, Alex Dobin, Pablo Prieto, Julien Lagarde, Giovanni Bussotti, Andrea Tanzer, Olgert Denas, Kanwei Li, M. A. Bender, Miaohua Zhang, Rachel Byron, Mark T. Groudine, David McCleary, Long Pham, Zhen Ye, Samantha Kuan, Lee Edsall, Yi Chieh Wu, Matthew D. Rasmussen, Mukul S. Bansal, Manolis Kellis, Cheryl A. Keller, Christapher S. Morrissey, Tejaswini Mishra, Deepti Jain, Nergiz Dogan, Robert S. Harris, Philip Cayting, Trupti Kawli, Alan P. Boyle, Ghia Euskirchen, Anshul Kundaje, Shin Lin, Yiing Lin, Camden Jansen, Venkat S. Malladi, Melissa S. Cline, Drew T. Erickson, Vanessa M. Kirkup, Katrina Learned, Cricket A. Sloan, Kate R. Rosenbloom, Beatriz Lacerda De Sousa, Kathryn Beal, Miguel Pignatelli, Paul Flicek, Jin Lian, Tamer Kahveci, Dongwon Lee, W. James Kent, Miguel Ramalho Santos, Javier Herrero, Cedric Notredame, Audra Johnson, Shinny Vong, Kristen Lee, Daniel Bates, Fidencio Neri, Morgan Diegel, Theresa Canfield, Peter J. Sabo, Matthew S. Wilken, Thomas A. Reh, Erika Giste, Anthony Shafer, Tanya Kutyavin, Eric Haugen, Douglas Dunn, Alex P. Reynolds, Shane Neph, Richard Humbert, R. Scott Hansen, Marella De Bruijn, Licia Selleri, Alexander Rudensky, Steven Josefowicz, Robert Samstein, Evan E. Eichler, Stuart H. Orkin, Dana Levasseur, Thalia Papayannopoulou, Kai Hsin Chang, Arthur Skoultchi, Srikanta Gosh, Christine Disteche, Piper Treuting, Yanli Wang, Mitchell J. Weiss, Gerd A. Blobel, Xiaoyi Cao, Sheng Zhong, Ting Wang, Peter J. Good, Rebecca F. Lowdon, Leslie B. Adams, Xiao Qiao Zhou, Michael J. Pazin, Elise A. Feingold, Barbara Wold, James Taylor, Ali Mortazavi, Sherman M. Weissman, John A. Stamatoyannopoulos, Michael P. Snyder, Roderic Guigo, Thomas R. Gingeras, David M. Gilbert, Ross C. Hardison, Michael A. Beer, Bing Ren

Cell Biology

Research output: Contribution to journal › Article

648 Scopus citations

Abstract

The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases.

Original language	English (US)
Pages (from-to)	355-364
Number of pages	10
Journal	Nature
Volume	515
Issue number	7527
DOIs	https://doi.org/10.1038/nature13992
State	Published - Nov 20 2014

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Yue, F., Cheng, Y., Breschi, A., Vierstra, J., Wu, W., Ryba, T., Sandstrom, R., Ma, Z., Davis, C., Pope, B. D., Shen, Y., Pervouchine, D. D., Djebali, S., Thurman, R. E., Kaul, R., Rynes, E., Kirilusha, A., Marinov, G. K., Williams, B. A., ... Ren, B. (2014). A comparative encyclopedia of DNA elements in the mouse genome. Nature, 515(7527), 355-364. https://doi.org/10.1038/nature13992

A comparative encyclopedia of DNA elements in the mouse genome. / Yue, Feng; Cheng, Yong; Breschi, Alessandra; Vierstra, Jeff; Wu, Weisheng; Ryba, Tyrone; Sandstrom, Richard; Ma, Zhihai; Davis, Carrie; Pope, Benjamin D.; Shen, Yin; Pervouchine, Dmitri D.; Djebali, Sarah; Thurman, Robert E.; Kaul, Rajinder; Rynes, Eric; Kirilusha, Anthony; Marinov, Georgi K.; Williams, Brian A.; Trout, Diane; Amrhein, Henry; Fisher-Aylor, Katherine; Antoshechkin, Igor; DeSalvo, Gilberto; See, Lei Hoon; Fastuca, Meagan; Drenkow, Jorg; Zaleski, Chris; Dobin, Alex; Prieto, Pablo; Lagarde, Julien; Bussotti, Giovanni; Tanzer, Andrea; Denas, Olgert; Li, Kanwei; Bender, M. A.; Zhang, Miaohua; Byron, Rachel; Groudine, Mark T.; McCleary, David; Pham, Long; Ye, Zhen; Kuan, Samantha; Edsall, Lee; Wu, Yi Chieh; Rasmussen, Matthew D.; Bansal, Mukul S.; Kellis, Manolis; Keller, Cheryl A.; Morrissey, Christapher S.; Mishra, Tejaswini; Jain, Deepti; Dogan, Nergiz; Harris, Robert S.; Cayting, Philip; Kawli, Trupti; Boyle, Alan P.; Euskirchen, Ghia; Kundaje, Anshul; Lin, Shin; Lin, Yiing; Jansen, Camden; Malladi, Venkat S.; Cline, Melissa S.; Erickson, Drew T.; Kirkup, Vanessa M.; Learned, Katrina; Sloan, Cricket A.; Rosenbloom, Kate R.; De Sousa, Beatriz Lacerda; Beal, Kathryn; Pignatelli, Miguel; Flicek, Paul; Lian, Jin; Kahveci, Tamer; Lee, Dongwon; Kent, W. James; Santos, Miguel Ramalho; Herrero, Javier; Notredame, Cedric; Johnson, Audra; Vong, Shinny; Lee, Kristen; Bates, Daniel; Neri, Fidencio; Diegel, Morgan; Canfield, Theresa; Sabo, Peter J.; Wilken, Matthew S.; Reh, Thomas A.; Giste, Erika; Shafer, Anthony; Kutyavin, Tanya; Haugen, Eric; Dunn, Douglas; Reynolds, Alex P.; Neph, Shane; Humbert, Richard; Hansen, R. Scott; De Bruijn, Marella; Selleri, Licia; Rudensky, Alexander; Josefowicz, Steven; Samstein, Robert; Eichler, Evan E.; Orkin, Stuart H.; Levasseur, Dana; Papayannopoulou, Thalia; Chang, Kai Hsin; Skoultchi, Arthur; Gosh, Srikanta; Disteche, Christine; Treuting, Piper; Wang, Yanli; Weiss, Mitchell J.; Blobel, Gerd A.; Cao, Xiaoyi; Zhong, Sheng; Wang, Ting; Good, Peter J.; Lowdon, Rebecca F.; Adams, Leslie B.; Zhou, Xiao Qiao; Pazin, Michael J.; Feingold, Elise A.; Wold, Barbara; Taylor, James; Mortazavi, Ali; Weissman, Sherman M.; Stamatoyannopoulos, John A.; Snyder, Michael P.; Guigo, Roderic; Gingeras, Thomas R.; Gilbert, David M.; Hardison, Ross C.; Beer, Michael A.; Ren, Bing.

In: Nature, Vol. 515, No. 7527, 20.11.2014, p. 355-364.

Research output: Contribution to journal › Article

Yue, F, Cheng, Y, Breschi, A, Vierstra, J, Wu, W, Ryba, T, Sandstrom, R, Ma, Z, Davis, C, Pope, BD, Shen, Y, Pervouchine, DD, Djebali, S, Thurman, RE, Kaul, R, Rynes, E, Kirilusha, A, Marinov, GK, Williams, BA, Trout, D, Amrhein, H, Fisher-Aylor, K, Antoshechkin, I, DeSalvo, G, See, LH, Fastuca, M, Drenkow, J, Zaleski, C, Dobin, A, Prieto, P, Lagarde, J, Bussotti, G, Tanzer, A, Denas, O, Li, K, Bender, MA, Zhang, M, Byron, R, Groudine, MT, McCleary, D, Pham, L, Ye, Z, Kuan, S, Edsall, L, Wu, YC, Rasmussen, MD, Bansal, MS, Kellis, M, Keller, CA, Morrissey, CS, Mishra, T, Jain, D, Dogan, N, Harris, RS, Cayting, P, Kawli, T, Boyle, AP, Euskirchen, G, Kundaje, A, Lin, S, Lin, Y, Jansen, C, Malladi, VS, Cline, MS, Erickson, DT, Kirkup, VM, Learned, K, Sloan, CA, Rosenbloom, KR, De Sousa, BL, Beal, K, Pignatelli, M, Flicek, P, Lian, J, Kahveci, T, Lee, D, Kent, WJ, Santos, MR, Herrero, J, Notredame, C, Johnson, A, Vong, S, Lee, K, Bates, D, Neri, F, Diegel, M, Canfield, T, Sabo, PJ, Wilken, MS, Reh, TA, Giste, E, Shafer, A, Kutyavin, T, Haugen, E, Dunn, D, Reynolds, AP, Neph, S, Humbert, R, Hansen, RS, De Bruijn, M, Selleri, L, Rudensky, A, Josefowicz, S, Samstein, R, Eichler, EE, Orkin, SH, Levasseur, D, Papayannopoulou, T, Chang, KH, Skoultchi, A, Gosh, S, Disteche, C, Treuting, P, Wang, Y, Weiss, MJ, Blobel, GA, Cao, X, Zhong, S, Wang, T, Good, PJ, Lowdon, RF, Adams, LB, Zhou, XQ, Pazin, MJ, Feingold, EA, Wold, B, Taylor, J, Mortazavi, A, Weissman, SM, Stamatoyannopoulos, JA, Snyder, MP, Guigo, R, Gingeras, TR, Gilbert, DM, Hardison, RC, Beer, MA & Ren, B 2014, 'A comparative encyclopedia of DNA elements in the mouse genome', Nature, vol. 515, no. 7527, pp. 355-364. https://doi.org/10.1038/nature13992

Yue, Feng ; Cheng, Yong ; Breschi, Alessandra ; Vierstra, Jeff ; Wu, Weisheng ; Ryba, Tyrone ; Sandstrom, Richard ; Ma, Zhihai ; Davis, Carrie ; Pope, Benjamin D. ; Shen, Yin ; Pervouchine, Dmitri D. ; Djebali, Sarah ; Thurman, Robert E. ; Kaul, Rajinder ; Rynes, Eric ; Kirilusha, Anthony ; Marinov, Georgi K. ; Williams, Brian A. ; Trout, Diane ; Amrhein, Henry ; Fisher-Aylor, Katherine ; Antoshechkin, Igor ; DeSalvo, Gilberto ; See, Lei Hoon ; Fastuca, Meagan ; Drenkow, Jorg ; Zaleski, Chris ; Dobin, Alex ; Prieto, Pablo ; Lagarde, Julien ; Bussotti, Giovanni ; Tanzer, Andrea ; Denas, Olgert ; Li, Kanwei ; Bender, M. A. ; Zhang, Miaohua ; Byron, Rachel ; Groudine, Mark T. ; McCleary, David ; Pham, Long ; Ye, Zhen ; Kuan, Samantha ; Edsall, Lee ; Wu, Yi Chieh ; Rasmussen, Matthew D. ; Bansal, Mukul S. ; Kellis, Manolis ; Keller, Cheryl A. ; Morrissey, Christapher S. ; Mishra, Tejaswini ; Jain, Deepti ; Dogan, Nergiz ; Harris, Robert S. ; Cayting, Philip ; Kawli, Trupti ; Boyle, Alan P. ; Euskirchen, Ghia ; Kundaje, Anshul ; Lin, Shin ; Lin, Yiing ; Jansen, Camden ; Malladi, Venkat S. ; Cline, Melissa S. ; Erickson, Drew T. ; Kirkup, Vanessa M. ; Learned, Katrina ; Sloan, Cricket A. ; Rosenbloom, Kate R. ; De Sousa, Beatriz Lacerda ; Beal, Kathryn ; Pignatelli, Miguel ; Flicek, Paul ; Lian, Jin ; Kahveci, Tamer ; Lee, Dongwon ; Kent, W. James ; Santos, Miguel Ramalho ; Herrero, Javier ; Notredame, Cedric ; Johnson, Audra ; Vong, Shinny ; Lee, Kristen ; Bates, Daniel ; Neri, Fidencio ; Diegel, Morgan ; Canfield, Theresa ; Sabo, Peter J. ; Wilken, Matthew S. ; Reh, Thomas A. ; Giste, Erika ; Shafer, Anthony ; Kutyavin, Tanya ; Haugen, Eric ; Dunn, Douglas ; Reynolds, Alex P. ; Neph, Shane ; Humbert, Richard ; Hansen, R. Scott ; De Bruijn, Marella ; Selleri, Licia ; Rudensky, Alexander ; Josefowicz, Steven ; Samstein, Robert ; Eichler, Evan E. ; Orkin, Stuart H. ; Levasseur, Dana ; Papayannopoulou, Thalia ; Chang, Kai Hsin ; Skoultchi, Arthur ; Gosh, Srikanta ; Disteche, Christine ; Treuting, Piper ; Wang, Yanli ; Weiss, Mitchell J. ; Blobel, Gerd A. ; Cao, Xiaoyi ; Zhong, Sheng ; Wang, Ting ; Good, Peter J. ; Lowdon, Rebecca F. ; Adams, Leslie B. ; Zhou, Xiao Qiao ; Pazin, Michael J. ; Feingold, Elise A. ; Wold, Barbara ; Taylor, James ; Mortazavi, Ali ; Weissman, Sherman M. ; Stamatoyannopoulos, John A. ; Snyder, Michael P. ; Guigo, Roderic ; Gingeras, Thomas R. ; Gilbert, David M. ; Hardison, Ross C. ; Beer, Michael A. ; Ren, Bing. / A comparative encyclopedia of DNA elements in the mouse genome. In: Nature. 2014 ; Vol. 515, No. 7527. pp. 355-364.

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title = "A comparative encyclopedia of DNA elements in the mouse genome",

abstract = "The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases.",

author = "Feng Yue and Yong Cheng and Alessandra Breschi and Jeff Vierstra and Weisheng Wu and Tyrone Ryba and Richard Sandstrom and Zhihai Ma and Carrie Davis and Pope, {Benjamin D.} and Yin Shen and Pervouchine, {Dmitri D.} and Sarah Djebali and Thurman, {Robert E.} and Rajinder Kaul and Eric Rynes and Anthony Kirilusha and Marinov, {Georgi K.} and Williams, {Brian A.} and Diane Trout and Henry Amrhein and Katherine Fisher-Aylor and Igor Antoshechkin and Gilberto DeSalvo and See, {Lei Hoon} and Meagan Fastuca and Jorg Drenkow and Chris Zaleski and Alex Dobin and Pablo Prieto and Julien Lagarde and Giovanni Bussotti and Andrea Tanzer and Olgert Denas and Kanwei Li and Bender, {M. A.} and Miaohua Zhang and Rachel Byron and Groudine, {Mark T.} and David McCleary and Long Pham and Zhen Ye and Samantha Kuan and Lee Edsall and Wu, {Yi Chieh} and Rasmussen, {Matthew D.} and Bansal, {Mukul S.} and Manolis Kellis and Keller, {Cheryl A.} and Morrissey, {Christapher S.} and Tejaswini Mishra and Deepti Jain and Nergiz Dogan and Harris, {Robert S.} and Philip Cayting and Trupti Kawli and Boyle, {Alan P.} and Ghia Euskirchen and Anshul Kundaje and Shin Lin and Yiing Lin and Camden Jansen and Malladi, {Venkat S.} and Cline, {Melissa S.} and Erickson, {Drew T.} and Kirkup, {Vanessa M.} and Katrina Learned and Sloan, {Cricket A.} and Rosenbloom, {Kate R.} and {De Sousa}, {Beatriz Lacerda} and Kathryn Beal and Miguel Pignatelli and Paul Flicek and Jin Lian and Tamer Kahveci and Dongwon Lee and Kent, {W. James} and Santos, {Miguel Ramalho} and Javier Herrero and Cedric Notredame and Audra Johnson and Shinny Vong and Kristen Lee and Daniel Bates and Fidencio Neri and Morgan Diegel and Theresa Canfield and Sabo, {Peter J.} and Wilken, {Matthew S.} and Reh, {Thomas A.} and Erika Giste and Anthony Shafer and Tanya Kutyavin and Eric Haugen and Douglas Dunn and Reynolds, {Alex P.} and Shane Neph and Richard Humbert and Hansen, {R. Scott} and {De Bruijn}, Marella and Licia Selleri and Alexander Rudensky and Steven Josefowicz and Robert Samstein and Eichler, {Evan E.} and Orkin, {Stuart H.} and Dana Levasseur and Thalia Papayannopoulou and Chang, {Kai Hsin} and Arthur Skoultchi and Srikanta Gosh and Christine Disteche and Piper Treuting and Yanli Wang and Weiss, {Mitchell J.} and Blobel, {Gerd A.} and Xiaoyi Cao and Sheng Zhong and Ting Wang and Good, {Peter J.} and Lowdon, {Rebecca F.} and Adams, {Leslie B.} and Zhou, {Xiao Qiao} and Pazin, {Michael J.} and Feingold, {Elise A.} and Barbara Wold and James Taylor and Ali Mortazavi and Weissman, {Sherman M.} and Stamatoyannopoulos, {John A.} and Snyder, {Michael P.} and Roderic Guigo and Gingeras, {Thomas R.} and Gilbert, {David M.} and Hardison, {Ross C.} and Beer, {Michael A.} and Bing Ren",

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AU - Yue, Feng

AU - Cheng, Yong

AU - Breschi, Alessandra

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AU - Wu, Weisheng

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AU - Sandstrom, Richard

AU - Ma, Zhihai

AU - Davis, Carrie

AU - Pope, Benjamin D.

AU - Shen, Yin

AU - Pervouchine, Dmitri D.

AU - Djebali, Sarah

AU - Thurman, Robert E.

AU - Kaul, Rajinder

AU - Rynes, Eric

AU - Kirilusha, Anthony

AU - Marinov, Georgi K.

AU - Williams, Brian A.

AU - Trout, Diane

AU - Amrhein, Henry

AU - Fisher-Aylor, Katherine

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AU - Drenkow, Jorg

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AU - Prieto, Pablo

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AU - Bussotti, Giovanni

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AU - Denas, Olgert

AU - Li, Kanwei

AU - Bender, M. A.

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AU - Byron, Rachel

AU - Groudine, Mark T.

AU - McCleary, David

AU - Pham, Long

AU - Ye, Zhen

AU - Kuan, Samantha

AU - Edsall, Lee

AU - Wu, Yi Chieh

AU - Rasmussen, Matthew D.

AU - Bansal, Mukul S.

AU - Kellis, Manolis

AU - Keller, Cheryl A.

AU - Morrissey, Christapher S.

AU - Mishra, Tejaswini

AU - Jain, Deepti

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AU - Harris, Robert S.

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AU - Euskirchen, Ghia

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AU - Hansen, R. Scott

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AU - Gosh, Srikanta

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