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1. Spin Coupling Effect on Geometry-Dependent X‑Ray Absorption of Diradicals

Author

Garner, Scott M, Haugen, Eric A, Leone, Stephen R, and Neuscamman, Eric

Subjects
Chemical Sciences, Physical Chemistry, Theoretical and Computational Chemistry, General Chemistry, Chemical sciences, Engineering
Abstract

We theoretically investigate the influence of diradical electron spin coupling on the time-resolved X-ray absorption spectra of the photochemical ring opening of furanone. We predict geometry-dependent carbon K-edge signals involving transitions from core orbitals to both singly and unoccupied molecular orbitals. The most obvious features of the ring opening come from the carbon atom directly involved in the bond breaking through its transition to both the newly formed singly occupied and the available lowest unoccupied molecular orbitals (SOMO and LUMO, respectively). In addition to this primary feature, the singlet spin coupling of four unpaired electrons that arises in the core-to-LUMO states creates additional geometry dependence in some spectral features with both oscillator strengths and relative excitation energies varying observably as a function of the ring opening. We attribute this behavior to a spin-occupancy-induced selection rule, which occurs when singlet spin coupling is enforced in the diradical state. Notably, one of these geometry-sensitive core-to-LUMO transitions excites core electrons from a backbone carbon not involved in the bond breaking, providing a novel nonlocal X-ray probe of chemical dynamics arising from electron spin coupling.

Published
2024

2. Spin Coupling Effect on Geometry-Dependent X-ray Absorption of Diradicals

Author

Garner, Scott M., Haugen, Eric A., Leone, Stephen R., and Neuscamman, Eric

Subjects
Physics - Chemical Physics
Abstract

We theoretically investigate the influence of diradical electron spin coupling on the time-resolved X-ray absorption spectra of the photochemical ring opening of furanone. We predict geometry dependent carbon K-edge signals involving transitions from core orbitals to both singly and unoccupied molecular orbitals. The most obvious features of the ring opening come from the carbon atom directly involved in the bond breaking, through its transition to both the newly formed SOMO and the available LUMO state. In addition to this primary feature, the singlet spin coupling of four unpaired electrons that arises in the core-to-LUMO states creates additional geometry dependence in some spectral features, with both oscillator strengths and relative excitation energies varying observably as a function of the ring opening. We attribute this behavior to a spin-occupancy-induced selection rule, which occurs when singlet spin coupling is enforced in the diradical state. Notably, one of these geometry-sensitive core-to-LUMO transitions excites core electrons from a backbone carbon not involved in the bond breaking, providing a novel non-local X-ray probe of chemical dynamics arising from electron spin coupling., Comment: 52 Pages, 13 Figures

Published
2023

4. Femtosecond Symmetry Breaking and Coherent Relaxation of Methane Cations at the Carbon K-Edge

Author

Ridente, Enrico, Hait, Diptarka, Haugen, Eric A., Ross, Andrew D., Neumark, Daniel M., Head-Gordon, Martin, and Leone, Stephen R.

Subjects
Physics - Chemical Physics, Quantum Physics
Abstract

Understanding the relaxation pathways of photoexcited molecules is essential to gain atomistic level insight into photochemistry. Herein, we perform a time-resolved study of ultrafast molecular symmetry breaking via geometric relaxation (Jahn-Teller distortion) on the methane cation. Attosecond transient absorption spectroscopy with soft X-rays at the carbon K-edge reveals that the distortion occurs within $10\pm 2$ femtoseconds after few-femtosecond strong-field ionization of methane. The distortion activates coherent oscillations in the scissoring vibrational mode of the symmetry broken cation, which are detected in the X-ray signal. These oscillations are damped within $58\pm13$ femtoseconds, as vibrational coherence is lost with the energy redistributing into lower-frequency vibrational modes. This study completely reconstructs the molecular relaxation dynamics of this prototypical example and opens new avenues for exploring complex systems.

Published
2022
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5. Femtosecond symmetry breaking and coherent relaxation of methane cations via x-ray spectroscopy

Author

Ridente, Enrico, Hait, Diptarka, Haugen, Eric A, Ross, Andrew D, Neumark, Daniel M, Head-Gordon, Martin, and Leone, Stephen R

Subjects
Physical Sciences, Chemical Sciences, Physical Chemistry, Theoretical and Computational Chemistry, CSD-01-AMOS-A, CSD-46-All CSGB, CSD-04-GPCP-A, General Science & Technology
Abstract

Understanding the relaxation pathways of photoexcited molecules is essential to gain atomistic-level insight into photochemistry. We performed a time-resolved study of ultrafast molecular symmetry breaking through geometric relaxation (Jahn-Teller distortion) on the methane cation. Attosecond transient absorption spectroscopy with soft x-rays at the carbon K-edge revealed that the distortion occurred within 10 ± 2 femtoseconds after few-femtosecond strong-field ionization of methane. The distortion activated coherent oscillations in the asymmetric scissoring vibrational mode of the symmetry-broken cation, which were detected in the x-ray signal. These oscillations were damped within 58 ± 13 femtoseconds because vibrational coherence was lost with the energy redistributing into lower-frequency vibrational modes. This study completely reconstructs the molecular relaxation dynamics of this prototypical example and opens avenues for exploring complex systems.

Published
2023

6. Ultrafast X-ray Spectroscopy of Intersystem Crossing in Hexafluoroacetylacetone: Chromophore Photophysics and Spectral Changes in the Face of Electron Withdrawing Groups

Author

Haugen, Eric A., Hait, Diptarka, Scutelnic, Valeriu, Xue, Tian, Head-Gordon, Martin, and Leone, Stephen R.

Subjects
Physics - Chemical Physics
Abstract

Intersystem crossings between singlet and triplet states represent a crucial relaxation pathway in photochemical processes. Herein, we probe the intersystem crossing in hexafluoro-acetylacetone with ultrafast X-ray transient absorption spectroscopy at the carbon K-edge. We observe the excited state dynamics following excitation with 266 nm UV light to the $^1\pi\pi^{*}$ (S$_2$) state with element and site-specificity using a broadband soft X-ray pulse produced by high harmonic generation. These results are compared to X-ray spectra computed from orbital optimized density functional theory methods. It is found that the electron withdrawing fluorine atoms decongest the X-ray absorption spectrum by enhancing separation between features originating from different carbon atoms. This facilitates the elucidation of structural and electronic dynamics at the chromophore. The evolution of the core-to-valence resonances at the carbon K-edge reveals an ultrafast population transfer between the $^1n\pi^{*}$ (S$_1$) and $^3\pi\pi^{*}$ (T$_1$) states on a $1.6\pm0.4$ ps timescale, which is similar to the 1.5 ps timescale earlier observed for acetylacetone [J. Am. Chem. Soc. 139, 16576 (2017)]. It therefore appears that terminal fluorination has little influence on the intersystem crossing rate of the acetylacetone chromophore. In addition, the significant role of hydrogen-bond opened and twisted rotational isomers is elucidated in the excited state dynamics by comparison of the experimental transient X-ray spectra with theory.

Published
2022
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7. Ultrafast X‑ray Spectroscopy of Intersystem Crossing in Hexafluoroacetylacetone: Chromophore Photophysics and Spectral Changes in the Face of Electron-Withdrawing Groups

Author

Haugen, Eric A, Hait, Diptarka, Scutelnic, Valeriu, Xue, Tian, Head-Gordon, Martin, and Leone, Stephen R

Subjects
Chemical Sciences, Physical Chemistry, Theoretical and Computational Chemistry, Physical Sciences, Atomic, Molecular and Optical Physics, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Physical Chemistry (incl. Structural), Physical chemistry, Theoretical and computational chemistry, Atomic, molecular and optical physics
Abstract

Intersystem crossings between singlet and triplet states represent a crucial relaxation pathway in photochemical processes. Herein, we probe the intersystem crossing in hexafluoro-acetylacetone with ultrafast X-ray transient absorption spectroscopy at the carbon K-edge. We observe the excited state dynamics following excitation with 266 nm UV light to the 1ππ* (S2) state with element and site-specificity using a broadband soft X-ray pulse produced by high harmonic generation. These results are compared to X-ray spectra computed from orbital optimized density functional theory methods. It is found that the electron-withdrawing fluorine atoms decongest the X-ray absorption spectrum by enhancing separation between features originating from different carbon atoms. This facilitates the elucidation of structural and electronic dynamics at the chromophore. The evolution of the core-to-valence resonances at the carbon K-edge reveals an ultrafast population transfer between the 1nπ* (S1) and 3ππ* (T1) states on a 1.6 ± 0.4 ps time scale, which is similar to the 1.5 ps time scale earlier observed for acetylacetone [ J. Am. Chem. Soc. 2017, 139, 16576-16583, DOI: 10.1021/jacs.7b07532]. It therefore appears that terminal fluorination has little influence on the intersystem crossing rate of the acetylacetone chromophore. In addition, the significant role of hydrogen-bond opened and twisted rotational isomers is elucidated in the excited state dynamics by comparison of the experimental transient X-ray spectra with theory.

Published
2023

8. Jahn-Teller Distortion and Dissociation of CCl$_4^+$ by Transient X-ray Spectroscopy Simultaneously at the Carbon K- and Chlorine L-Edge

Author

Ross, Andrew D., Hait, Diptarka, Scutelnic, Valeriu, Haugen, Eric A., Ridente, Enrico, Balkew, Mikias B., Neumark, Daniel M., Head-Gordon, Martin, and Leone, Stephen R.

Subjects
Physics - Chemical Physics
Abstract

X-ray Transient Absorption Spectroscopy (XTAS) and theoretical calculations are used to study CCl$_4^+$ prepared by 800 nm strong-field ionization. XTAS simultaneously probes atoms at the carbon K-edge (280-300 eV) and chlorine L-edge (195-220 eV). Comparison of experiment to X-ray spectra computed by orbital-optimized density functional theory (OO-DFT) indicates that after ionization, CCl$_4^+$ undergoes symmetry breaking driven by Jahn-Teller distortion away from the initial tetrahedral structure (T$_d$) in 6$\pm$2 fs. The resultant symmetry-broken covalently bonded form subsequently separates to a noncovalently bound complex between CCl$_3^+$ and Cl over 90$\pm$10 fs, which is again predicted by theory. Finally, after more than 800 fs, L-edge signals for atomic Cl are observed, indicating dissociation to free CCl$_3^+$ and Cl. The results for Jahn-Teller distortion to the symmetry-broken form of CCl$_4^+$ and formation of the Cl -- CCl$_3^+$ complex characterize previously unobserved new species along the route to dissociation.

Published
2022
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10. Jahn-Teller distortion and dissociation of CCl 4 + by transient X-ray spectroscopy simultaneously at the carbon K- and chlorine L-edge

Author

Ross, Andrew D, Hait, Diptarka, Scutelnic, Valeriu, Haugen, Eric A, Ridente, Enrico, Balkew, Mikias B, Neumark, Daniel M, Head-Gordon, Martin, and Leone, Stephen R

Subjects
Chemical Sciences, Physical Chemistry, CSD-04-GPCP-A, CSD-46-All CSGB, Chemical sciences
Abstract

X-ray Transient Absorption Spectroscopy (XTAS) and theoretical calculations are used to study CCl4 + prepared by 800 nm strong-field ionization. XTAS simultaneously probes atoms at the carbon K-edge (280-300 eV) and chlorine L-edge (195-220 eV). Comparison of experiment to X-ray spectra computed by orbital-optimized density functional theory (OO-DFT) indicates that after ionization, CCl4 + undergoes symmetry breaking driven by Jahn-Teller distortion away from the initial tetrahedral structure (Td) in 6 ± 2 fs. The resultant symmetry-broken covalently bonded form subsequently separates to a noncovalently bound complex between CCl3 + and Cl over 90 ± 10 fs, which is again predicted by theory. Finally, after more than 800 fs, L-edge signals for atomic Cl are observed, indicating dissociation to free CCl3 + and Cl. The results for Jahn-Teller distortion to the symmetry-broken form of CCl4 + and formation of the Cl-CCl+ 3 complex characterize previously unobserved new species along the route to dissociation.

Published
2022

11. Jahn-Teller Distortion and Dissociation of CCl$_4^+$ by Transient X-ray Spectroscopy Simultaneously at the Carbon K- and Chlorine L-Edge

Author

Ross, Andrew D, Hait, Diptarka, Scutelnic, Valeriu, Haugen, Eric A, Ridente, Enrico, Balkew, Mikias B, Neumark, Daniel M, Head-Gordon, Martin, and Leone, Stephen R

Subjects
physics.chem-ph
Abstract

X-ray Transient Absorption Spectroscopy (XTAS) and theoretical calculationsare used to study CCl$_4^+$ prepared by 800 nm strong-field ionization. XTASsimultaneously probes atoms at the carbon K-edge (280-300 eV) and chlorineL-edge (195-220 eV). Comparison of experiment to X-ray spectra computed byorbital-optimized density functional theory (OO-DFT) indicates that afterionization, CCl$_4^+$ undergoes symmetry breaking driven by Jahn-Tellerdistortion away from the initial tetrahedral structure (T$_d$) in 6$\pm$2 fs.The resultant symmetry-broken covalently bonded form subsequently separates toa noncovalently bound complex between CCl$_3^+$ and Cl over 90$\pm$10 fs, whichis again predicted by theory. Finally, after more than 800 fs, L-edge signalsfor atomic Cl are observed, indicating dissociation to free CCl$_3^+$ and Cl.The results for Jahn-Teller distortion to the symmetry-broken form of CCl$_4^+$and formation of the Cl -- CCl$_3^+$ complex characterize previously unobservednew species along the route to dissociation.

Published
2022

12. Accurate prediction of core-level spectra of radicals at density functional theory cost via square gradient minimization and recoupling of mixed configurations

Author

Hait, Diptarka, Haugen, Eric A., Yang, Zheyue, Oosterbaan, Katherine J., Leone, Stephen R., and Head-Gordon, Martin

Subjects
Physics - Chemical Physics, Physics - Atomic Physics
Abstract

State-specific orbital optimized approaches are more accurate at predicting core-level spectra than traditional linear-response protocols, but their utility had been restricted on account of the risk of `variational collapse' down to the ground state. We employ the recently developed square gradient minimization (SGM, J. Chem. Theory Comput. 16, 1699-1710, 2020) algorithm to reliably avoid variational collapse and study the effectiveness of orbital optimized density functional theory (DFT) at predicting second period element 1s core-level spectra of open-shell systems. Several density functionals (including SCAN, B3LYP and $\omega$B97X-D3) are found to predict excitation energies from the core to singly occupied levels to high accuracy ($\le 0.3$ eV RMS error), against available experimental data. Higher excited states are however more challenging by virtue of being intrinsically multiconfigurational. We thus present a CI inspired route to self-consistently recouple single determinant mixed configurations obtained from DFT, in order to obtain approximate doublet states. This recoupling scheme is used to predict the C K-edge spectra of the allyl radical, the O K-edge spectra of CO$^+$ and the N K-edge of NO$_2$ to high accuracy relative to experiment, indicating substantial promise in using this approach for computation of core-level spectra for doublet species (vs more traditional time dependent DFT, EOM-CCSD or using unrecoupled mixed configurations). We also present general guidelines for computing core-excited states from orbital optimized DFT., Comment: Added more data

Published
2020
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13. X-ray transient absorption reveals the 1Au (nπ*) state of pyrazine in electronic relaxation.

Author

Scutelnic, Valeriu, Tsuru, Shota, Pápai, Mátyás, Yang, Zheyue, Epshtein, Michael, Xue, Tian, Haugen, Eric, Kobayashi, Yuki, Krylov, Anna I, Møller, Klaus B, Coriani, Sonia, and Leone, Stephen R

Abstract

Electronic relaxation in organic chromophores often proceeds via states not directly accessible by photoexcitation. We report on the photoinduced dynamics of pyrazine that involves such states, excited by a 267 nm laser and probed with X-ray transient absorption spectroscopy in a table-top setup. In addition to the previously characterized 1B2u (ππ*) (S2) and 1B3u (nπ*) (S1) states, the participation of the optically dark 1Au (nπ*) state is assigned by a combination of experimental X-ray core-to-valence spectroscopy, electronic structure calculations, nonadiabatic dynamics simulations, and X-ray spectral computations. Despite 1Au (nπ*) and 1B3u (nπ*) states having similar energies at relaxed geometry, their X-ray absorption spectra differ largely in transition energy and oscillator strength. The 1Au (nπ*) state is populated in 200 ± 50 femtoseconds after electronic excitation and plays a key role in the relaxation of pyrazine to the ground state.

Published
2021

14. Ultraviolet Induced Photophysics of Organic Molecules Probed with Ultrafast X-ray Spectroscopy

Author

Haugen, Eric Arne

Subjects
Chemistry, Physical chemistry
Abstract

The measurement of ultrafast chemical dynamics has long been a goal of physical chemists. The ability to resolve both molecular and electronic dynamics occurring within a chemical reaction in real-time, with atomic specificity, represents a significant stepping stone towards resolving chemical dynamics. In this dissertation, ultrafast x-ray transient absorption spectroscopy will be utilized to elucidate photo-induced dynamics in a variety of molecular systems, with a focus on molecules excited with ultraviolet light. The dissertation will outline an experimental apparatus used to conducted attosecond soft x-ray transient absorption spectroscopy. Furthermore, the design and implementation of a novel ultraviolet pump arm, delivering 15 - 25 fs deep ultraviolet pulses (250 - 290 nm) for these transient absorption measurements will also be detailed. Several different molecular systems will be studied within this dissertation. First off, the intersystem crossing mechanism of hexafluoroacetylacetone will be discussed in addition to the influence of the fluorine atoms on the ultrafast photophysics. Here it was found that the terminal fluorine atoms play only a minor role in the ensuing dynamics but nevertheless disentangle the spectral signals of the x-ray spectrum. Following this, preliminary results on photoexcited butadiene will shed light on the predominant pathway for its non-adiabatic relaxation. Next the passage through a conical intersection and thereby directly mapping the never before resolved internal conversion of acetylacetone will be displayed, demonstrating the viability of the short ultraviolet pump pulse to resolve rapid dynamics in organic chromophores. Following this, the ultrafast dissociation of allyl iodide and the real-time observation of a resonance stabilization occurring within a molecular system will be studied. Molecular vibrations are clearly observed in the transient x-ray measurement of the allyl iodide dissociation, providing information towards additional mechanisms driving the relaxation process. Lastly the ultrafast Jahn-Teller distortion within the methane cation will be measured, resolving the Jahn-Teller effect in real time in the prototypical methane molecule. Here it was found that the methane cation underwent Jahn-Teller distortion in 10 fs and displayed coherent vibrational motion for ≈ 60 fs before these vibrations were dissipated via a intramolecular vibrational energy redistribution mechanism.

Published
2024

16. Capturing ring opening in photoexcited enolic acetylacetone upon hydrogen bond dissociation by ultrafast electron diffraction

Author

Leone, Stephen, primary, Scutelnic, Valeriu, additional, Tikhonov, Denis, additional, Poullain, Sonia Marggi, additional, Haugen, Eric, additional, Attar, Andrew, additional, Barreau, Lou, additional, Chang, Kristina, additional, Fidler, Ashley, additional, Gaynor, James, additional, Lin, Yen-Cheng, additional, Yang, Jie, additional, Champenois, Elio, additional, Wang, Xijie, additional, Shen, Xiaozhe, additional, Luo, Duan, additional, Ji, Fuhao, additional, Weathersby, Stephen, additional, Vishnevsky, Yury, additional, Schnell, Melanie, additional, Wolf, Thomas, additional, and Lin, Ming-Fu, additional

Published
2024
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17. 52 Genetic Loci Influencing Myocardial Mass

Author

van der Harst, Pim, van Setten, Jessica, Verweij, Niek, Vogler, Georg, Franke, Lude, Maurano, Matthew T, Wang, Xinchen, Leach, Irene Mateo, Eijgelsheim, Mark, Sotoodehnia, Nona, Hayward, Caroline, Sorice, Rossella, Meirelles, Osorio, Lyytikäinen, Leo-Pekka, Polašek, Ozren, Tanaka, Toshiko, Arking, Dan E, Ulivi, Sheila, Trompet, Stella, Müller-Nurasyid, Martina, Smith, Albert V, Dörr, Marcus, Kerr, Kathleen F, Magnani, Jared W, Del Greco M., Fabiola, Zhang, Weihua, Nolte, Ilja M, Silva, Claudia T, Padmanabhan, Sandosh, Tragante, Vinicius, Esko, Tõnu, Abecasis, Gonçalo R, Adriaens, Michiel E, Andersen, Karl, Barnett, Phil, Bis, Joshua C, Bodmer, Rolf, Buckley, Brendan M, Campbell, Harry, Cannon, Megan V, Chakravarti, Aravinda, Chen, Lin Y, Delitala, Alessandro, Devereux, Richard B, Doevendans, Pieter A, Dominiczak, Anna F, Ferrucci, Luigi, Ford, Ian, Gieger, Christian, Harris, Tamara B, Haugen, Eric, Heinig, Matthias, Hernandez, Dena G, Hillege, Hans L, Hirschhorn, Joel N, Hofman, Albert, Hubner, Norbert, Hwang, Shih-Jen, Iorio, Annamaria, Kähönen, Mika, Kellis, Manolis, Kolcic, Ivana, Kooner, Ishminder K, Kooner, Jaspal S, Kors, Jan A, Lakatta, Edward G, Lage, Kasper, Launer, Lenore J, Levy, Daniel, Lundby, Alicia, Macfarlane, Peter W, May, Dalit, Meitinger, Thomas, Metspalu, Andres, Nappo, Stefania, Naitza, Silvia, Neph, Shane, Nord, Alex S, Nutile, Teresa, Okin, Peter M, Olsen, Jesper V, Oostra, Ben A, Penninger, Josef M, Pennacchio, Len A, Pers, Tune H, Perz, Siegfried, Peters, Annette, Pinto, Yigal M, Pfeufer, Arne, Pilia, Maria Grazia, Pramstaller, Peter P, Prins, Bram P, Raitakari, Olli T, Raychaudhuri, Soumya, Rice, Ken M, Rossin, Elizabeth J, Rotter, Jerome I, Schafer, Sebastian, Schlessinger, David, and Schmidt, Carsten O

Subjects
Medical Physiology, Biomedical and Clinical Sciences, Genetics, Heart Disease - Coronary Heart Disease, Cardiovascular, Heart Disease, Biotechnology, Human Genome, 2.1 Biological and endogenous factors, Animals, Cardiomegaly, Genetic Loci, Genome-Wide Association Study, Humans, electrocardiogram, genetic association study, heart failure, left ventricular hypertrophy, QRS, Cardiorespiratory Medicine and Haematology, Public Health and Health Services, Cardiovascular System & Hematology, Cardiovascular medicine and haematology
Abstract

BackgroundMyocardial mass is a key determinant of cardiac muscle function and hypertrophy. Myocardial depolarization leading to cardiac muscle contraction is reflected by the amplitude and duration of the QRS complex on the electrocardiogram (ECG). Abnormal QRS amplitude or duration reflect changes in myocardial mass and conduction, and are associated with increased risk of heart failure and death.ObjectivesThis meta-analysis sought to gain insights into the genetic determinants of myocardial mass.MethodsWe carried out a genome-wide association meta-analysis of 4 QRS traits in up to 73,518 individuals of European ancestry, followed by extensive biological and functional assessment.ResultsWe identified 52 genomic loci, of which 32 are novel, that are reliably associated with 1 or more QRS phenotypes at p < 1 × 10(-8). These loci are enriched in regions of open chromatin, histone modifications, and transcription factor binding, suggesting that they represent regions of the genome that are actively transcribed in the human heart. Pathway analyses provided evidence that these loci play a role in cardiac hypertrophy. We further highlighted 67 candidate genes at the identified loci that are preferentially expressed in cardiac tissue and associated with cardiac abnormalities in Drosophila melanogaster and Mus musculus. We validated the regulatory function of a novel variant in the SCN5A/SCN10A locus in vitro and in vivo.ConclusionsTaken together, our findings provide new insights into genes and biological pathways controlling myocardial mass and may help identify novel therapeutic targets.

Published
2016

18. Index and biological spectrum of human DNase I hypersensitive sites

Author

Meuleman, Wouter, Muratov, Alexander, Rynes, Eric, Halow, Jessica, Lee, Kristen, Bates, Daniel, Diegel, Morgan, Dunn, Douglas, Neri, Fidencio, Teodosiadis, Athanasios, Reynolds, Alex, Haugen, Eric, Nelson, Jemma, Johnson, Audra, Frerker, Mark, Buckley, Michael, Sandstrom, Richard, Vierstra, Jeff, Kaul, Rajinder, and Stamatoyannopoulos, John

Published
2020
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19. Global reference mapping of human transcription factor footprints

Author

Vierstra, Jeff, Lazar, John, Sandstrom, Richard, Halow, Jessica, Lee, Kristen, Bates, Daniel, Diegel, Morgan, Dunn, Douglas, Neri, Fidencio, Haugen, Eric, Rynes, Eric, Reynolds, Alex, Nelson, Jemma, Johnson, Audra, Frerker, Mark, Buckley, Michael, Kaul, Rajinder, Meuleman, Wouter, and Stamatoyannopoulos, John A.

Published
2020
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20. Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

Author

Vierstra, Jeff, Rynes, Eric, Sandstrom, Richard, Zhang, Miaohua, Canfield, Theresa, Hansen, R Scott, Stehling-Sun, Sandra, Sabo, Peter J, Byron, Rachel, Humbert, Richard, Thurman, Robert E, Johnson, Audra K, Vong, Shinny, Lee, Kristen, Bates, Daniel, Neri, Fidencio, Diegel, Morgan, Giste, Erika, Haugen, Eric, Dunn, Douglas, Wilken, Matthew S, Josefowicz, Steven, Samstein, Robert, Chang, Kai-Hsin, Eichler, Evan E, De Bruijn, Marella, Reh, Thomas A, Skoultchi, Arthur, Rudensky, Alexander, Orkin, Stuart H, Papayannopoulou, Thalia, Treuting, Piper M, Selleri, Licia, Kaul, Rajinder, Groudine, Mark, Bender, MA, and Stamatoyannopoulos, John A

Subjects
Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Biological Sciences, Biotechnology, Human Genome, Genetics, Generic health relevance, Animals, Base Sequence, Conserved Sequence, DNA, Deoxyribonuclease I, Evolution, Molecular, Genome, Human, Humans, Mice, Regulatory Sequences, Nucleic Acid, Restriction Mapping, Transcription Factors, General Science & Technology
Abstract

To study the evolutionary dynamics of regulatory DNA, we mapped >1.3 million deoxyribonuclease I-hypersensitive sites (DHSs) in 45 mouse cell and tissue types, and systematically compared these with human DHS maps from orthologous compartments. We found that the mouse and human genomes have undergone extensive cis-regulatory rewiring that combines branch-specific evolutionary innovation and loss with widespread repurposing of conserved DHSs to alternative cell fates, and that this process is mediated by turnover of transcription factor (TF) recognition elements. Despite pervasive evolutionary remodeling of the location and content of individual cis-regulatory regions, within orthologous mouse and human cell types the global fraction of regulatory DNA bases encoding recognition sites for each TF has been strictly conserved. Our findings provide new insights into the evolutionary forces shaping mammalian regulatory DNA landscapes.

Published
2014

21. Comprehensive Transposon Mutant Library of Pseudomonas aeruginosa

Author

Jacobs, Michael A., Alwood, Ashley, Thaipisuttikul, Iyarit, Spencer, David, Haugen, Eric, Ernst, Stephen, Will, Oliver, Kaul, Rajinder, Raymond, Christopher, Levy, Ruth, Chun-Rong, Liu, Guenthner, Donald, Bovee, Donald, Olson, Maynard V., and Manoil, Colin

Published
2003

22. The impact of rare variation on gene expression across tissues

Author

Li, Xin, Kim, Yungil, Tsang, Emily K., Davis, Joe R., Damani, Farhan N., Chiang, Colby, Hess, Gaelen T., Zappala, Zachary, Strober, Benjamin J., Scott, Alexandra J., Li, Amy, Ganna, Andrea, Bassik, Michael C., Merker, Jason D., Aguet, Franois, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Chen, Lin S., Conrad, Donald F., Cox, Nancy J., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D.H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Sul, Jae Hoon, Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Billy Li, Jin, Li, Qin, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, and Zhu, Jingchun

Subjects
Disease susceptibility -- Genetic aspects, Genetic variation -- Observations, Gene expression -- Observations, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Xin Li [1]; Yungil Kim [2]; Emily K. Tsang [1, 3]; Joe R. Davis [1, 4]; Farhan N. Damani [2]; Colby Chiang [5]; Gaelen T. Hess [4]; Zachary Zappala [...]

Published
2017
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23. Dynamic landscape and regulation of RNA editing in mammals

Author

Tan, Meng How, Li, Qin, Shanmugam, Raghuvaran, Piskol, Robert, Kohler, Jennefer, Young, Amy N., Liu, Kaiwen Ivy, Zhang, Rui, Ramaswami, Gokul, Ariyoshi, Kentaro, Gupte, Ankita, Keegan, Liam P., George, Cyril X., Ramu, Avinash, Huang, Ni, Pollina, Elizabeth A., Leeman, Dena S., Rustighi, Alessandra, Goh, Y. P. Sharon, Aguet, Franois, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Cox, Nancy J., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D. H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J., Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Sul, Jae Hoon, Tsang, Emily K., Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zappala, Zachary, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Li, Jin Billy, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Chawla, Ajay, Del Sal, Giannino, Peltz, Gary, Brunet, Anne, Samuel, Charles E., OConnell, Mary A., Walkley, Carl R., and Nishikura, Kazuko

Subjects
Genetic research, Mammals -- Genetic aspects, RNA processing -- Research, Genetic regulation, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Meng How Tan (corresponding author) [1, 2, 3]; Qin Li [1]; Raghuvaran Shanmugam [2, 3]; Robert Piskol [1]; Jennefer Kohler [1]; Amy N. Young [1]; Kaiwen Ivy Liu [3]; [...]

Published
2017
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24. Landscape of X chromosome inactivation across human tissues

Author

Tukiainen, Taru, Villani, Alexandra-Chlo, Yen, Angela, Rivas, Manuel A., Marshall, Jamie L., Satija, Rahul, Aguirre, Matt, Gauthier, Laura, Fleharty, Mark, Kirby, Andrew, Cummings, Beryl B., Castel, Stephane E., Karczewski, Konrad J., Aguet, Franois, Byrnes, Andrea, Ardlie, Kristin G., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Cox, Nancy J., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D. H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J., Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Sul, Jae Hoon, Tsang, Emily K., Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zappala, Zachary, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Li, Jin Billy, Li, Qin, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Regev, Aviv, and Hacohen, Nir

Subjects
Chromosomes -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Taru Tukiainen (corresponding author) [1, 2]; Alexandra-Chlo Villani [2, 3]; Angela Yen [2, 4]; Manuel A. Rivas [1, 2, 5]; Jamie L. Marshall [1, 2]; Rahul Satija [2, 6, [...]

Published
2017
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25. FORGEdb: systematic analysis of candidate causal variants to uncover target genes and mechanisms in complex traits

Author

Breeze, Charles E., primary, Haugen, Eric, additional, Gutierrez-Arcelus, María, additional, Yao, Xiaozheng, additional, Teschendorff, Andrew, additional, Beck, Stephan, additional, Dunham, Ian, additional, Stamatoyannopoulos, John, additional, Franceschini, Nora, additional, Machiela, Mitchell J., additional, and Berndt, Sonja I., additional

Published
2022
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27. Jahn-Teller distortion and dissociation of CCl4 + by transient X-ray spectroscopy simultaneously at the carbon K- and chlorine L-edge.

Author

Ross, Andrew D, Ross, Andrew D, Hait, Diptarka, Scutelnic, Valeriu, Haugen, Eric A, Ridente, Enrico, Balkew, Mikias B, Neumark, Daniel M, Head-Gordon, Martin, Leone, Stephen R, Ross, Andrew D, Ross, Andrew D, Hait, Diptarka, Scutelnic, Valeriu, Haugen, Eric A, Ridente, Enrico, Balkew, Mikias B, Neumark, Daniel M, Head-Gordon, Martin, and Leone, Stephen R

Abstract

X-ray Transient Absorption Spectroscopy (XTAS) and theoretical calculations are used to study CCl4 + prepared by 800 nm strong-field ionization. XTAS simultaneously probes atoms at the carbon K-edge (280-300 eV) and chlorine L-edge (195-220 eV). Comparison of experiment to X-ray spectra computed by orbital-optimized density functional theory (OO-DFT) indicates that after ionization, CCl4 + undergoes symmetry breaking driven by Jahn-Teller distortion away from the initial tetrahedral structure (Td) in 6 ± 2 fs. The resultant symmetry-broken covalently bonded form subsequently separates to a noncovalently bound complex between CCl3 + and Cl over 90 ± 10 fs, which is again predicted by theory. Finally, after more than 800 fs, L-edge signals for atomic Cl are observed, indicating dissociation to free CCl3 + and Cl. The results for Jahn-Teller distortion to the symmetry-broken form of CCl4 + and formation of the Cl-CCl+ 3 complex characterize previously unobserved new species along the route to dissociation.

Published
2022

28. Correction: Jahn-Teller distortion and dissociation of CCl4 + by transient X-ray spectroscopy simultaneously at the carbon K- and chlorine L-edge.

Author

Ross, Andrew D, Ross, Andrew D, Hait, Diptarka, Scutelnic, Valeriu, Haugen, Eric A, Ridente, Enrico, Balkew, Mikias B, Neumark, Daniel M, Head-Gordon, Martin, Leone, Stephen R, Ross, Andrew D, Ross, Andrew D, Hait, Diptarka, Scutelnic, Valeriu, Haugen, Eric A, Ridente, Enrico, Balkew, Mikias B, Neumark, Daniel M, Head-Gordon, Martin, and Leone, Stephen R

Abstract

[This corrects the article DOI: 10.1039/D2SC02402K.].

Published
2022

29. Genetic effects on gene expression across human tissues

Author

Aguet, François, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segrè, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Cox, Nancy J., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frésard, Laure, Gamazon, Eric R., Garrido-Martín, Diego, Gewirtz, Ariel D.H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Im, Hae Kyung, Jo, Brian, Kang, Eun Yong, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muñoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J., Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Sul, Jae Hoon, Tsang, Emily K., Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zappala, Zachary, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Li, Jin Billy, Li, Qin, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, Roger A., Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, James W., Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Brown, Andrew A., Nguyen, Duyen Y., Sullivan, Timothy J., Addington, Anjene, Koester, Susan, Lockhart, Nicole C., Roe, Bryan, Valley, Dana, Gewirtz, Ariel D. H., He, Amy Z., Quon, Gerald, Ripke, Stephan, Shimko, Tyler C., Teran, Nicole A., Zhang, Hailei, Bustamante, Carlos D., and Guigó, Roderic

Published
2017
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30. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

Author

Maurano, Matthew T., Humbert, Richard, Rynes, Eric, Thurman, Robert E., Haugen, Eric, Wang, Hao, Reynolds, Alex P., Sandstrom, Richard, Qu, Hongzhu, Brody, Jennifer, Shafer, Anthony, Neri, Fidencio, Lee, Kristen, Kutyavin, Tanya, Stehling-Sun, Sandra, Johnson, Audra K., Canfield, Theresa K., Giste, Erika, Diegel, Morgan, Bates, Daniel, Hansen, R. Scott, Neph, Shane, Sabo, Peter J., Heimfeld, Shelly, Raubitschek, Antony, Ziegler, Steven, Cotsapas, Chris, Sotoodehnia, Nona, Glass, Ian, Sunyaev, Shamil R., Kaul, Rajinder, and Stamatoyannopoulos, John A.

Published
2012
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31. Associations Between Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants and Risk of Coronavirus Disease 2019 (COVID-19) Hospitalization Among Confirmed Cases in Washington State: A Retrospective Cohort Study

Author

Paredes, Miguel I, primary, Lunn, Stephanie M, additional, Famulare, Michael, additional, Frisbie, Lauren A, additional, Painter, Ian, additional, Burstein, Roy, additional, Roychoudhury, Pavitra, additional, Xie, Hong, additional, Mohamed Bakhash, Shah A, additional, Perez, Ricardo, additional, Lukes, Maria, additional, Ellis, Sean, additional, Sathees, Saraswathi, additional, Mathias, Patrick C, additional, Greninger, Alexander, additional, Starita, Lea M, additional, Frazar, Chris D, additional, Ryke, Erica, additional, Zhong, Weizhi, additional, Gamboa, Luis, additional, Threlkeld, Machiko, additional, Lee, Jover, additional, McDermot, Evan, additional, Truong, Melissa, additional, Nickerson, Deborah A, additional, Bates, Daniel L, additional, Hartman, Matthew E, additional, Haugen, Eric, additional, Nguyen, Truong N, additional, Richards, Joshua D, additional, Rodriguez, Jacob L, additional, Stamatoyannopoulos, John A, additional, Thorland, Eric, additional, Melly, Geoff, additional, Dykema, Philip E, additional, MacKellar, Drew C, additional, Gray, Hannah K, additional, Singh, Avi, additional, Peterson, JohnAric M, additional, Russell, Denny, additional, Torres, Laura Marcela, additional, Lindquist, Scott, additional, Bedford, Trevor, additional, Allen, Krisandra J, additional, and Oltean, Hanna N, additional

Published
2022
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32. Differences in nanoscale organization of regulatory active and inactive human chromatin

Author

Brandstetter, Katharina, primary, Zülske, Tilo, additional, Ragoczy, Tobias, additional, Hörl, David, additional, Guirao-Ortiz, Miguel, additional, Steinek, Clemens, additional, Barnes, Toby, additional, Stumberger, Gabriela, additional, Schwach, Jonathan, additional, Haugen, Eric, additional, Rynes, Eric, additional, Korber, Philipp, additional, Stamatoyannopoulos, John A., additional, Leonhardt, Heinrich, additional, Wedemann, Gero, additional, and Harz, Hartmann, additional

Published
2022
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36. A comparative encyclopedia of DNA elements in the mouse genome

Author

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., Lacerda de Sousa, Beatriz, Beal, Kathryn, Pignatelli, Miguel, Flicek, Paul, Lian, Jin, Kahveci, Tamer, Lee, Dongwon, James Kent, W., Ramalho Santos, Miguel, 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, Scott Hansen, R., 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., and Ren, Bing

Subjects
Man -- Genetic aspects, Genetic research, Human beings -- Genetic aspects, Genomes -- Comparative analysis, Mice -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
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(s): Feng Yue [1, 2]; Yong Cheng [3]; Alessandra Breschi [4]; Jeff Vierstra [5]; Weisheng Wu [6]; Tyrone Ryba [7]; Richard Sandstrom [5]; Zhihai Ma [3]; Carrie Davis [8]; Benjamin [...]

Published
2014
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37. Conservation of trans-acting circuitry during mammalian regulatory evolution

Author

Stergachis, Andrew B., Neph, Shane, Sandstrom, Richard, Haugen, Eric, Reynolds, Alex P., Zhang, Miaohua, Byron, Rachel, Canfield, Theresa, Stelhing-Sun, Sandra, Lee, Kristen, Thurman, Robert E., Vong, Shinny, Bates, Daniel, Neri, Fidencio, Diegel, Morgan, Giste, Erika, Dunn, Douglas, Vierstra, Jeff, Hansen, R. Scott, Johnson, Audra K., Sabo, Peter J., Wilken, Matthew S., Reh, Thomas A., Treuting, Piper M., Kaul, Rajinder, Groudine, Mark, Bender, M. A., Borenstein, Elhanan, and Stamatoyannopoulos, John A.

Subjects
Evolution -- Genetic aspects, Genetic regulation -- Methods, Mammals -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The basic body plan and major physiological axes have been highly conserved during mammalian evolution, yet only a small fraction of the human genome sequence appears to be subject to evolutionary constraint. To quantify cis- versus trans-acting contributions to mammalian regulatory evolution, we performed genomic DNase I footprinting of the mouse genome across 25 cell and tissue types, collectively defining [similar]8.6 million transcription factor (TF) occupancy sites at nucleotide resolution. Here we show that mouse TF footprints conjointly encode a regulatory lexicon that is [similar]95% similar with that derived from human TF footprints. However, only [similar]20% of mouse TF footprints have human orthologues. Despite substantial turnover of the cis-regulatory landscape, nearly half of all pairwise regulatory interactions connecting mouse TF genes have been maintained in orthologous human cell types through evolutionary innovation of TF recognition sequences. Furthermore, the higher-level organization of mouse TF-to-TF connections into cellular network architectures is nearly identical with human. Our results indicate that evolutionary selection on mammalian gene regulation is targeted chiefly at the level of trans-regulatory circuitry, enabling and potentiating cis-regulatory plasticity., Author(s): Andrew B. Stergachis [1]; Shane Neph [1]; Richard Sandstrom [1]; Eric Haugen [1]; Alex P. Reynolds [1]; Miaohua Zhang [2]; Rachel Byron [2]; Theresa Canfield [1]; Sandra Stelhing-Sun [1]; [...]

Published
2014
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38. Associations between SARS-CoV-2 variants and risk of COVID-19 hospitalization among confirmed cases in Washington State: a retrospective cohort study

Author

Paredes, Miguel I., primary, Lunn, Stephanie M., additional, Famulare, Michael, additional, Frisbie, Lauren A., additional, Painter, Ian, additional, Burstein, Roy, additional, Roychoudhury, Pavitra, additional, Xie, Hong, additional, Bakhash, Shah A. Mohamed, additional, Perez, Ricardo, additional, Lukes, Maria, additional, Ellis, Sean, additional, Sathees, Saraswathi, additional, Mathias, Patrick C., additional, Greninger, Alexander, additional, Starita, Lea M., additional, Frazar, Chris D., additional, Ryke, Erica, additional, Zhong, Weizhi, additional, Gamboa, Luis, additional, Threlkeld, Machiko, additional, Lee, Jover, additional, McDermot, Evan, additional, Truong, Melissa, additional, Nickerson, Deborah A., additional, Bates, Daniel L., additional, Hartman, Matthew E., additional, Haugen, Eric, additional, Nguyen, Truong N., additional, Richards, Joshua D., additional, Rodriguez, Jacob L., additional, Stamatoyannopoulos, John A., additional, Thorland, Eric, additional, Melly, Geoff, additional, Dykema, Philip E., additional, MacKellar, Drew C., additional, Gray, Hannah K., additional, Singh, Avi, additional, Peterson, JohnAric M., additional, Russell, Denny, additional, Torres, Laura Marcela, additional, Lindquist, Scott, additional, Bedford, Trevor, additional, Allen, Krisandra J., additional, and Oltean, Hanna N., additional

Published
2021
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39. Integrative analysis of 111 reference human epigenomes

Author

Consortium, Roadmap Epigenomics, Kundaje, Anshul, Meuleman, Wouter, Ernst, Jason, Bilenky, Misha, Yen, Angela, Heravi-Moussavi, Alireza, Kheradpour, Pouya, Zhang, Zhizhuo, Wang, Jianrong, Ziller, Michael J., Whitaker, John W., Ward, Lucas D., Sarkar, Abhishek, Sandstrom, Richard S., Wu, Yi-Chieh, Pfenning, Andreas R., Wang, Xinchen, Claussnitzer, Melina, Liu, Yaping, Harris, Alan R., Epstein, Charles B., Leung, Danny, Hawkins, David R., Hong, Chibo, Mungall, Andrew J., Chuah, Eric, Hansen, Scott R., Bansal, Mukul S., Dixon, Jesse R., Feizi, Soheil, Kim, Ah-Ram, Li, Daofeng, Elliott, GiNell, Neph, Shane J., Polak, Paz, Ray, Pradipta, Siebenthall, Kyle T., Thurman, Robert E., Zhou, Xin, Boyer, Laurie A., De Jager, Philip L., Fisher, Susan J., Li, Wei, McManus, Michael T., Sunyaev, Shamil, Tlsty, Thea D., Wang, Wei, Waterland, Robert A., Costello, Joseph F., Hirst, Martin, Stamatoyannopoulos, John A., Wang, Ting, Amin, Viren, Schultz, Matthew D., Quon, Gerald, Eaton, Matthew L., Pfenning, Andreas, Liu, Melina ClaussnitzerYaping, Coarfa, Cristian, Shoresh, Noam, Gjoneska, Elizabeta, Xie, Wei, Lister, Ryan, Moore, Richard, Tam, Angela, Canfield, Theresa K., Kaul, Rajinder, Sabo, Peter J., Carles, Annaick, Farh, Kai-How, Karlic, Rosa, Kulkarni, Ashwinikumar, Lowdon, Rebecca, Mercer, Tim R., Onuchic, Vitor, Rajagopal, Nisha, Sallari, Richard C., Sinnott-Armstrong, Nicholas A., Stevens, Michael, Wu, Jie, Zhang, Bo, Abdennur, Nezar, Adli, Mazhar, Akerman, Martin, Barrera, Luis, Antosiewicz-Bourget, Jessica, Ballinger, Tracy, Barnes, Michael J., Bates, Daniel, Bell, Robert J. A., Bennett, David A., Bianco, Katherine, Bock, Christoph, Boyle, Patrick, Brinchmann, Jan, Caballero-Campo, Pedro, Camahort, Raymond, Carrasco-Alfonso, Marlene J., Charnecki, Timothy, Chen, Huaming, Chen, Zhao, Cheng, Jeffrey B., Cho, Stephanie, Chu, Andy, Chung, Wen-Yu, Cowan, Chad, Deng, Qixia Athena, Deshpande, Vikram, Diegel, Morgan, Ding, Bo, Durham, Timothy, Echipare, Lorigail, Edsall, Lee, Flowers, David, Genbacev-Krtolica, Olga, Gifford, Casey, Gillespie, Shawn, Giste, Erika, Glass, Ian A., Gnirke, Andreas, Gormley, Matthew, Gu, Hongcang, Gu, Junchen, Hafler, David A., Hangauer, Matthew J., Hariharan, Manoj, Hatan, Meital, Haugen, Eric, He, Yupeng, Heimfeld, Shelly, Herlofsen, Sarah, Hou, Zhonggang, Humbert, Richard, Issner, Robbyn, Jackson, Andrew R., Jia, Haiyang, Jiang, Peng, Johnson, Audra K., Kadlecek, Theresa, Kamoh, Baljit, Kapidzic, Mirhan, Kent, Jim, Kim, Audrey, Kleinewietfeld, Markus, Klugman, Sarit, Krishnan, Jayanth, Kuan, Samantha, Kutyavin, Tanya, Lee, Ah-Young, Lee, Kristen, Li, Jian, Li, Nan, Li, Yan, Ligon, Keith L., Lin, Shin, Lin, Yiing, Liu, Jie, Liu, Yuxuan, Luckey, John C., Ma, Yussanne P., Maire, Cecile, Marson, Alexander, Mattick, John S., Mayo, Michael, McMaster, Michael, Metsky, Hayden, Mikkelsen, Tarjei, Miller, Diane, Miri, Mohammad, Mukame, Eran, Nagarajan, Raman P., Neri, Fidencio, Nery, Joseph, Nguyen, Tung, OʼGeen, Henriette, Paithankar, Sameer, Papayannopoulou, Thalia, Pelizzola, Mattia, Plettner, Patrick, Propson, Nicholas E., Raghuraman, Sriram, Raney, Brian J., Raubitschek, Anthony, Reynolds, Alex P., Richards, Hunter, Riehle, Kevin, Rinaudo, Paolo, Robinson, Joshua F., Rockweiler, Nicole B., Rosen, Evan, Rynes, Eric, Schein, Jacqueline, Sears, Renee, Sejnowski, Terrence, Shafer, Anthony, Shen, Li, Shoemaker, Robert, Sigaroudinia, Mahvash, Slukvin, Igor, Stehling-Sun, Sandra, Stewart, Ron, Subramanian, Sai Lakshmi, Suknuntha, Kran, Swanson, Scott, Tian, Shulan, Tilden, Hannah, Tsai, Linus, Urich, Mark, Vaughn, Ian, Vierstra, Jeff, Vong, Shinny, Wagner, Ulrich, Wang, Hao, Wang, Tao, Wang, Yunfei, Weiss, Arthur, Whitton, Holly, Wildberg, Andre, Witt, Heather, Won, Kyoung-Jae, Xie, Mingchao, Xing, Xiaoyun, Xu, Iris, Xuan, Zhenyu, Ye, Zhen, Yen, Chia-an, Yu, Pengzhi, Zhang, Xian, Zhang, Xiaolan, Zhao, Jianxin, Zhou, Yan, Zhu, Jiang, Zhu, Yun, Ziegler, Steven, Beaudet, Arthur E., Farnham, Peggy J., Haussler, David, Jones, Steven J. M., Marra, Marco A., Thomson, James A., Tsai, Li-Huei, Zhang, Michael Q., Chadwick, Lisa H., Bernstein, Bradley E., Ecker, Joseph R., Meissner, Alexander, Milosavljevic, Aleksandar, Ren, Bing, and Kellis, Manolis

Published
2015
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41. An integrated encyclopedia of DNA elements in the human genome

Author

Dunham, Ian, Kundaje, Anshul, Aldred, Shelley F., Collins, Patrick J., Davis, Carrie A., Doyle, Francis, Epstein, Charles B., Frietze, Seth, Harrow, Jennifer, Kaul, Rajinder, Khatun, Jainab, Lajoie, Bryan R., Landt, Stephen G., Lee, Bum-Kyu, Pauli, Florencia, Rosenbloom, Kate R., Sabo, Peter, Safi, Alexias, Sanyal, Amartya, Shoresh, Noam, Simon, Jeremy M., Song, Lingyun, Trinklein, Nathan D., Altshuler, Robert C., Birney, Ewan, Brown, James B., Cheng, Chao, Djebali, Sarah, Dong, Xianjun, Ernst, Jason, Furey, Terrence S., Gerstein, Mark, Giardine, Belinda, Greven, Melissa, Hardison, Ross C., Harris, Robert S., Herrero, Javier, Hoffman, Michael M., Iyer, Sowmya, Kellis, Manolis, Kheradpour, Pouya, Lassmann, Timo, Li, Qunhua, Lin, Xinying, Marinov, Georgi K., Merkel, Angelika, Mortazavi, Ali, Parker, Stephen C. J., Reddy, Timothy E., Rozowsky, Joel, Schlesinger, Felix, Thurman, Robert E., Wang, Jie, Ward, Lucas D., Whitfield, Troy W., Wilder, Steven P., Wu, Weisheng, Xi, Hualin S., Yip, Kevin Y., Zhuang, Jiali, Bernstein, Bradley E., Green, Eric D., Gunter, Chris, Snyder, Michael, Pazin, Michael J., Lowdon, Rebecca F., Dillon, Laura A. L., Adams, Leslie B., Kelly, Caroline J., Zhang, Julia, Wexler, Judith R., Good, Peter J., Feingold, Elise A., Crawford, Gregory E., Dekker, Job, Elnitski, Laura, Farnham, Peggy J., Giddings, Morgan C., Gingeras, Thomas R., Guigo, Roderic, Hubbard, Timothy J., Kent, W. James, Lieb, Jason D., Margulies, Elliott H., Myers, Richard M., Stamatoyannopoulos, John A., Tenenbaum, Scott A., Weng, Zhiping, White, Kevin P., Wold, Barbara, Yu, Yanbao, Wrobel, John, Risk, Brian A., Gunawardena, Harsha P., Kuiper, Heather C., Maier, Christopher W., Xie, Ling, Chen, Xian, Mikkelsen, Tarjei S., Gillespie, Shawn, Goren, Alon, Ram, Oren, Zhang, Xiaolan, Wang, Li, Issner, Robbyn, Coyne, Michael J., Durham, Timothy, Ku, Manching, Truong, Thanh, Eaton, Matthew L., Dobin, Alex, Tanzer, Andrea, Lagarde, Julien, Lin, Wei, Xue, Chenghai, Williams, Brian A., Zaleski, Chris, Roder, Maik, Kokocinski, Felix, Abdelhamid, Rehab F., Alioto, Tyler, Antoshechkin, Igor, Baer, Michael T., Batut, Philippe, Bell, Ian, Bell, Kimberly, Chakrabortty, Sudipto, Chrast, Jacqueline, Curado, Joao, Derrien, Thomas, Drenkow, Jorg, Dumais, Erica, Dumais, Jackie, Duttagupta, Radha, Fastuca, Megan, Fejes-Toth, Kata, Ferreira, Pedro, Foissac, Sylvain, Fullwood, Melissa J., Gao, Hui, Gonzalez, David, Gordon, Assaf, Howald, Cedric, Jha, Sonali, Johnson, Rory, Kapranov, Philipp, King, Brandon, Kingswood, Colin, Li, Guoliang, Luo, Oscar J., Park, Eddie, Preall, Jonathan B., Presaud, Kimberly, Ribeca, Paolo, Robyr, Daniel, Ruan, Xiaoan, Sammeth, Michael, Sandhu, Kuljeet Singh, Schaeffer, Lorain, See, Lei-Hoon, Shahab, Atif, Skancke, Jorgen, Suzuki, Ana Maria, Takahashi, Hazuki, Tilgner, Hagen, Trout, Diane, Walters, Nathalie, Wang, Huaien, Hayashizaki, Yoshihide, Reymond, Alexandre, Antonarakis, Stylianos E., Hannon, Gregory J., Ruan, Yijun, Carninci, Piero, Sloan, Cricket A., Learned, Katrina, Malladi, Venkat S., Wong, Matthew C., Barber, Galt P., Cline, Melissa S., Dreszer, Timothy R., Heitner, Steven G., Karolchik, Donna, Kirkup, Vanessa M., Meyer, Laurence R., Long, Jeffrey C., Maddren, Morgan, Raney, Brian J., Grasfeder, Linda L., Giresi, Paul G., Battenhouse, Anna, Sheffield, Nathan C., Showers, Kimberly A., London, Darin, Bhinge, Akshay A., Shestak, Christopher, Schaner, Matthew R., Ki Kim, Seul, Zhang, Zhuzhu Z., Mieczkowski, Piotr A., Mieczkowska, Joanna O., Liu, Zheng, McDaniell, Ryan M., Ni, Yunyun, Rashid, Naim U., Kim, Min Jae, Adar, Sheera, Zhang, Zhancheng, Wang, Tianyuan, Winter, Deborah, Keefe, Damian, Iyer, Vishwanath R., Zheng, Meizhen, Wang, Ping, Gertz, Jason, Vielmetter, Jost, Partridge, E., Varley, Katherine E., Gasper, Clarke, Bansal, Anita, Pepke, Shirley, Jain, Preti, Amrhein, Henry, Bowling, Kevin M., Anaya, Michael, Cross, Marie K., Muratet, Michael A., Newberry, Kimberly M., McCue, Kenneth, Nesmith, Amy S., Fisher-Aylor, Katherine I., Pusey, Barbara, DeSalvo, Gilberto, Parker, Stephanie L., Balasubramanian, Sreeram, Davis, Nicholas S., Meadows, Sarah K., Eggleston, Tracy, Newberry, J. Scott, Levy, Shawn E., Absher, Devin M., Wong, Wing H., Blow, Matthew J., Visel, Axel, Pennachio, Len A., Petrykowska, Hanna M., Abyzov, Alexej, Aken, Bronwen, Barrell, Daniel, Barson, Gemma, Berry, Andrew, Bignell, Alexandra, Boychenko, Veronika, Bussotti, Giovanni, Davidson, Claire, Despacio-Reyes, Gloria, Diekhans, Mark, Ezkurdia, Iakes, Frankish, Adam, Gilbert, James, Gonzalez, Jose Manuel, Griffiths, Ed, Harte, Rachel, Hendrix, David A., Hunt, Toby, Jungreis, Irwin, Kay, Mike, Khurana, Ekta, Leng, Jing, Lin, Michael F., Loveland, Jane, Lu, Zhi, Manthravadi, Deepa, Mariotti, Marco, Mudge, Jonathan, Mukherjee, Gaurab, Notredame, Cedric, Pei, Baikang, Rodriguez, Jose Manuel, Saunders, Gary, Sboner, Andrea, Searle, Stephen, Sisu, Cristina, Snow, Catherine, Steward, Charlie, Tapanari, Electra, Tress, Michael L., van Baren, Marijke J., Washietl, Stefan, Wilming, Laurens, Zadissa, Amonida, Zhang, Zhengdong, Brent, Michael, Haussler, David, Valencia, Alfonso, Addleman, Nick, Alexander, Roger P., Auerbach, Raymond K., Balasubramanian, Suganthi, Bettinger, Keith, Bhardwaj, Nitin, Boyle, Alan P., Cao, Alina R., Cayting, Philip, Charos, Alexandra, Cheng, Yong, Eastman, Catharine, Euskirchen, Ghia, Fleming, Joseph D., Grubert, Fabian, Habegger, Lukas, Hariharan, Manoj, Harmanci, Arif, Iyengar, Sushma, Jin, Victor X., Karczewski, Konrad J., Kasowski, Maya, Lacroute, Phil, Lam, Hugo, Lamarre-Vincent, Nathan, Lian, Jin, Lindahl-Allen, Marianne, Min, Renqiang, Miotto, Benoit, Monahan, Hannah, Moqtaderi, Zarmik, Mu, Xinmeng J., Ouyang, Zhengqing, Patacsil, Dorrelyn, Raha, Debasish, Ramirez, Lucia, Reed, Brian, Shi, Minyi, Slifer, Teri, Witt, Heather, Wu, Linfeng, Xu, Xiaoqin, Yan, Koon-Kiu, Yang, Xinqiong, Struhl, Kevin, Weissman, Sherman M., Penalva, Luiz O., Karmakar, Subhradip, Bhanvadia, Raj R., Choudhury, Alina, Domanus, Marc, Ma, Lijia, Moran, Jennifer, Victorsen, Alec, Auer, Thomas, Centanin, Lazaro, Eichenlaub, Michael, Gruhl, Franziska, Heermann, Stephan, Hoeckendorf, Burkhard, Inoue, Daigo, Kellner, Tanja, Kirchmaier, Stephan, Mueller, Claudia, Reinhardt, Robert, Schertel, Lea, Schneider, Stephanie, Sinn, Rebecca, Wittbrodt, Beate, Wittbrodt, Jochen, Partridge, E. Christopher, Jain, Gaurav, Balasundaram, Gayathri, Bates, Daniel L., Byron, Rachel, Canfield, Theresa K., Diegel, Morgan J., Dunn, Douglas, Ebersol, Abigail K., Frum, Tristan, Garg, Kavita, Gist, Erica, Hansen, R. Scott, Boatman, Lisa, Haugen, Eric, Humbert, Richard, Johnson, Audra K., Johnson, Ericka M., Kutyavin, Tattyana V., Lee, Kristen, Lotakis, Dimitra, Maurano, Matthew T., Neph, Shane J., Neri, Fiedencio V., Nguyen, Eric D., Qu, Hongzhu, Reynolds, Alex P., Roach, Vaughn, Rynes, Eric, Sanchez, Minerva E., Sandstrom, Richard S., Shafer, Anthony O., Stergachis, Andrew B., Thomas, Sean, Vernot, Benjamin, Vierstra, Jeff, Vong, Shinny, Weaver, Molly A., Yan, Yongqi, Zhang, Miaohua, Akey, Joshua M., Bender, Michael, Dorschner, Michael O., Groudine, Mark, MacCoss, Michael J., Navas, Patrick, Stamatoyannopoulos, George, Beal, Kathryn, Brazma, Alvis, Flicek, Paul, Johnson, Nathan, Lukk, Margus, Luscombe, Nicholas M., Sobral, Daniel, Vaquerizas, Juan M., Batzoglou, Serafim, Sidow, Arend, Hussami, Nadine, Kyriazopoulou-Panagiotopoulou, Sofia, Libbrecht, Max W., Schaub, Marc A., Miller, Webb, Bickel, Peter J., Banfai, Balazs, Boley, Nathan P., Huang, Haiyan, Li, Jingyi Jessica, Noble, William Stafford, Bilmes, Jeffrey A., Buske, Orion J., Sahu, Avinash D., Kharchenko, Peter V., Park, Peter J., Baker, Dannon, Taylor, James, and Lochovsky, Lucas

Subjects
Genetic research, Human genome -- Research, Genetic transcription -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research., Author(s): The ENCODE Project Consortium; Overall coordination (data analysis coordination); Ian Dunham [2]; Anshul Kundaje [3, 82]; Data production leads (data production); Shelley F. Aldred [4]; Patrick J. Collins [4]; [...]

Published
2012
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42. The accessible chromatin landscape of the human genome

Author

Thurman, Robert E., Rynes, Eric, Humbert, Richard, Vierstra, Jeff, Maurano, Matthew T., Haugen, Eric, Sheffield, Nathan C., Stergachis, Andrew B., Vernot, Benjamin, Garg, Kavita, John, Sam, Sandstrom, Richard, Bates, Daniel, Boatman, Lisa, Canfield, Theresa K., Diegel, Morgan, Dunn, Douglas, Ebersol, Abigail K., Frum, Tristan, Giste, Erika, Johnson, Audra K., Johnson, Ericka M., Kutyavin, Tanya, Lajoie, Bryan, Lee, Bum-Kyu, Lee, Kristen, London, Darin, Lotakis, Dimitra, Neph, Shane, Neri, Fidencio, Nguyen, Eric D., Qu, Hongzhu, Reynolds, Alex P., Roach, Vaughn, Safi, Alexias, Sanchez, Minerva E., Sanyal, Amartya, Shafer, Anthony, Simon, Jeremy M., Song, Lingyun, Vong, Shinny, Weaver, Molly, Yan, Yongqi, Zhang, Zhancheng, Zhang, Zhuzhu, Lenhard, Boris, Tewari, Muneesh, Dorschner, Michael O., Hansen, R. Scott, Navas, Patrick A., Stamatoyannopoulos, George, Iyer, Vishwanath R., Lieb, Jason D., Sunyaev, Shamil R., Akey, Joshua M., Sabo, Peter J., Kaul, Rajinder, Furey, Terrence S., Dekker, Job, Crawford, Gregory E., and Stamatoyannopoulos, John A.

Subjects
Chromatin -- Physiological aspects, DNA -- Physiological aspects, Genetic research, Human genome -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify [similar]2.9 million DHSs that encompass virtually all known experimentally validated cis-regulatory sequences and expose a vast trove of novel elements, most with highly cell-selective regulation. Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns. We connect [similar]580,000 distal DHSs with their target promoters, revealing systematic pairing of different classes of distal DHSs and specific promoter types. Patterning of chromatin accessibility at many regulatory regions is organized with dozens to hundreds of co-activated elements, and the transcellular DNase I sensitivity pattern at a given region can predict cell-type-specific functional behaviours. The DHS landscape shows signatures of recent functional evolutionary constraint. However, the DHS compartment in pluripotent and immortalized cells exhibits higher mutation rates than that in highly differentiated cells, exposing an unexpected link between chromatin accessibility, proliferative potential and patterns of human variation., Author(s): Robert E. Thurman [1, 13]; Eric Rynes [1, 13]; Richard Humbert [1, 13]; Jeff Vierstra [1]; Matthew T. Maurano [1]; Eric Haugen [1]; Nathan C. Sheffield [2]; Andrew B. [...]

Published
2012
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43. An expansive human regulatory lexicon encoded in transcription factor footprints

Author

Neph, Shane, Vierstra, Jeff, Stergachis, Andrew B., Reynolds, Alex P., Haugen, Eric, Vernot, Benjamin, Thurman, Robert E., John, Sam, Sandstrom, Richard, Johnson, Audra K., Maurano, Matthew T., Humbert, Richard, Rynes, Eric, Vong, Shinny, Lee, Kristen, Bates, Daniel, Diegel, Morgan, Roach, Vaughn, Dunn, Douglas, Neri, Jun, Schafer, Anthony, Hansen, R. Scott, Kutyavin, Tanya, Giste, Erika, Weaver, Molly, Canfield, Theresa, Sabo, Peter, Zhang, Miaohua, Balasundaram, Gayathri, Byron, Rachel, MacCoss, Michael J., Akey, Joshua M., Bender, M. A., Groudine, Mark, Kaul, Rajinder, and Stamatoyannopoulos, John A.

Subjects
Genetic research, Genetic regulation -- Research, Transcription factors -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting across 41 diverse cell and tissue types, we detected 45 million transcription factor occupancy events within regulatory regions, representing differential binding to 8.4 million distinct short sequence elements. Here we show that this small genomic sequence compartment, roughly twice the size of the exome, encodes an expansive repertoire of conserved recognition sequences for DNA-binding proteins that nearly doubles the size of the human cis-regulatory lexicon. We find that genetic variants affecting allelic chromatin states are concentrated in footprints, and that these elements are preferentially sheltered from DNA methylation. High-resolution DNase I cleavage patterns mirror nucleotide-level evolutionary conservation and track the crystallographic topography of protein-DNA interfaces, indicating that transcription factor structure has been evolutionarily imprinted on the human genome sequence. We identify a stereotyped 50-base-pair footprint that precisely defines the site of transcript origination within thousands of human promoters. Finally, we describe a large collection of novel regulatory factor recognition motifs that are highly conserved in both sequence and function, and exhibit cell-selective occupancy patterns that closely parallel major regulators of development, differentiation and pluripotency., Author(s): Shane Neph [1, 7]; Jeff Vierstra [1, 7]; Andrew B. Stergachis [1, 7]; Alex P. Reynolds [1, 7]; Eric Haugen [1]; Benjamin Vernot [1]; Robert E. Thurman [1]; Sam [...]

Published
2012
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44. MOUSE GENOMICS: Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

Author

Vierstra, Jeff, Rynes, Eric, Sandstrom, Richard, Zhang, Miaohua, Canfield, Theresa, Hansen, Scott R., Stehling-Sun, Sandra, Sabo, Peter J., Byron, Rachel, Humbert, Richard, Thurman, Robert E., Johnson, Audra K., Vong, Shinny, Lee, Kristen, Bates, Daniel, Neri, Fidencio, Diegel, Morgan, Giste, Erika, Haugen, Eric, Dunn, Douglas, Wilken, Matthew S., Josefowicz, Steven, Samstein, Robert, Chang, Kai-Hsin, Eichler, Evan E., De Bruijn, Marella, Reh, Thomas A., Skoultchi, Arthur, Rudensky, Alexander, Orkin, Stuart H., Papayannopoulou, Thalia, Treuting, Piper M., Selleri, Licia, Kaul, Rajinder, Groudine, Mark, Bender, M. A., and Stamatoyannopoulos, John A.

Published
2014
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49. Prognostic value of dobutamine stress echocardiography in patients with chronic kidney disease

Author

Bergeron, SeBastien, Hillis, Graham S., Haugen, Eric N., Oh, Jae K., Bailey, Kent R., and Pellikka, Patricia A.

Subjects
Kidney diseases -- Care and treatment, Kidney diseases -- Prognosis, Health
Abstract

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ahj.2006.11.012 Byline: Sebastien Bergeron (a), Graham S. Hillis (a), Eric N. Haugen (b), Jae K. Oh (a), Kent R. Bailey (c), Patricia A. Pellikka (a) Abstract: Although dobutamine stress echocardiography (DSE) is cited in clinical guidelines for the evaluation of patients with chronic kidney disease (CKD), there are limited data regarding its prognostic utility in this setting. The current study assesses the prognostic value of DSE in patients with CKD. Author Affiliation: (a) Division of Cardiovascular Diseases, Mayo Clinic Rochester, MN (b) Division of Nephrology, Mayo Clinic Rochester, MN (c) Department of Biostatistics, Mayo Clinic Rochester, MN Article History: Received 16 August 2006; Accepted 21 November 2006 Article Note: (footnote) Dr Bergeron was supported by a grant from Laval University, Quebec, Canada, and Dr Hillis by a grant from the British Heart Foundation. The study was supported by a grant from the Mayo Foundation.

Published
2007

50. The DNA sequence, annotation and analysis of human chromosome 3

Author

Muzny, Donna M., Scherer, Steven E., Kaul, Rajinder, Wang, Jing, Yu, Jun, Sudbrak, Ralf, Buhay, Christian J., Chen, Rui, Cree, Andrew, Ding, Yan, Dugan-Rocha, Shannon, Gill, Rachel, Gunaratne, Preethi, Harris, R. Alan, Hawes, Alicia C., Hernandez, Judith, Hodgson, Anne V., Hume, Jennifer, Jackson, Andrew, Khan, Ziad Mohid, Kovar-Smith, Christie, Lewis, Lora R., Lozado, Ryan J., Metzker, Michael L., Milosavljevic, Aleksandar, Miner, George R., Morgan, Margaret B., Nazareth, Lynne V., Scott, Graham, Sodergren, Erica, Song, Xing-Zhi, Steffen, David, Wei, Sharon, Wheeler, David A., Wright, Mathew W., Worley, Kim C., Yuan, Ye, Zhang, Zhengdong, Adams, Charles Q., Ansari-Lari, M. Ali, Ayele, Mulu, Brown, Mary J., Chen, Guan, Chen, Zhijian, Clendenning, James, Clerc-Blankenburg, Kerstin P., Chen, Runsheng, Chen, Zhu, Davis, Clay, Delgado, Oliver, Dinh, Huyen H., Dong, Wei, Draper, Heather, Ernst, Stephen, Fu, Gang, Gonzalez-Garay, Manuel L., Garcia, Dawn K., Gillett, Will, Gu, Jun, Hao, Bailin, Haugen, Eric, Havlak, Paul, He, Xin, Hennig, Steffen, Hu, Songnian, Huang, Wei, Jackson, Laronda R., Jacob, Leni S., Kelly, Susan H., Kube, Michael, Levy, Ruth, Li, Zhangwan, Liu, Bin, Liu, Jing, Liu, Wen, Lu, Jing, Maheshwari, Manjula, Nguyen, Bao-Viet, Okwuonu, Geoffrey O., Palmeiri, Anthony, Pasternak, Shiran, Perez, Lesette M., Phelps, Karen A., Plopper, Farah J. H., Qiang, Boqin, Raymond, Christopher, Rodriguez, Ruben, Saenphimmachak, Channakhone, Santibanez, Jireh, Shen, Hua, Shen, Yan, Subramanian, Sandhya, Tabor, Paul E., Verduzco, Daniel, Waldron, Lenee, Wang, Jian, Wang, Jun, Wang, Qiaoyan, Williams, Gabrielle A., Wong, Gane K.-S., Yao, Zhijian, Zhang, JingKun, Zhang, Xiuqing, Zhao, Guoping, Zhou, Jianling, Zhou, Yang, contributors, further, Nelson, David, Lehrach, Hans, Reinhardt, Richard, Naylor, Susan L., Yang, Huanming, Olson, Maynard, Weinstock, George, and Gibbs, Richard A.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Donna M. Muzny [1]; Steven E. Scherer (corresponding author) [1]; Rajinder Kaul [2]; Jing Wang [3]; Jun Yu [3]; Ralf Sudbrak [4, 5]; Christian J. Buhay [1]; Rui Chen [...]

Published
2006
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