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3D genomics across the tree of life reveals condensin II as a determinant of architecture type 期刊论文
Science, 2021
作者:  Claire Hoencamp;  Olga Dudchenko;  Ahmed M. O. Elbatsh;  Sumitabha Brahmachari;  Jonne A. Raaijmakers;  Tom van Schaik;  Ángela Sedeño Cacciatore;  Vinícius G. Contessoto;  Roy G. H. P. van Heesbeen;  Bram van den Broek;  Aditya N. Mhaskar;  Hans Teunissen;  Brian Glenn St Hilaire;  David Weisz;  Arina D. Omer;  Melanie Pham;  Zane Colaric;  Zhenzhen Yang;  Suhas S. P. Rao;  Namita Mitra;  Christopher Lui;  Weijie Yao;  Ruqayya Khan;  Leonid L. Moroz;  Andrea Kohn;  Judy St. Leger;  Alexandria Mena;  Karen Holcroft;  Maria Cristina Gambetta;  Fabian Lim;  Emma Farley;  Nils Stein;  Alexander Haddad;  Daniel Chauss;  Ayse Sena Mutlu;  Meng C. Wang;  Neil D. Young;  Evin Hildebrandt;  Hans H. Cheng;  Christopher J. Knight;  Theresa L. U. Burnham;  Kevin A. Hovel;  Andrew J. Beel;  Pierre-Jean Mattei;  Roger D. Kornberg;  Wesley C. Warren;  Gregory Cary;  José Luis Gómez-Skarmeta;  Veronica Hinman;  Kerstin Lindblad-Toh;  Federica Di Palma;  Kazuhiro Maeshima;  Asha S. Multani;  Sen Pathak;  Liesl Nel-Themaat;  Richard R. Behringer;  Parwinder Kaur;  René H. Medema;  Bas van Steensel;  Elzo de Wit;  José N. Onuchic;  Michele Di Pierro;  Erez Lieberman Aiden;  Benjamin D. Rowland
收藏  |  浏览/下载:37/0  |  提交时间:2021/06/07
Observational constraints on warm cloud microphysical processes using machine learning and optimization techniques 期刊论文
Geophysical Research Letters, 2020
作者:  J. Christine Chiu;  C. Kevin Yang;  Peter J. van Leeuwen;  Graham Feingold;  Robert Wood;  Yann Blanchard;  Fan Mei;  Jian Wang
收藏  |  浏览/下载:25/0  |  提交时间:2020/12/22
Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms 期刊论文
Science, 2020
作者:  David E. Gordon;  Joseph Hiatt;  Mehdi Bouhaddou;  Veronica V. Rezelj;  Svenja Ulferts;  Hannes Braberg;  Alexander S. Jureka;  Kirsten Obernier;  Jeffrey Z. Guo;  Jyoti Batra;  Robyn M. Kaake;  Andrew R. Weckstein;  Tristan W. Owens;  Meghna Gupta;  Sergei Pourmal;  Erron W. Titus;  Merve Cakir;  Margaret Soucheray;  Michael McGregor;  Zeynep Cakir;  Gwendolyn Jang;  Matthew J. O’Meara;  Tia A. Tummino;  Ziyang Zhang;  Helene Foussard;  Ajda Rojc;  Yuan Zhou;  Dmitry Kuchenov;  Ruth Hüttenhain;  Jiewei Xu;  Manon Eckhardt;  Danielle L. Swaney;  Jacqueline M. Fabius;  Manisha Ummadi;  Beril Tutuncuoglu;  Ujjwal Rathore;  Maya Modak;  Paige Haas;  Kelsey M. Haas;  Zun Zar Chi Naing;  Ernst H. Pulido;  Ying Shi;  Inigo Barrio-Hernandez;  Danish Memon;  Eirini Petsalaki;  Alistair Dunham;  Miguel Correa Marrero;  David Burke;  Cassandra Koh;  Thomas Vallet;  Jesus A. Silvas;  Caleigh M. Azumaya;  Christian Billesbølle;  Axel F. Brilot;  Melody G. Campbell;  Amy Diallo;  Miles Sasha Dickinson;  Devan Diwanji;  Nadia Herrera;  Nick Hoppe;  Huong T. Kratochvil;  Yanxin Liu;  Gregory E. Merz;  Michelle Moritz;  Henry C. Nguyen;  Carlos Nowotny;  Cristina Puchades;  Alexandrea N. Rizo;  Ursula Schulze-Gahmen;  Amber M. Smith;  Ming Sun;  Iris D. Young;  Jianhua Zhao;  Daniel Asarnow;  Justin Biel;  Alisa Bowen;  Julian R. Braxton;  Jen Chen;  Cynthia M. Chio;  Un Seng Chio;  Ishan Deshpande;  Loan Doan;  Bryan Faust;  Sebastian Flores;  Mingliang Jin;  Kate Kim;  Victor L. Lam;  Fei Li;  Junrui Li;  Yen-Li Li;  Yang Li;  Xi Liu;  Megan Lo;  Kyle E. Lopez;  Arthur A. Melo;  Frank R. Moss;  Phuong Nguyen;  Joana Paulino;  Komal Ishwar Pawar;  Jessica K. Peters;  Thomas H. Pospiech;  Maliheh Safari;  Smriti Sangwan;  Kaitlin Schaefer;  Paul V. Thomas;  Aye C. Thwin;  Raphael Trenker;  Eric Tse;  Tsz Kin Martin Tsui;  Feng Wang;  Natalie Whitis;  Zanlin Yu;  Kaihua Zhang;  Yang Zhang;  Fengbo Zhou;  Daniel Saltzberg;  QCRG Structural Biology Consortium12†;  Anthony J. Hodder;  Amber S. Shun-Shion;  Daniel M. Williams;  Kris M. White;  Romel Rosales;  Thomas Kehrer;  Lisa Miorin;  Elena Moreno;  Arvind H. Patel;  Suzannah Rihn;  Mir M. Khalid;  Albert Vallejo-Gracia;  Parinaz Fozouni;  Camille R. Simoneau;  Theodore L. Roth;  David Wu;  Mohd Anisul Karim;  Maya Ghoussaini;  Ian Dunham;  Francesco Berardi;  Sebastian Weigang;  Maxime Chazal;  Jisoo Park;  James Logue;  Marisa McGrath;  Stuart Weston;  Robert Haupt;  C. James Hastie;  Matthew Elliott;  Fiona Brown;  Kerry A. Burness;  Elaine Reid;  Mark Dorward;  Clare Johnson;  Stuart G. Wilkinson;  Anna Geyer;  Daniel M. Giesel;  Carla Baillie;  Samantha Raggett;  Hannah Leech;  Rachel Toth;  Nicola Goodman;  Kathleen C. Keough;  Abigail L. Lind;  Zoonomia Consortium‡;  Reyna J. Klesh;  Kafi R. Hemphill;  Jared Carlson-Stevermer;  Jennifer Oki;  Kevin Holden;  Travis Maures;  Katherine S. Pollard;  Andrej Sali;  David A. Agard;  Yifan Cheng;  James S. Fraser;  Adam Frost;  Natalia Jura;  Tanja Kortemme;  Aashish Manglik;  Daniel R. Southworth;  Robert M. Stroud;  Dario R. Alessi;  Paul Davies;  Matthew B. Frieman;  Trey Ideker;  Carmen Abate;  Nolwenn Jouvenet;  Georg Kochs;  Brian Shoichet;  Melanie Ott;  Massimo Palmarini;  Kevan M. Shokat;  Adolfo García-Sastre;  Jeremy A. Rassen;  Robert Grosse;  Oren S. Rosenberg;  Kliment A. Verba;  Christopher F. Basler;  Marco Vignuzzi;  Andrew A. Peden;  Pedro Beltrao;  Nevan J. Krogan
收藏  |  浏览/下载:74/0  |  提交时间:2020/12/07
Live-animal imaging of native haematopoietic stem and progenitor cells 期刊论文
NATURE, 2020, 578 (7794) : 278-+
作者:  Gerstung, Moritz;  Jolly, Clemency;  Leshchiner, Ignaty;  Dentro, Stefan C.;  Gonzalez, Santiago;  Rosebrock, Daniel;  Mitchell, Thomas J.;  Rubanova, Yulia;  Anur, Pavana;  Yu, Kaixian;  Tarabichi, Maxime;  Deshwar, Amit;  Wintersinger, Jeff;  Kleinheinz, Kortine;  Vazquez-Garcia, Ignacio;  Haase, Kerstin;  Jerman, Lara;  Sengupta, Subhajit;  Macintyre, Geoff;  Malikic, Salem;  Donmez, Nilgun;  Livitz, Dimitri G.;  Cmero, Marek;  Demeulemeester, Jonas;  Schumacher, Steven;  Fan, Yu;  Yao, Xiaotong;  Lee, Juhee;  Schlesner, Matthias;  Boutros, Paul C.;  Bowtell, David D.;  Zhu, Hongtu;  Getz, Gad;  Imielinski, Marcin;  Beroukhim, Rameen;  Sahinalp, S. Cenk;  Ji, Yuan;  Peifer, Martin;  Markowetz, Florian;  Mustonen, Ville;  Yuan, Ke;  Wang, Wenyi;  Morris, Quaid D.;  Spellman, Paul T.;  Wedge, David C.;  Van Loo, Peter;  Deshwar, Amit G.;  Adams, David J.;  Campbell, Peter J.;  Cao, Shaolong;  Christie, Elizabeth L.;  Cun, Yupeng;  Dawson, Kevin J.;  Drews, Ruben M.;  Eils, Roland;  Fittall, Matthew;  Garsed, Dale W.;  Ha, Gavin;  Lee-Six, Henry;  Martincorena, Inigo;  Oesper, Layla;  Peto, Myron;  Raphael, Benjamin J.;  Salcedo, Adriana;  Shi, Ruian;  Shin, Seung Jun;  Spiro, Oliver;  Stein, Lincoln D.;  Vembu, Shankar;  Wheeler, David A.;  Yang, Tsun-Po
收藏  |  浏览/下载:45/0  |  提交时间:2020/07/03

The biology of haematopoietic stem cells (HSCs) has predominantly been studied under transplantation conditions(1,2). It has been particularly challenging to study dynamic HSC behaviour, given that the visualization of HSCs in the native niche in live animals has not, to our knowledge, been achieved. Here we describe a dual genetic strategy in mice that restricts reporter labelling to a subset of the most quiescent long-term HSCs (LT-HSCs) and that is compatible with current intravital imaging approaches in the calvarial bone marrow(3-5). We show that this subset of LT-HSCs resides close to both sinusoidal blood vessels and the endosteal surface. By contrast, multipotent progenitor cells (MPPs) show greater variation in distance from the endosteum and are more likely to be associated with transition zone vessels. LT-HSCs are not found in bone marrow niches with the deepest hypoxia and instead are found in hypoxic environments similar to those of MPPs. In vivo time-lapse imaging revealed that LT-HSCs at steady-state show limited motility. Activated LT-HSCs show heterogeneous responses, with some cells becoming highly motile and a fraction of HSCs expanding clonally within spatially restricted domains. These domains have defined characteristics, as HSC expansion is found almost exclusively in a subset of bone marrow cavities with bone-remodelling activity. By contrast, cavities with low bone-resorbing activity do not harbour expanding HSCs. These findings point to previously unknown heterogeneity within the bone marrow microenvironment, imposed by the stages of bone turnover. Our approach enables the direct visualization of HSC behaviours and dissection of heterogeneity in HSC niches.


A dual genetic strategy enables the labelling and in vivo imaging of native long-term haematopoietic stem cells in the mouse calvarial bone marrow.


  
Design of an invitro biocatalytic cascade for the manufacture of islatravir 期刊论文
SCIENCE, 2019, 366 (6470) : 1255-+
作者:  Huffman, Mark A.;  Fryszkowska, Anna;  Alvizo, Oscar;  Borra-Garske, Margie;  Campos, Kevin R.;  Canada, Keith A.;  Devine, Paul N.;  Duan, Da;  Forstater, Jacob H.;  Grosser, Shane T.;  Halsey, Holst M.;  Hughes, Gregory J.;  Jo, Junyong;  Joyce, Leo A.;  Kolev, Joshua N.;  Liang, Jack;  Maloney, Kevin M.;  Mann, Benjamin F.;  Marshall, Nicholas M.;  McLaughlin, Mark;  Moore, Jeffrey C.;  Murphy, Grant S.;  Nawrat, Christopher C.;  Nazor, Jovana;  Novick, Scott;  Patel, Niki R.;  Rodriguez-Granillo, Agustina;  Robaire, Sandra A.;  Sherer, Edward C.;  Truppo, Matthew D.;  Whittaker, Aaron M.;  Verma, Deeptak;  Xiao, Li;  Xu, Yingju;  Yang, Hao
收藏  |  浏览/下载:47/0  |  提交时间:2020/02/17
Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders 期刊论文
NATURE COMMUNICATIONS, 2019, 10
作者:  Saffouri, George B.;  Shields-Cutler, Robin R.;  Chen, Jun;  Yang, Yi;  Lekatz, Heather R.;  Hale, Vanessa L.;  Cho, Janice M.;  Battaglioli, Eric J.;  Bhattarai, Yogesh;  Thompson, Kevin J.;  Kalari, Krishna K.;  Behera, Gaurav;  Berry, Jonathan C.;  Peters, Stephanie A.;  Patel, Robin;  Schuetz, Audrey N.;  Faith, Jeremiah J.;  Camilleri, Michael;  Sonnenburg, Justin L.;  Farrugia, Gianrico;  Swann, Jonathan R.;  Grover, Madhusudan;  Knights, Dan;  Kashyap, Purna C.
收藏  |  浏览/下载:16/0  |  提交时间:2019/11/27
Natural, incidental, and engineered nanomaterials and their impacts on the Earth system 期刊论文
SCIENCE, 2019, 363 (6434) : 1414-+
作者:  Hochella, Michael F., Jr.;  Mogk, David W.;  Ranville, James;  Allen, Irving C.;  Luther, George W.;  Marr, Linsey C.;  McGrail, B. Peter;  Murayama, Mitsu;  Qafoku, Nikolla P.;  Rosso, Kevin M.;  Sahai, Nita;  Schroeder, Paul A.;  Vikesland, Peter;  Westerhoff, Paul;  Yang, Yi
收藏  |  浏览/下载:35/0  |  提交时间:2019/11/27
Comprehensive functional genomic resource and integrative model for the human brain 期刊论文
SCIENCE, 2018, 362 (6420) : 1266-+
作者:  Wang, Daifeng;  Liu, Shuang;  Warrell, Jonathan;  Won, Hyejung;  Shi, Xu;  Navarro, Fabio C. P.;  Clarke, Declan;  Gu, Mengting;  Emani, Prashant;  Yang, Yucheng T.;  Xu, Min;  Gandal, Michael J.;  Lou, Shaoke;  Zhang, Jing;  Park, Jonathan J.;  Yan, Chengfei;  Rhie, Suhn Kyong;  Manakongtreecheep, Kasidet;  Zhou, Holly;  Nathan, Aparna;  Peters, Mette;  Mattei, Eugenio;  Fitzgerald, Dominic;  Brunetti, Tonya;  Moore, Jill;  Jiang, Yan;  Girdhar, Kiran;  Hoffman, Gabriel E.;  Kalayci, Selim;  Gumus, Zeynep H.;  Crawford, Gregory E.;  Roussos, Panos;  Akbarian, Schahram;  Jaffe, Andrew E.;  White, Kevin P.;  Weng, Zhiping;  Sestan, Nenad;  Geschwind, Daniel H.;  Knowles, James A.;  Gerstein, Mark B.
收藏  |  浏览/下载:37/0  |  提交时间:2019/11/27
Frontiers in alley cropping: Transformative solutions for temperate agriculture 期刊论文
GLOBAL CHANGE BIOLOGY, 2018, 24 (3) : 883-894
作者:  Wolz, Kevin J.;  Lovell, Sarah T.;  Branham, Bruce E.;  Eddy, William C.;  Keeley, Keefe;  Revord, Ronald S.;  Wander, Michelle M.;  Yang, Wendy H.;  DeLucia, Evan H.
收藏  |  浏览/下载:25/0  |  提交时间:2019/04/09
agroforestry  land-use alternatives  multispecies systems  perennialization  permaculture  polyculture  silvoarable  sustainable agriculture  tree crops  tree-based intercropping  
Fabrication of fillable microparticles and other complex 3D microstructures 期刊论文
SCIENCE, 2017, 357 (6356) : 1138-+
作者:  McHugh, Kevin J.;  Nguyen, Thanh D.;  Linehan, Allison R.;  Yang, David;  Behrens, Adam M.;  Rose, Sviatlana;  Tochka, Zachary L.;  Tzeng, Stephany Y.;  Norman, James J.;  Anselmo, Aaron C.;  Xu, Xian;  Tomasic, Stephanie;  Taylor, Matthew A.;  Lu, Jennifer;  Guarecuco, Rohiverth;  Langer, Robert;  Jaklenec, Ana
收藏  |  浏览/下载:22/0  |  提交时间:2019/11/27