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Eric Lander

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https://www.readbyqxmd.com/read/28070282/the-database-of-the-predicts-projecting-responses-of-ecological-diversity-in-changing-terrestrial-systems-project
#1
Lawrence N Hudson, Tim Newbold, Sara Contu, Samantha L L Hill, Igor Lysenko, Adriana De Palma, Helen R P Phillips, Tamera I Alhusseini, Felicity E Bedford, Dominic J Bennett, Hollie Booth, Victoria J Burton, Charlotte W T Chng, Argyrios Choimes, David L P Correia, Julie Day, Susy Echeverría-Londoño, Susan R Emerson, Di Gao, Morgan Garon, Michelle L K Harrison, Daniel J Ingram, Martin Jung, Victoria Kemp, Lucinda Kirkpatrick, Callum D Martin, Yuan Pan, Gwilym D Pask-Hale, Edwin L Pynegar, Alexandra N Robinson, Katia Sanchez-Ortiz, Rebecca A Senior, Benno I Simmons, Hannah J White, Hanbin Zhang, Job Aben, Stefan Abrahamczyk, Gilbert B Adum, Virginia Aguilar-Barquero, Marcelo A Aizen, Belén Albertos, E L Alcala, Maria Del Mar Alguacil, Audrey Alignier, Marc Ancrenaz, Alan N Andersen, Enrique Arbeláez-Cortés, Inge Armbrecht, Víctor Arroyo-Rodríguez, Tom Aumann, Jan C Axmacher, Badrul Azhar, Adrián B Azpiroz, Lander Baeten, Adama Bakayoko, András Báldi, John E Banks, Sharad K Baral, Jos Barlow, Barbara I P Barratt, Lurdes Barrico, Paola Bartolommei, Diane M Barton, Yves Basset, Péter Batáry, Adam J Bates, Bruno Baur, Erin M Bayne, Pedro Beja, Suzan Benedick, Åke Berg, Henry Bernard, Nicholas J Berry, Dinesh Bhatt, Jake E Bicknell, Jochen H Bihn, Robin J Blake, Kadiri S Bobo, Roberto Bóçon, Teun Boekhout, Katrin Böhning-Gaese, Kevin J Bonham, Paulo A V Borges, Sérgio H Borges, Céline Boutin, Jérémy Bouyer, Cibele Bragagnolo, Jodi S Brandt, Francis Q Brearley, Isabel Brito, Vicenç Bros, Jörg Brunet, Grzegorz Buczkowski, Christopher M Buddle, Rob Bugter, Erika Buscardo, Jörn Buse, Jimmy Cabra-García, Nilton C Cáceres, Nicolette L Cagle, María Calviño-Cancela, Sydney A Cameron, Eliana M Cancello, Rut Caparrós, Pedro Cardoso, Dan Carpenter, Tiago F Carrijo, Anelena L Carvalho, Camila R Cassano, Helena Castro, Alejandro A Castro-Luna, Cerda B Rolando, Alexis Cerezo, Kim Alan Chapman, Matthieu Chauvat, Morten Christensen, Francis M Clarke, Daniel F R Cleary, Giorgio Colombo, Stuart P Connop, Michael D Craig, Leopoldo Cruz-López, Saul A Cunningham, Biagio D'Aniello, Neil D'Cruze, Pedro Giovâni da Silva, Martin Dallimer, Emmanuel Danquah, Ben Darvill, Jens Dauber, Adrian L V Davis, Jeff Dawson, Claudio de Sassi, Benoit de Thoisy, Olivier Deheuvels, Alain Dejean, Jean-Louis Devineau, Tim Diekötter, Jignasu V Dolia, Erwin Domínguez, Yamileth Dominguez-Haydar, Silvia Dorn, Isabel Draper, Niels Dreber, Bertrand Dumont, Simon G Dures, Mats Dynesius, Lars Edenius, Paul Eggleton, Felix Eigenbrod, Zoltán Elek, Martin H Entling, Karen J Esler, Ricardo F de Lima, Aisyah Faruk, Nina Farwig, Tom M Fayle, Antonio Felicioli, Annika M Felton, Roderick J Fensham, Ignacio C Fernandez, Catarina C Ferreira, Gentile F Ficetola, Cristina Fiera, Bruno K C Filgueiras, Hüseyin K Fırıncıoğlu, David Flaspohler, Andreas Floren, Steven J Fonte, Anne Fournier, Robert E Fowler, Markus Franzén, Lauchlan H Fraser, Gabriella M Fredriksson, Geraldo B Freire, Tiago L M Frizzo, Daisuke Fukuda, Dario Furlani, René Gaigher, Jörg U Ganzhorn, Karla P García, Juan C Garcia-R, Jenni G Garden, Ricardo Garilleti, Bao-Ming Ge, Benoit Gendreau-Berthiaume, Philippa J Gerard, Carla Gheler-Costa, Benjamin Gilbert, Paolo Giordani, Simonetta Giordano, Carly Golodets, Laurens G L Gomes, Rachelle K Gould, Dave Goulson, Aaron D Gove, Laurent Granjon, Ingo Grass, Claudia L Gray, James Grogan, Weibin Gu, Moisès Guardiola, Nihara R Gunawardene, Alvaro G Gutierrez, Doris L Gutiérrez-Lamus, Daniela H Haarmeyer, Mick E Hanley, Thor Hanson, Nor R Hashim, Shombe N Hassan, Richard G Hatfield, Joseph E Hawes, Matt W Hayward, Christian Hébert, Alvin J Helden, John-André Henden, Philipp Henschel, Lionel Hernández, James P Herrera, Farina Herrmann, Felix Herzog, Diego Higuera-Diaz, Branko Hilje, Hubert Höfer, Anke Hoffmann, Finbarr G Horgan, Elisabeth Hornung, Roland Horváth, Kristoffer Hylander, Paola Isaacs-Cubides, Hiroaki Ishida, Masahiro Ishitani, Carmen T Jacobs, Víctor J Jaramillo, Birgit Jauker, F Jiménez Hernández, McKenzie F Johnson, Virat Jolli, Mats Jonsell, S Nur Juliani, Thomas S Jung, Vena Kapoor, Heike Kappes, Vassiliki Kati, Eric Katovai, Klaus Kellner, Michael Kessler, Kathryn R Kirby, Andrew M Kittle, Mairi E Knight, Eva Knop, Florian Kohler, Matti Koivula, Annette Kolb, Mouhamadou Kone, Ádám Kőrösi, Jochen Krauss, Ajith Kumar, Raman Kumar, David J Kurz, Alex S Kutt, Thibault Lachat, Victoria Lantschner, Francisco Lara, Jesse R Lasky, Steven C Latta, William F Laurance, Patrick Lavelle, Violette Le Féon, Gretchen LeBuhn, Jean-Philippe Légaré, Valérie Lehouck, María V Lencinas, Pia E Lentini, Susan G Letcher, Qi Li, Simon A Litchwark, Nick A Littlewood, Yunhui Liu, Nancy Lo-Man-Hung, Carlos A López-Quintero, Mounir Louhaichi, Gabor L Lövei, Manuel Esteban Lucas-Borja, Victor H Luja, Matthew S Luskin, M Cristina MacSwiney G, Kaoru Maeto, Tibor Magura, Neil Aldrin Mallari, Louise A Malone, Patrick K Malonza, Jagoba Malumbres-Olarte, Salvador Mandujano, Inger E Måren, Erika Marin-Spiotta, Charles J Marsh, E J P Marshall, Eliana Martínez, Guillermo Martínez Pastur, David Moreno Mateos, Margaret M Mayfield, Vicente Mazimpaka, Jennifer L McCarthy, Kyle P McCarthy, Quinn S McFrederick, Sean McNamara, Nagore G Medina, Rafael Medina, Jose L Mena, Estefania Mico, Grzegorz Mikusinski, Jeffrey C Milder, James R Miller, Daniel R Miranda-Esquivel, Melinda L Moir, Carolina L Morales, Mary N Muchane, Muchai Muchane, Sonja Mudri-Stojnic, A Nur Munira, Antonio Muoñz-Alonso, B F Munyekenye, Robin Naidoo, A Naithani, Michiko Nakagawa, Akihiro Nakamura, Yoshihiro Nakashima, Shoji Naoe, Guiomar Nates-Parra, Dario A Navarrete Gutierrez, Luis Navarro-Iriarte, Paul K Ndang'ang'a, Eike L Neuschulz, Jacqueline T Ngai, Violaine Nicolas, Sven G Nilsson, Norbertas Noreika, Olivia Norfolk, Jorge Ari Noriega, David A Norton, Nicole M Nöske, A Justin Nowakowski, Catherine Numa, Niall O'Dea, Patrick J O'Farrell, William Oduro, Sabine Oertli, Caleb Ofori-Boateng, Christopher Omamoke Oke, Vicencio Oostra, Lynne M Osgathorpe, Samuel Eduardo Otavo, Navendu V Page, Juan Paritsis, Alejandro Parra-H, Luke Parry, Guy Pe'er, Peter B Pearman, Nicolás Pelegrin, Raphaël Pélissier, Carlos A Peres, Pablo L Peri, Anna S Persson, Theodora Petanidou, Marcell K Peters, Rohan S Pethiyagoda, Ben Phalan, T Keith Philips, Finn C Pillsbury, Jimmy Pincheira-Ulbrich, Eduardo Pineda, Joan Pino, Jaime Pizarro-Araya, A J Plumptre, Santiago L Poggio, Natalia Politi, Pere Pons, Katja Poveda, Eileen F Power, Steven J Presley, Vânia Proença, Marino Quaranta, Carolina Quintero, Romina Rader, B R Ramesh, Martha P Ramirez-Pinilla, Jai Ranganathan, Claus Rasmussen, Nicola A Redpath-Downing, J Leighton Reid, Yana T Reis, José M Rey Benayas, Juan Carlos Rey-Velasco, Chevonne Reynolds, Danilo Bandini Ribeiro, Miriam H Richards, Barbara A Richardson, Michael J Richardson, Rodrigo Macip Ríos, Richard Robinson, Carolina A Robles, Jörg Römbke, Luz Piedad Romero-Duque, Matthias Rös, Loreta Rosselli, Stephen J Rossiter, Dana S Roth, T'ai H Roulston, Laurent Rousseau, André V Rubio, Jean-Claude Ruel, Jonathan P Sadler, Szabolcs Sáfián, Romeo A Saldaña-Vázquez, Katerina Sam, Ulrika Samnegård, Joana Santana, Xavier Santos, Jade Savage, Nancy A Schellhorn, Menno Schilthuizen, Ute Schmiedel, Christine B Schmitt, Nicole L Schon, Christof Schüepp, Katharina Schumann, Oliver Schweiger, Dawn M Scott, Kenneth A Scott, Jodi L Sedlock, Steven S Seefeldt, Ghazala Shahabuddin, Graeme Shannon, Douglas Sheil, Frederick H Sheldon, Eyal Shochat, Stefan J Siebert, Fernando A B Silva, Javier A Simonetti, Eleanor M Slade, Jo Smith, Allan H Smith-Pardo, Navjot S Sodhi, Eduardo J Somarriba, Ramón A Sosa, Grimaldo Soto Quiroga, Martin-Hugues St-Laurent, Brian M Starzomski, Constanti Stefanescu, Ingolf Steffan-Dewenter, Philip C Stouffer, Jane C Stout, Ayron M Strauch, Matthew J Struebig, Zhimin Su, Marcela Suarez-Rubio, Shinji Sugiura, Keith S Summerville, Yik-Hei Sung, Hari Sutrisno, Jens-Christian Svenning, Tiit Teder, Caragh G Threlfall, Anu Tiitsaar, Jacqui H Todd, Rebecca K Tonietto, Ignasi Torre, Béla Tóthmérész, Teja Tscharntke, Edgar C Turner, Jason M Tylianakis, Marcio Uehara-Prado, Nicolas Urbina-Cardona, Denis Vallan, Adam J Vanbergen, Heraldo L Vasconcelos, Kiril Vassilev, Hans A F Verboven, Maria João Verdasca, José R Verdú, Carlos H Vergara, Pablo M Vergara, Jort Verhulst, Massimiliano Virgilio, Lien Van Vu, Edward M Waite, Tony R Walker, Hua-Feng Wang, Yanping Wang, James I Watling, Britta Weller, Konstans Wells, Catrin Westphal, Edward D Wiafe, Christopher D Williams, Michael R Willig, John C Z Woinarski, Jan H D Wolf, Volkmar Wolters, Ben A Woodcock, Jihua Wu, Joseph M Wunderle, Yuichi Yamaura, Satoko Yoshikura, Douglas W Yu, Andrey S Zaitsev, Juliane Zeidler, Fasheng Zou, Ben Collen, Rob M Ewers, Georgina M Mace, Drew W Purves, Jörn P W Scharlemann, Andy Purvis
The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3...
January 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28031487/comprehensive-population-based-genome-sequencing-provides-insight-into-hematopoietic-regulatory-mechanisms
#2
Michael H Guo, Satish K Nandakumar, Jacob C Ulirsch, Seyedeh M Zekavat, Jason D Buenrostro, Pradeep Natarajan, Rany M Salem, Roberto Chiarle, Mario Mitt, Mart Kals, Kalle Pärn, Krista Fischer, Lili Milani, Reedik Mägi, Priit Palta, Stacey B Gabriel, Andres Metspalu, Eric S Lander, Sekar Kathiresan, Joel N Hirschhorn, Tõnu Esko, Vijay G Sankaran
Genetic variants affecting hematopoiesis can influence commonly measured blood cell traits. To identify factors that affect hematopoiesis, we performed association studies for blood cell traits in the population-based Estonian Biobank using high-coverage whole-genome sequencing (WGS) in 2,284 samples and SNP genotyping in an additional 14,904 samples. Using up to 7,134 samples with available phenotype data, our analyses identified 17 associations across 14 blood cell traits. Integration of WGS-based fine-mapping and complementary epigenomic datasets provided evidence for causal mechanisms at several loci, including at a previously undiscovered basophil count-associated locus near the master hematopoietic transcription factor CEBPA The fine-mapped variant at this basophil count association near CEBPA overlapped an enhancer active in common myeloid progenitors and influenced its activity...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28007139/phenotypic-characterization-of-genetically%C3%A2-lowered-human-lipoprotein-a-levels
#3
Connor A Emdin, Amit V Khera, Pradeep Natarajan, Derek Klarin, Hong-Hee Won, Gina M Peloso, Nathan O Stitziel, Akihiro Nomura, Seyedeh M Zekavat, Alexander G Bick, Namrata Gupta, Rosanna Asselta, Stefano Duga, Piera Angelica Merlini, Adolfo Correa, Thorsten Kessler, James G Wilson, Matthew J Bown, Alistair S Hall, Peter S Braund, Nilesh J Samani, Heribert Schunkert, Jaume Marrugat, Roberto Elosua, Ruth McPherson, Martin Farrall, Hugh Watkins, Cristen Willer, Gonçalo R Abecasis, Janine F Felix, Ramachandran S Vasan, Eric Lander, Daniel J Rader, John Danesh, Diego Ardissino, Stacey Gabriel, Danish Saleheen, Sekar Kathiresan
BACKGROUND: Genomic analyses have suggested that the LPA gene and its associated plasma biomarker, lipoprotein(a) (Lp[a]), represent a causal risk factor for coronary heart disease (CHD). As such, lowering Lp(a) levels has emerged as a therapeutic strategy. Beyond target identification, human genetics may contribute to the development of new therapies by defining the full spectrum of beneficial and adverse consequences and by developing a dose-response curve of target perturbation. OBJECTIVES: The goal of this study was to establish the full phenotypic impact of LPA gene variation and to estimate a dose-response curve between genetically altered plasma Lp(a) and risk for CHD...
December 27, 2016: Journal of the American College of Cardiology
https://www.readbyqxmd.com/read/27992415/a-genome-wide-crispr-screen-identifies-a-restricted-set-of-hiv-host-dependency-factors
#4
Ryan J Park, Tim Wang, Dylan Koundakjian, Judd F Hultquist, Pedro Lamothe-Molina, Blandine Monel, Kathrin Schumann, Haiyan Yu, Kevin M Krupzcak, Wilfredo Garcia-Beltran, Alicja Piechocka-Trocha, Nevan J Krogan, Alexander Marson, David M Sabatini, Eric S Lander, Nir Hacohen, Bruce D Walker
Host proteins are essential for HIV entry and replication and can be important nonviral therapeutic targets. Large-scale RNA interference (RNAi)-based screens have identified nearly a thousand candidate host factors, but there is little agreement among studies and few factors have been validated. Here we demonstrate that a genome-wide CRISPR-based screen identifies host factors in a physiologically relevant cell system. We identify five factors, including the HIV co-receptors CD4 and CCR5, that are required for HIV infection yet are dispensable for cellular proliferation and viability...
December 19, 2016: Nature Genetics
https://www.readbyqxmd.com/read/27984732/perturb-seq-dissecting-molecular-circuits-with-scalable-single-cell-rna-profiling-of-pooled-genetic-screens
#5
Atray Dixit, Oren Parnas, Biyu Li, Jenny Chen, Charles P Fulco, Livnat Jerby-Arnon, Nemanja D Marjanovic, Danielle Dionne, Tyler Burks, Raktima Raychowdhury, Britt Adamson, Thomas M Norman, Eric S Lander, Jonathan S Weissman, Nir Friedman, Aviv Regev
Genetic screens help infer gene function in mammalian cells, but it has remained difficult to assay complex phenotypes-such as transcriptional profiles-at scale. Here, we develop Perturb-seq, combining single-cell RNA sequencing (RNA-seq) and clustered regularly interspaced short palindromic repeats (CRISPR)-based perturbations to perform many such assays in a pool. We demonstrate Perturb-seq by analyzing 200,000 cells in immune cells and cell lines, focusing on transcription factors regulating the response of dendritic cells to lipopolysaccharide (LPS)...
December 15, 2016: Cell
https://www.readbyqxmd.com/read/27851748/chromosomal-instability-estimation-based-on-next-generation-sequencing-and-single-cell-genome-wide-copy-number-variation-analysis
#6
Stephanie B Greene, Angel E Dago, Laura J Leitz, Yipeng Wang, Jerry Lee, Shannon L Werner, Steven Gendreau, Premal Patel, Shidong Jia, Liangxuan Zhang, Eric K Tucker, Michael Malchiodi, Ryon P Graf, Ryan Dittamore, Dena Marrinucci, Mark Landers
Genomic instability is a hallmark of cancer often associated with poor patient outcome and resistance to targeted therapy. Assessment of genomic instability in bulk tumor or biopsy can be complicated due to sample availability, surrounding tissue contamination, or tumor heterogeneity. The Epic Sciences circulating tumor cell (CTC) platform utilizes a non-enrichment based approach for the detection and characterization of rare tumor cells in clinical blood samples. Genomic profiling of individual CTCs could provide a portrait of cancer heterogeneity, identify clonal and sub-clonal drivers, and monitor disease progression...
2016: PloS One
https://www.readbyqxmd.com/read/27783602/local-regulation-of-gene-expression-by-lncrna-promoters-transcription-and-splicing
#7
Jesse M Engreitz, Jenna E Haines, Elizabeth M Perez, Glen Munson, Jenny Chen, Michael Kane, Patrick E McDonel, Mitchell Guttman, Eric S Lander
Mammalian genomes are pervasively transcribed to produce thousands of long non-coding RNAs (lncRNAs). A few of these lncRNAs have been shown to recruit regulatory complexes through RNA-protein interactions to influence the expression of nearby genes, and it has been suggested that many other lncRNAs can also act as local regulators. Such local functions could explain the observation that lncRNA expression is often correlated with the expression of nearby genes. However, these correlations have been challenging to dissect and could alternatively result from processes that are not mediated by the lncRNA transcripts themselves...
November 17, 2016: Nature
https://www.readbyqxmd.com/read/27774369/perchlorate-formation-on-mars-through-surface-radiolysis-initiated-atmospheric-chemistry-a-potential-mechanism
#8
Eric H Wilson, Sushil K Atreya, Ralf I Kaiser, Paul R Mahaffy
Recent observations of the Martian surface by the Phoenix lander and the Sample Analysis at Mars indicate the presence of perchlorate (ClO4(-)). The abundance and isotopic composition of these perchlorates suggest that the mechanisms responsible for their formation in the Martian environment may be unique in our solar system. With this in mind, we propose a potential mechanism for the production of Martian perchlorate: the radiolysis of the Martian surface by galactic cosmic rays, followed by the sublimation of chlorine oxides into the atmosphere and their subsequent synthesis to form perchloric acid (HClO4) in the atmosphere, and the surface deposition and subsequent mineralization of HClO4 in the regolith to form surface perchlorates...
August 2016: Journal of Geophysical Research. Planets
https://www.readbyqxmd.com/read/27760322/genomic-correlates-of-immune-cell-infiltrates-in-colorectal-carcinoma
#9
Marios Giannakis, Xinmeng Jasmine Mu, Sachet A Shukla, Zhi Rong Qian, Ofir Cohen, Reiko Nishihara, Samira Bahl, Yin Cao, Ali Amin-Mansour, Mai Yamauchi, Yasutaka Sukawa, Chip Stewart, Mara Rosenberg, Kosuke Mima, Kentaro Inamura, Katsuhiko Nosho, Jonathan A Nowak, Michael S Lawrence, Edward L Giovannucci, Andrew T Chan, Kimmie Ng, Jeffrey A Meyerhardt, Eliezer M Van Allen, Gad Getz, Stacey B Gabriel, Eric S Lander, Catherine J Wu, Charles S Fuchs, Shuji Ogino, Levi A Garraway
No abstract text is available yet for this article.
October 18, 2016: Cell Reports
https://www.readbyqxmd.com/read/27720232/distance-from-a-comprehensive-cancer-center-a-proxy-for-poor-cervical-cancer-outcomes
#10
David A Barrington, Sarah E Dilley, Emily E Landers, Eric D Thomas, Jonathon D Boone, J Michael Straughn, Gerald McGwin, Charles A Leath
OBJECTIVE: To evaluate the potential relationship between outcomes in cervical cancer patients based on distance from our Comprehensive Cancer Center (CCC). METHODS: A retrospective cohort study of cervical cancer patients was performed. Abstracted data included: demographics, clinicopathologic variables, treatment, and survival. Analyses both by quartiles and distance <100 and ≥100miles from our institution were performed. Data were analyzed using SAS version 9...
December 2016: Gynecologic Oncology
https://www.readbyqxmd.com/read/27708057/systematic-mapping-of-functional-enhancer-promoter-connections-with-crispr-interference
#11
Charles P Fulco, Mathias Munschauer, Rockwell Anyoha, Glen Munson, Sharon R Grossman, Elizabeth M Perez, Michael Kane, Brian Cleary, Eric S Lander, Jesse M Engreitz
Gene expression in mammals is regulated by noncoding elements that can affect physiology and disease, yet the functions and target genes of most noncoding elements remain unknown. We present a high-throughput approach that uses clustered regularly interspaced short palindromic repeats (CRISPR) interference (CRISPRi) to discover regulatory elements and identify their target genes. We assess >1 megabase of sequence in the vicinity of two essential transcription factors, MYC and GATA1, and identify nine distal enhancers that control gene expression and cellular proliferation...
November 11, 2016: Science
https://www.readbyqxmd.com/read/27681617/mutant-pfn1-causes-als-phenotypes-and-progressive-motor-neuron-degeneration-in-mice-by-a-gain-of-toxicity
#12
Chunxing Yang, Eric W Danielson, Tao Qiao, Jake Metterville, Robert H Brown, John E Landers, Zuoshang Xu
Mutations in the profilin 1 (PFN1) gene cause amyotrophic lateral sclerosis (ALS), a neurodegenerative disease caused by the loss of motor neurons leading to paralysis and eventually death. PFN1 is a small actin-binding protein that promotes formin-based actin polymerization and regulates numerous cellular functions, but how the mutations in PFN1 cause ALS is unclear. To investigate this problem, we have generated transgenic mice expressing either the ALS-associated mutant (C71G) or wild-type protein. Here, we report that mice expressing the mutant, but not the wild-type, protein had relentless progression of motor neuron loss with concomitant progressive muscle weakness ending in paralysis and death...
October 11, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27467250/juicebox-provides-a-visualization-system-for-hi-c-contact-maps-with-unlimited-zoom
#13
Neva C Durand, James T Robinson, Muhammad S Shamim, Ido Machol, Jill P Mesirov, Eric S Lander, Erez Lieberman Aiden
Hi-C experiments study how genomes fold in 3D, generating contact maps containing features as small as 20 bp and as large as 200 Mb. Here we introduce Juicebox, a tool for exploring Hi-C and other contact map data. Juicebox allows users to zoom in and out of Hi-C maps interactively, just as a user of Google Earth might zoom in and out of a geographic map. Maps can be compared to one another, or to 1D tracks or 2D feature sets.
July 2016: Cell Systems
https://www.readbyqxmd.com/read/27467249/juicer-provides-a-one-click-system-for-analyzing-loop-resolution-hi-c-experiments
#14
Neva C Durand, Muhammad S Shamim, Ido Machol, Suhas S P Rao, Miriam H Huntley, Eric S Lander, Erez Lieberman Aiden
Hi-C experiments explore the 3D structure of the genome, generating terabases of data to create high-resolution contact maps. Here, we introduce Juicer, an open-source tool for analyzing terabase-scale Hi-C datasets. Juicer allows users without a computational background to transform raw sequence data into normalized contact maps with one click. Juicer produces a hic file containing compressed contact matrices at many resolutions, facilitating visualization and analysis at multiple scales. Structural features, such as loops and domains, are automatically annotated...
July 2016: Cell Systems
https://www.readbyqxmd.com/read/27466172/outcomes-with-anti-tumour-necrosis-factor-alpha-therapy-and-serology-in-patients-with-denovo-crohn-s-disease-after-ileal-pouch-anal-anastomosis
#15
Lori Robbins, Karen Zaghiyan, Gil Melmed, Eric Vasiliauskas, Shahzad Ahmed, Dermot McGovern, Shervin Rabizadeh, Namita Singh, Carol Landers, Andrew Ippoliti, David Shih, Stephan Targan, Phillip Fleshner
BACKGROUND AND AIMS: A subset of patients who undergo ileal pouch-anal anastomosis [IPAA] for ulcerative colitis [UC] will later be diagnosed with denovo Crohn's disease [CD]. These patients have a higher risk of pouch failure. In this study we evaluated inflammatory bowel disease [IBD] serology in patients with denovo CD and examined the success of anti-tumour necrosis factor-alpha [anti-TNFα] therapy in preventing ileostomy in denovo CD patients who failed anti-TNFα therapy before IPAA...
January 2017: Journal of Crohn's & Colitis
https://www.readbyqxmd.com/read/27432957/deletion-of-dxz4-on-the-human-inactive-x-chromosome-alters-higher-order-genome-architecture
#16
Emily M Darrow, Miriam H Huntley, Olga Dudchenko, Elena K Stamenova, Neva C Durand, Zhuo Sun, Su-Chen Huang, Adrian L Sanborn, Ido Machol, Muhammad Shamim, Andrew P Seberg, Eric S Lander, Brian P Chadwick, Erez Lieberman Aiden
During interphase, the inactive X chromosome (Xi) is largely transcriptionally silent and adopts an unusual 3D configuration known as the "Barr body." Despite the importance of X chromosome inactivation, little is known about this 3D conformation. We recently showed that in humans the Xi chromosome exhibits three structural features, two of which are not shared by other chromosomes. First, like the chromosomes of many species, Xi forms compartments. Second, Xi is partitioned into two huge intervals, called "superdomains," such that pairs of loci in the same superdomain tend to colocalize...
August 2, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27398621/the-genetic-architecture-of-type-2-diabetes
#17
Christian Fuchsberger, Jason Flannick, Tanya M Teslovich, Anubha Mahajan, Vineeta Agarwala, Kyle J Gaulton, Clement Ma, Pierre Fontanillas, Loukas Moutsianas, Davis J McCarthy, Manuel A Rivas, John R B Perry, Xueling Sim, Thomas W Blackwell, Neil R Robertson, N William Rayner, Pablo Cingolani, Adam E Locke, Juan Fernandez Tajes, Heather M Highland, Josee Dupuis, Peter S Chines, Cecilia M Lindgren, Christopher Hartl, Anne U Jackson, Han Chen, Jeroen R Huyghe, Martijn van de Bunt, Richard D Pearson, Ashish Kumar, Martina Müller-Nurasyid, Niels Grarup, Heather M Stringham, Eric R Gamazon, Jaehoon Lee, Yuhui Chen, Robert A Scott, Jennifer E Below, Peng Chen, Jinyan Huang, Min Jin Go, Michael L Stitzel, Dorota Pasko, Stephen C J Parker, Tibor V Varga, Todd Green, Nicola L Beer, Aaron G Day-Williams, Teresa Ferreira, Tasha Fingerlin, Momoko Horikoshi, Cheng Hu, Iksoo Huh, Mohammad Kamran Ikram, Bong-Jo Kim, Yongkang Kim, Young Jin Kim, Min-Seok Kwon, Juyoung Lee, Selyeong Lee, Keng-Han Lin, Taylor J Maxwell, Yoshihiko Nagai, Xu Wang, Ryan P Welch, Joon Yoon, Weihua Zhang, Nir Barzilai, Benjamin F Voight, Bok-Ghee Han, Christopher P Jenkinson, Teemu Kuulasmaa, Johanna Kuusisto, Alisa Manning, Maggie C Y Ng, Nicholette D Palmer, Beverley Balkau, Alena Stancáková, Hanna E Abboud, Heiner Boeing, Vilmantas Giedraitis, Dorairaj Prabhakaran, Omri Gottesman, James Scott, Jason Carey, Phoenix Kwan, George Grant, Joshua D Smith, Benjamin M Neale, Shaun Purcell, Adam S Butterworth, Joanna M M Howson, Heung Man Lee, Yingchang Lu, Soo-Heon Kwak, Wei Zhao, John Danesh, Vincent K L Lam, Kyong Soo Park, Danish Saleheen, Wing Yee So, Claudia H T Tam, Uzma Afzal, David Aguilar, Rector Arya, Tin Aung, Edmund Chan, Carmen Navarro, Ching-Yu Cheng, Domenico Palli, Adolfo Correa, Joanne E Curran, Denis Rybin, Vidya S Farook, Sharon P Fowler, Barry I Freedman, Michael Griswold, Daniel Esten Hale, Pamela J Hicks, Chiea-Chuen Khor, Satish Kumar, Benjamin Lehne, Dorothée Thuillier, Wei Yen Lim, Jianjun Liu, Yvonne T van der Schouw, Marie Loh, Solomon K Musani, Sobha Puppala, William R Scott, Loïc Yengo, Sian-Tsung Tan, Herman A Taylor, Farook Thameem, Gregory Wilson, Tien Yin Wong, Pål Rasmus Njølstad, Jonathan C Levy, Massimo Mangino, Lori L Bonnycastle, Thomas Schwarzmayr, João Fadista, Gabriela L Surdulescu, Christian Herder, Christopher J Groves, Thomas Wieland, Jette Bork-Jensen, Ivan Brandslund, Cramer Christensen, Heikki A Koistinen, Alex S F Doney, Leena Kinnunen, Tõnu Esko, Andrew J Farmer, Liisa Hakaste, Dylan Hodgkiss, Jasmina Kravic, Valeriya Lyssenko, Mette Hollensted, Marit E Jørgensen, Torben Jørgensen, Claes Ladenvall, Johanne Marie Justesen, Annemari Käräjämäki, Jennifer Kriebel, Wolfgang Rathmann, Lars Lannfelt, Torsten Lauritzen, Narisu Narisu, Allan Linneberg, Olle Melander, Lili Milani, Matt Neville, Marju Orho-Melander, Lu Qi, Qibin Qi, Michael Roden, Olov Rolandsson, Amy Swift, Anders H Rosengren, Kathleen Stirrups, Andrew R Wood, Evelin Mihailov, Christine Blancher, Mauricio O Carneiro, Jared Maguire, Ryan Poplin, Khalid Shakir, Timothy Fennell, Mark DePristo, Martin Hrabé de Angelis, Panos Deloukas, Anette P Gjesing, Goo Jun, Peter Nilsson, Jacquelyn Murphy, Robert Onofrio, Barbara Thorand, Torben Hansen, Christa Meisinger, Frank B Hu, Bo Isomaa, Fredrik Karpe, Liming Liang, Annette Peters, Cornelia Huth, Stephen P O'Rahilly, Colin N A Palmer, Oluf Pedersen, Rainer Rauramaa, Jaakko Tuomilehto, Veikko Salomaa, Richard M Watanabe, Ann-Christine Syvänen, Richard N Bergman, Dwaipayan Bharadwaj, Erwin P Bottinger, Yoon Shin Cho, Giriraj R Chandak, Juliana C N Chan, Kee Seng Chia, Mark J Daly, Shah B Ebrahim, Claudia Langenberg, Paul Elliott, Kathleen A Jablonski, Donna M Lehman, Weiping Jia, Ronald C W Ma, Toni I Pollin, Manjinder Sandhu, Nikhil Tandon, Philippe Froguel, Inês Barroso, Yik Ying Teo, Eleftheria Zeggini, Ruth J F Loos, Kerrin S Small, Janina S Ried, Ralph A DeFronzo, Harald Grallert, Benjamin Glaser, Andres Metspalu, Nicholas J Wareham, Mark Walker, Eric Banks, Christian Gieger, Erik Ingelsson, Hae Kyung Im, Thomas Illig, Paul W Franks, Gemma Buck, Joseph Trakalo, David Buck, Inga Prokopenko, Reedik Mägi, Lars Lind, Yossi Farjoun, Katharine R Owen, Anna L Gloyn, Konstantin Strauch, Tiinamaija Tuomi, Jaspal Singh Kooner, Jong-Young Lee, Taesung Park, Peter Donnelly, Andrew D Morris, Andrew T Hattersley, Donald W Bowden, Francis S Collins, Gil Atzmon, John C Chambers, Timothy D Spector, Markku Laakso, Tim M Strom, Graeme I Bell, John Blangero, Ravindranath Duggirala, E Shyong Tai, Gilean McVean, Craig L Hanis, James G Wilson, Mark Seielstad, Timothy M Frayling, James B Meigs, Nancy J Cox, Rob Sladek, Eric S Lander, Stacey Gabriel, Noël P Burtt, Karen L Mohlke, Thomas Meitinger, Leif Groop, Goncalo Abecasis, Jose C Florez, Laura J Scott, Andrew P Morris, Hyun Min Kang, Michael Boehnke, David Altshuler, Mark I McCarthy
The genetic architecture of common traits, including the number, frequency, and effect sizes of inherited variants that contribute to individual risk, has been long debated. Genome-wide association studies have identified scores of common variants associated with type 2 diabetes, but in aggregate, these explain only a fraction of the heritability of this disease. Here, to test the hypothesis that lower-frequency variants explain much of the remainder, the GoT2D and T2D-GENES consortia performed whole-genome sequencing in 2,657 European individuals with and without diabetes, and exome sequencing in 12,940 individuals from five ancestry groups...
August 4, 2016: Nature
https://www.readbyqxmd.com/read/27365150/pet-ownership-and-cancer-risk-in-the-women-s-health-initiative
#18
David O Garcia, Eric M Lander, Betsy C Wertheim, JoAnn E Manson, Stella L Volpe, Rowan T Chlebowski, Marcia L Stefanick, Lawrence S Lessin, Lewis H Kuller, Cynthia A Thomson
BACKGROUND: Pet ownership and cancer are both highly prevalent in the United States. Evidence suggests that associations may exist between this potentially modifiable factor and cancer prevention, though studies are sparse. The present report examined whether pet ownership (dog, cat, or bird) is associated with lower risk for total cancer and site-specific obesity-related cancers. METHODS: This was a prospective analysis of 123,560 participants (20,981 dog owners; 19,288 cat owners; 1,338 bird owners; and 81,953 non-pet owners) enrolled in the Women's Health Initiative observational study and clinical trials...
September 2016: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/27306663/natural-history-of-the-infant-gut-microbiome-and-impact-of-antibiotic-treatment-on-bacterial-strain-diversity-and-stability
#19
Moran Yassour, Tommi Vatanen, Heli Siljander, Anu-Maaria Hämäläinen, Taina Härkönen, Samppa J Ryhänen, Eric A Franzosa, Hera Vlamakis, Curtis Huttenhower, Dirk Gevers, Eric S Lander, Mikael Knip, Ramnik J Xavier
The gut microbial community is dynamic during the first 3 years of life, before stabilizing to an adult-like state. However, little is known about the impact of environmental factors on the developing human gut microbiome. We report a longitudinal study of the gut microbiome based on DNA sequence analysis of monthly stool samples and clinical information from 39 children, about half of whom received multiple courses of antibiotics during the first 3 years of life. Whereas the gut microbiome of most children born by vaginal delivery was dominated by Bacteroides species, the four children born by cesarean section and about 20% of vaginally born children lacked Bacteroides in the first 6 to 18 months of life...
June 15, 2016: Science Translational Medicine
https://www.readbyqxmd.com/read/27259153/direct-identification-of-hundreds-of-expression-modulating-variants-using-a-multiplexed-reporter-assay
#20
Ryan Tewhey, Dylan Kotliar, Daniel S Park, Brandon Liu, Sarah Winnicki, Steven K Reilly, Kristian G Andersen, Tarjei S Mikkelsen, Eric S Lander, Stephen F Schaffner, Pardis C Sabeti
Although studies have identified hundreds of loci associated with human traits and diseases, pinpointing causal alleles remains difficult, particularly for non-coding variants. To address this challenge, we adapted the massively parallel reporter assay (MPRA) to identify variants that directly modulate gene expression. We applied it to 32,373 variants from 3,642 cis-expression quantitative trait loci and control regions. Detection by MPRA was strongly correlated with measures of regulatory function. We demonstrate MPRA's capabilities for pinpointing causal alleles, using it to identify 842 variants showing differential expression between alleles, including 53 well-annotated variants associated with diseases and traits...
June 2, 2016: Cell
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