Learning Influential Genes on Cancer Gene Expression Data with Stacked Denoising Autoencoders

Institute of Electrical and Electronics Engineers (IEEE) (2017) 1201-1205

Authors:

Vítor Teixeira, Rui Camacho, Pedro G Ferreira

Co-expression networks reveal the tissue-specific regulation of transcription and splicing

Genome Research Cold Spring Harbor Laboratory 27:11 (2017) 1843-1858

Authors:

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

Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis

Genome Research Cold Spring Harbor Laboratory 27:11 (2017) 1859-1871

Authors:

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

KiDS-450 + 2dFLenS: Cosmological parameter constraints from weak gravitational lensing tomography and overlapping redshift-space galaxy clustering

Monthly Notices of the Royal Astronomical Society Oxford University Press 474:4 (2017) 4894-4924

Authors:

Shahab Joudaki, C Blake, A Johnson, A Amon, M Asgari, A Choi, T Erben, K Glazebrook, J Harnois-Déraps, C Heymans, H Hildebrandt, H Hoekstra, D Klaes, K Kuijken, C Lidman, A Mead, Lance Miller, D Parkinson, GB Poole, P Schneider, M Viola, C Wolf

Abstract:

We perform a combined analysis of cosmic shear tomography, galaxy-galaxy lensing tomography, and redshift-space multipole power spectra (monopole and quadrupole) using 450 deg$^2$ of imaging data by the Kilo Degree Survey (KiDS) overlapping with two spectroscopic surveys: the 2-degree Field Lensing Survey (2dFLenS) and the Baryon Oscillation Spectroscopic Survey (BOSS). We restrict the galaxy-galaxy lensing and multipole power spectrum measurements to the overlapping regions with KiDS, and self-consistently compute the full covariance between the different observables using a large suite of $N$-body simulations. We methodically analyze different combinations of the observables, finding that galaxy-galaxy lensing measurements are particularly useful in improving the constraint on the intrinsic alignment amplitude (by 30%, positive at $3.5\sigma$ in the fiducial data analysis), while the multipole power spectra are useful in tightening the constraints along the lensing degeneracy direction (e.g. factor of two stronger matter density constraint in the fiducial analysis). The fully combined constraint on $S_8 \equiv \sigma_8 \sqrt{\Omega_{\rm m}/0.3} = 0.742 \pm 0.035$, which is an improvement by 20% compared to KiDS alone, corresponds to a $2.6\sigma$ discordance with Planck, and is not significantly affected by fitting to a more conservative set of scales. Given the tightening of the parameter space, we are unable to resolve the discordance with an extended cosmology that is simultaneously favored in a model selection sense, including the sum of neutrino masses, curvature, evolving dark energy, and modified gravity. The complementarity of our observables allows for constraints on modified gravity degrees of freedom that are not simultaneously bounded with either probe alone, and up to a factor of three improvement in the $S_8$ constraint in the extended cosmology compared to KiDS alone.

Next Generation Virgo Cluster Survey. XXI. The weak lensing masses of the CFHTLS and NGVS RedGOLD galaxy clusters and calibration of the optical richness

Astrophysical Journal American Astronomical Society 848:2 (2017) 114

Authors:

C Parroni, S Mei, T Erben, LV Waerbeke, A Raichoor, J Ford, R Licitra, M Meneghetti, H Hildebrandt, Lance Miller, P Côté, G Covone, J-C Cuillandre, P-A Duc, L Ferrarese, SDJ Gwyn, TH Puzia

Abstract:

We measured stacked weak lensing cluster masses for a sample of 1323 galaxy clusters detected by the RedGOLD algorithm in the Canada–France–Hawaii Telescope Legacy Survey W1 and the Next Generation Virgo Cluster Survey at $0.2\lt z\lt 0.5$, in the optical richness range $10\lt \lambda \lt 70$. This is the most comprehensive lensing study of a $\sim 100 \% $ complete and $\sim 80 \% $ pure optical cluster catalog in this redshift range. We test different mass models, and our final model includes a basic halo model with a Navarro Frenk and White profile, as well as correction terms that take into account cluster miscentering, non-weak shear, the two-halo term, the contribution of the Brightest Cluster Galaxy, and an a posteriori correction for the intrinsic scatter in the mass–richness relation. With this model, we obtain a mass–richness relation of $\mathrm{log}{M}_{200}/{M}_{\odot }\,=(14.46\pm 0.02)+(1.04\pm 0.09)\mathrm{log}(\lambda /40)$ (statistical uncertainties). This result is consistent with other published lensing mass–richness relations. We give the coefficients of the scaling relations between the lensing mass and X-ray mass proxies, L X and T X, and compare them with previous results. When compared to X-ray masses and mass proxies, our results are in agreement with most previous results and simulations, and consistent with the expected deviations from self-similarity.