@article {HPA2015,
	author = {Uhl{\'e}n, Mathias and Fagerberg, Linn and Hallstr{\"o}m, Bj{\"o}rn M. and Lindskog, Cecilia and Oksvold, Per and Mardinoglu, Adil and Sivertsson, {\r A}sa and Kampf, Caroline and Sj{\"o}stedt, Evelina and Asplund, Anna and Olsson, IngMarie and Edlund, Karolina and Lundberg, Emma and Navani, Sanjay and Szigyarto, Cristina Al-Khalili and Odeberg, Jacob and Djureinovic, Dijana and Takanen, Jenny Ottosson and Hober, Sophia and Alm, Tove and Edqvist, Per-Henrik and Berling, Holger and Tegel, Hanna and Mulder, Jan and Rockberg, Johan and Nilsson, Peter and Schwenk, Jochen M. and Hamsten, Marica and von Feilitzen, Kalle and Forsberg, Mattias and Persson, Lukas and Johansson, Fredric and Zwahlen, Martin and von Heijne, Gunnar and Nielsen, Jens and Pont{\'e}n, Fredrik},
	title = {Tissue-based map of the human proteome},
	volume = {347},
	number = {6220},
	year = {2015},
	doi = {10.1126/science.1260419},
	publisher = {American Association for the Advancement of Science},
	issn = {0036-8075},
	URL = {http://science.sciencemag.org/content/347/6220/1260419},
	eprint = {http://science.sciencemag.org/content/347/6220/1260419.full.pdf},
	journal = {Science}
}


@article {GTEx2015,
	author = {Ardlie, Kristin G. and Deluca, David S. and Segr{\`e}, Ayellet V. and Sullivan, Timothy J. and Young, Taylor R. and Gelfand, Ellen T. and Trowbridge, Casandra A. and Maller, Julian B. and Tukiainen, Taru and Lek, Monkol and Ward, Lucas D. and Kheradpour, Pouya and Iriarte, Benjamin and Meng, Yan and Palmer, Cameron D. and Esko, T{\~o}nu and Winckler, Wendy and Hirschhorn, Joel N. and Kellis, Manolis and MacArthur, Daniel G. and Getz, Gad and Shabalin, Andrey A. and Li, Gen and Zhou, Yi-Hui and Nobel, Andrew B. and Rusyn, Ivan and Wright, Fred A. and Lappalainen, Tuuli and Ferreira, Pedro G. and Ongen, Halit and Rivas, Manuel A. and Battle, Alexis and Mostafavi, Sara and Monlong, Jean and Sammeth, Michael and Mele, Marta and Reverter, Ferran and Goldmann, Jakob M. and Koller, Daphne and Guig{\'o}, Roderic and McCarthy, Mark I. and Dermitzakis, Emmanouil T. and Gamazon, Eric R. and Im, Hae Kyung and Konkashbaev, Anuar and Nicolae, Dan L. and Cox, Nancy J. and Flutre, Timoth{\'e}e and Wen, Xiaoquan and Stephens, Matthew and Pritchard, Jonathan K. and Tu, Zhidong and Zhang, Bin and Huang, Tao and Long, Quan and Lin, Luan and Yang, Jialiang and Zhu, Jun and Liu, Jun and Brown, Amanda and Mestichelli, Bernadette and Tidwell, Denee and Lo, Edmund and Salvatore, Mike and Shad, Saboor and Thomas, Jeffrey A. and Lonsdale, John T. and Moser, Michael T. and Gillard, Bryan M. and Karasik, Ellen and Ramsey, Kimberly and Choi, Christopher and Foster, Barbara A. and Syron, John and Fleming, Johnell and Magazine, Harold and Hasz, Rick and Walters, Gary D. and Bridge, Jason P. and Miklos, Mark and Sullivan, Susan and Barker, Laura K. and Traino, Heather M. and Mosavel, Maghboeba and Siminoff, Laura A. and Valley, Dana R. and Rohrer, Daniel C. and Jewell, Scott D. and Branton, Philip A. and Sobin, Leslie H. and Barcus, Mary and Qi, Liqun and McLean, Jeffrey and Hariharan, Pushpa and Um, Ki Sung and Wu, Shenpei and Tabor, David and Shive, Charles and Smith, Anna M. and Buia, Stephen A. and Undale, Anita H. and Robinson, Karna L. and Roche, Nancy and Valentino, Kimberly M. and Britton, Angela and Burges, Robin and Bradbury, Debra and Hambright, Kenneth W. and Seleski, John and Korzeniewski, Greg E. and Erickson, Kenyon and Marcus, Yvonne and Tejada, Jorge and Taherian, Mehran and Lu, Chunrong and Basile, Margaret and Mash, Deborah C. and Volpi, Simona and Struewing, Jeffery P. and Temple, Gary F. and Boyer, Joy and Colantuoni, Deborah and Little, Roger and Koester, Susan and Carithers, Latarsha J. and Moore, Helen M. and Guan, Ping and Compton, Carolyn and Sawyer, Sherilyn J. and Demchok, Joanne P. and Vaught, Jimmie B. and Rabiner, Chana A. and Lockhart, Nicole C. and Ardlie, Kristin G. and Getz, Gad and Wright, Fred A. and Kellis, Manolis and Volpi, Simona and Dermitzakis, Emmanouil T.},
	title = {The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans},
	volume = {348},
	number = {6235},
	pages = {648--660},
	year = {2015},
	doi = {10.1126/science.1262110},
	publisher = {American Association for the Advancement of Science},
	issn = {0036-8075},
	URL = {http://science.sciencemag.org/content/348/6235/648},
	eprint = {http://science.sciencemag.org/content/348/6235/648.full.pdf},
	journal = {Science}
}


@article{ENCODE2012,
  author = {Shen, Yin and Yue, Feng and McCleary, David F. and Ye, Zhen and Edsall, Lee and Kuan, Samantha and Wagner, Ulrich and Dixon, Jesse and Lee, Leonard and Lobanenkov, Victor V. and Ren, Bing},
  journal = {Nature},
  title = {{A map of the cis-regulatory sequences in the mouse genome}},
  url = {http://www.nature.com/articles/nature11243},
  year = 2012,
  volume = 448,
  issue = 7409
}

@article{Petropoulos2016,
abstract = {Mouse studies have been instrumental in forming our current understanding of early cell-lineage decisions; however, similar insights into the early human development are severely limited. Here, we present a comprehensive transcriptional map of human embryo development, including the sequenced transcriptomes of 1,529 individual cells from 88 human preimplantation embryos. These data show that cells undergo an intermediate state of co-expression of lineage-specific genes, followed by a concurrent establishment of the trophectoderm, epiblast, and primitive endoderm lineages, which coincide with blastocyst formation. Female cells of all three lineages achieve dosage compensation of X chromosome RNA levels prior to implantation. However, in contrast to the mouse, XIST is transcribed from both alleles throughout the progression of this expression dampening, and X chromosome genes maintain biallelic expression while dosage compensation proceeds. We envision broad utility of this transcriptional atlas in future studies on human development as well as in stem cell research.},
author = {Petropoulos, Sophie and Edsg{\"{a}}rd, Daniel and Reinius, Bj{\"{o}}rn and Deng, Qiaolin and Panula, Sarita Pauliina and Codeluppi, Simone and {Plaza Reyes}, Alvaro and Linnarsson, Sten and Sandberg, Rickard and Lanner, Fredrik},
doi = {10.1016/j.cell.2016.03.023},
file = {:Users/jain/Library/Application Support/Mendeley Desktop/Downloaded/Petropoulos et al. - 2016 - Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos(2).pdf:pdf},
issn = {1097-4172},
journal = {Cell},
month = {may},
number = {4},
pages = {1012--26},
pmid = {27062923},
publisher = {Elsevier},
title = {{Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/27062923 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4868821},
volume = {165},
year = {2016}
}

@article{Aken2016,
abstract = {The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.Database URL: http://www.ensembl.org/index.html.},
author = {Aken, Bronwen L and Ayling, Sarah and Barrell, Daniel and Clarke, Laura and Curwen, Valery and Fairley, Susan and {Fernandez Banet}, Julio and Billis, Konstantinos and {Garc{\'{i}}a Gir{\'{o}}n}, Carlos and Hourlier, Thibaut and Howe, Kevin and K{\"{a}}h{\"{a}}ri, Andreas and Kokocinski, Felix and Martin, Fergal J and Murphy, Daniel N and Nag, Rishi and Ruffier, Magali and Schuster, Michael and Tang, Y Amy and Vogel, Jan-Hinnerk and White, Simon and Zadissa, Amonida and Flicek, Paul and Searle, Stephen M J},
doi = {10.1093/database/baw093},
issn = {1758-0463},
journal = {Database : the journal of biological databases and curation},
pmid = {27337980},
publisher = {Oxford University Press},
title = {{The Ensembl gene annotation system.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/27337980 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4919035},
volume = {2016},
year = {2016}
}

