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1. Bingo as a Novel Approach to Skill Building in the Initial Months of Surgical Internship: A Pilot Implementation

Author

DIMITRA LOTAKIS, MARK WALLACK, and SAMIR GADEPALLI

Subjects
surgery, internship, residency, teaching, procedure, Education (General), L7-991, Medicine (General), R5-920
Abstract

Introduction: We have observed inconsistencies in residents’experiences regarding important procedures and tasks necessary for patient care. We aimed to improve individual motivation tolearn and become facile with specific practices earlier in the timeline of the internship years.Methods: Intern Bingo was implemented in a single general surgery residency. Two sites, both tertiary care centers with institutional practices, were utilized. Twenty-four procedures/tasks important to clinical practice were identified, including but not limited to Nasogastric Tube placement, IV insertion, incision and drainage, laceration repair, vascular doppler exam, andclinical documentation. Bingo cards were randomly generated. To assess comprehension, interns taught back necessary components to a senior resident or attending to complete each bingo square; including indications, supplies, steps, troubleshooting techniques, and complications. First, the residents were awarded prizes to complete a row and a full card (a cloth scrub cap and portable pulse-oximeter, respectively). A Likert-scale survey assessing satisfaction was administered following the completion of the internship period.Results: The first row was completed in two weeks and the first full card at four weeks. All participants finished the cards within 8 weeks. 54% of the participants returned the survey and100% reported positive experiences. 50% felt that bingo created a healthy learning environment with improved teaching, and the remaining 50% were neutral. 75% reported that Bingo positivelyinfluenced decisions to seek out opportunities. 100% conveyed a desire to repeat Bingo as mentors. Feedback from the attendings was gathered, with positive assessments of the interns’ skills and confidence.Conclusion: Bingo is a simple and easily implemented educational tool that works to alleviate variations in experience early in the internship period. It represents a novel and effective way tomotivate the interns to learn important procedures and tasks within the first two months of residency. Cards may be effortlessly tailored to a variety of residency programs and rotations.

Published
2024
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3. Histologic type predicts disparate outcomes in pediatric hepatocellular neoplasms: A Pediatric Surgical Oncology Research Collaborative study

Author

Scott S. Short, Zachary J. Kastenberg, Guo Wei, Alex Bondoc, Roshni Dasgupta, Greg M. Tiao, Erin Watters, Todd E. Heaton, Dimitra Lotakis, Michael P. La Quaglia, Andrew J. Murphy, Andrew M. Davidoff, Sara A. Mansfield, Max R. Langham, Timothy B. Lautz, Riccardo A. Superina, Katherine C. Ott, Marcus M. Malek, Katrina M. Morgan, Eugene S. Kim, Abigail Zamora, Danny Lascano, Jonathan Roach, Joseph T. Murphy, David H. Rothstein, Sanjeev A. Vasudevan, Richard Whitlock, Dave R. Lal, Brian Hallis, Andreana Bütter, Reto M. Baertschiger, Eveline Lapidus‐Krol, Juan Putra, Elisabeth R. Tracy, Jennifer H. Aldrink, Jordan Apfeld, Hau D. Le, Keon Y. Park, Barrie S. Rich, Richard D. Glick, Elizabeth A. Fialkowski, Alan F. Utria, Rebecka L. Meyers, and Kimberly J. Riehle

Subjects
Cancer Research, Carcinoma, Hepatocellular, Surgical Oncology, Oncology, Liver Neoplasms, Humans, Neoplasm Recurrence, Local, Child, Neoplasm Staging, Retrospective Studies
Abstract

Hepatocellular carcinoma (HCC) is a rare cancer in children, with various histologic subtypes and a paucity of data to guide clinical management and predict prognosis.A multi-institutional review of children with hepatocellular neoplasms was performed, including demographic, staging, treatment, and outcomes data. Patients were categorized as having conventional HCC (cHCC) with or without underlying liver disease, fibrolamellar carcinoma (FLC), and hepatoblastoma with HCC features (HB-HCC). Univariate and multivariate analyses identified predictors of mortality and relapse.In total, 262 children were identified; and an institutional histologic review revealed 110 cHCCs (42%; 69 normal background liver, 34 inflammatory/cirrhotic, 7 unknown), 119 FLCs (45%), and 33 HB-HCCs (12%). The authors observed notable differences in presentation and behavior among tumor subtypes, including increased lymph node involvement in FLC and higher stage in cHCC. Factors associated with mortality included cHCC (hazard ratio [HR], 1.63; P = .038), elevated α-fetoprotein (HR, 3.1; P = .014), multifocality (HR, 2.4; P.001), and PRETEXT (pretreatment extent of disease) stage IV (HR, 5.76; P.001). Multivariate analysis identified increased mortality in cHCC versus FLC (HR, 2.2; P = .004) and in unresectable tumors (HR, 3.4; P.001). Disease-free status at any point predicted survival.This multi-institutional, detailed data set allowed a comprehensive analysis of outcomes for children with these rare hepatocellular neoplasms. The current data demonstrated that pediatric HCC subtypes are not equivalent entities because FLC and cHCC have distinct anatomic patterns and outcomes in concert with their known molecular differences. This data set will be further used to elucidate the impact of histology on specific treatment responses, with the goal of designing risk-stratified algorithms for children with HCC.This is the largest reported granular data set on children with hepatocellular carcinoma. The study evaluates different subtypes of hepatocellular carcinoma and identifies key differences between subtypes. This information is pivotal in improving understanding of these rare cancers and may be used to improve clinical management and subsequent outcome in children with these rare malignancies.

Published
2022

4. Contributors

Author

Babak Abai, James F. Abdo, Faryal G. Afridi, Olamide Alabi, Sarah Brown, Victoria Burton, Stephanie Carr, Venita Chandra, Vina Chhaya, Dawn M. Coleman, Michol A. Cooper, Alan Dardik, Sarah E. Deery, Ellen D. Dillavou, Laura M. Drudi, Audra Duncan, Jennifer L. Ellis, Yana Etkin, Amanda C. Filiberto, Julie Ann Freischlag, Vivian Gahtan, Mingjie Gao, Elizabeth L. George, Natalia O. Glebova, Philip Goodney, Jolanta Gorecka, Bernadette Goudreau, Linda M. Harris, Christine A. Heisler, Caitlin W. Hicks, Milan Ho, Vy Ho, Nicole Ilonzo, Sadia Ilyas, Brendan A. Jones, Enjae Jung, Manasa Kanneganti, Melina R. Kibbe, Misaki M. Kiguchi, Tanner I. Kim, Gregg S. Landis, Jason T. Lee, Jia Liu, Joann M. Lohr, Dimitra Lotakis, Natalia Rodriguez Luquerna, Pallavi Manvar-Singh, Christina L. Marcaccio, Katharine L. McGinigle, Pringl Miller, Samantha Minc, Erica L. Mitchell, Karina Newhall, Bao-Ngoc Nguyen, Sonya S. Noor, Cassius Iyad Ochoa Chaar, J. Westley Ohman, Kathleen J. Ozsvath, Georgina M. Pappas, Bruce A. Perler, Emily S. Reardon, Sudie-Ann Robinson, Meagan L. Rosenberg, Ethan S. Rosenfeld, Jessica R. Rouan, Danielle Salazar, Oonagh Scallan, Marc L. Schermerhorn, Palma M. Shaw, Jeffrey E. Silpe, Niten Singh, Brigitte Smith, Michael C. Soult, Elizabeth H. Stephens, Varuna Sundaram, Sarah M. Temkin, Robert W. Thompson, Britt H. Tonnessen, Margaret Tracci, Kaspar Trocha, Ashley K. Vavra, Gabriela Velazquez-Ramirez, Ageliki G. Vouyouka, Grace J. Wang, Tahlia L. Weis, Kimberly Zamor, and Pamela M. Zimmerman-Owen

Published
2021

6. Meckel’s Diverticulum, A Rare Presentation in a Neonate

Author

Jesse Honig, Ariel Figueroa, Rebecca Castro, Dimitra Lotakis, Mahrukh Bamji, Marc Wallack, and Arthur Cooper

Subjects
General Medicine, digestive system, digestive system diseases
Abstract

Meckel’s diverticulum is commonly symptomatic the first 2 years of life. Complications associated with Meckel’s diverticulum are due to gastrointestinal (GI) bleeding or obstruction. A 5-day-old male presented to the emergency department (ED) with an episode of bright red blood per rectum (BRBPR) associated with emesis. Vital signs were normal and abdomen soft and non-distended. Serial abdominal radiographs progressed to show distention of small bowel and air fluid levels. Operative intervention was undertaken with diagnosis of intestinal obstruction. On exploratory laparotomy, 24 cm of a fibrosed, ischemic closed-loop ileal segment densely adherent to the tip of a Meckel’s diverticulum was identified and resected, followed by primary reanastamosis. Histologic findings confirmed ectopic gastric tissue. Symptomatic Meckel’s diverticulum is often secondary to intestinal obstruction and hematochezia, findings which are caused by incarcerated inguinal hernia or ileocolic intussusception. Our patient presented with a closed loop, which has not been previously reported.

Published
2022

7. Genetic origins of the Minoans and Mycenaeans

Author

P. J. P. McGeorge, Ron Pinhasi, Kristin Stewardson, Yannis Tzedakis, Manolis Michalodimitrakis, Alexander Peltzer, Yannis Maniatis, Songül Alpaslan Roodenberg, Daniel Fernandes, Cosimo Posth, Patrick A. Navas, Eleni Konsolaki-Yannopoulou, David Reich, Anastasia Papathanasiou, Holley Martlew, Philipp W. Stockhammer, Michael P. Richards, John A. Stamatoyannopoulos, Johannes Krause, Dimitra Lotakis, Andonis Vasilakis, George N. Korres, Swapan Mallick, Anja Furtwängler, George Stamatoyannopoulos, Mehmet Özsait, Nadin Rohland, Saskia Pfrengle, Robert Arnott, Iosif Lazaridis, Alissa Mittnik, Nick Patterson, Jeffery R. Hughey, and Nesrin Özsait

Subjects
0301 basic medicine, Male, Chromosomes, Human, X, Principal Component Analysis, Multidisciplinary, geography.geographical_feature_category, Greece, Steppe, Human Migration, Ancient history, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Geography, Bronze Age, Ethnicity, Humans, Mainland, Female, 030217 neurology & neurosurgery, History, Ancient, Phylogeny
Abstract

The origins of the Bronze Age Minoan and Mycenaean cultures have puzzled archaeologists for more than a century. We assembled genome-wide data from nineteen ancient individuals, including Minoans from Crete, Mycenaeans from mainland Greece, and their eastern neighbours from southwestern Anatolia. We show that Minoans and Mycenaeans were genetically similar, having at least three quarters of their ancestry from the first Neolithic farmers of western Anatolia and the Aegean1,2, and most of the remainder from ancient populations like those of the Caucasus3 and Iran4,5. However, the Mycenaeans differed from Minoans in deriving additional ancestry from an ultimate source related to the hunter-gatherers of eastern Europe and Siberia6–8, introduced via a proximal source related to either the inhabitants of either the Eurasian steppe1,6,9 or Armenia4,9. Modern Greeks resemble the Mycenaeans, but with some additional dilution of the early Neolithic ancestry. Our results support the idea of continuity but not isolation in the history of populations of the Aegean, before and after the time of its earliest civilizations.

Published
2016

8. The accessible chromatin landscape of the human genome

Author

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

Subjects
Encyclopedias as Topic, Transcription, Genetic, DNA Footprinting, ATAC-seq, Computational biology, Regulatory Sequences, Nucleic Acid, Biology, DNase-Seq, Article, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Mutation Rate, Deoxyribonuclease I, Humans, Promoter Regions, Genetic, Enhancer, 030304 developmental biology, Genetics, 0303 health sciences, Multidisciplinary, Genome, Human, Molecular Sequence Annotation, Promoter, DNA, Genomics, DNA Methylation, Chromatin, DNA-Binding Proteins, DNA methylation, Human genome, DNase I hypersensitive site, Transcription Initiation Site, 030217 neurology & neurosurgery, Transcription Factors
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 ∼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 ∼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. An extensive map of human DNase I hypersensitive sites, markers of regulatory DNA, in 125 diverse cell and tissue types is described; integration of this information with other ENCODE-generated data sets identifies new relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns. This paper describes the first extensive map of human DNaseI hypersensitive sites — markers of regulatory DNA — in 125 diverse cell and tissue types. Integration of this information with other data sets generated by ENCODE (Encyclopedia of DNA Elements) identified new relationships between chromatin accessibility, transcription, DNA methylation and regulatory-factor occupancy patterns. Evolutionary-conservation analysis revealed signatures of recent functional constraint within DNaseI hypersensitive sites.

Published
2012

9. A European population in Minoan Bronze Age Crete

Author

Manolis Michalodimitrakis, Dimitra Lotakis, Donald Mastropaolo, Patrick A. Navas, John A. Stamatoyannopoulos, Jeffery R. Hughey, Peristera Paschou, George Stamatoyannopoulos, and Petros Drineas

Subjects
Time Factors, media_common.quotation_subject, Molecular Sequence Data, Population, General Physics and Astronomy, Ancient history, DNA, Mitochondrial, Article, General Biochemistry, Genetics and Molecular Biology, Ossuary, Cave, Bronze Age, Ethnicity, Humans, education, Minoan civilization, media_common, Principal Component Analysis, geography, education.field_of_study, Multidisciplinary, geography.geographical_feature_category, Plateau, Middle East, Civilization, Geography, Greece, General Chemistry, Europe, Genetics, Population, Haplotypes
Abstract

The first advanced Bronze Age civilization of Europe was established by the Minoans about 5,000 years before present. Since Sir Arthur Evans exposed the Minoan civic centre of Knossos, archaeologists have speculated on the origin of the founders of the civilization. Evans proposed a North African origin; Cycladic, Balkan, Anatolian and Middle Eastern origins have also been proposed. Here we address the question of the origin of the Minoans by analysing mitochondrial DNA from Minoan osseous remains from a cave ossuary in the Lassithi plateau of Crete dated 4,400–3,700 years before present. Shared haplotypes, principal component and pairwise distance analyses refute the Evans North African hypothesis. Minoans show the strongest relationships with Neolithic and modern European populations and with the modern inhabitants of the Lassithi plateau. Our data are compatible with the hypothesis of an autochthonous development of the Minoan civilization by the descendants of the Neolithic settlers of the island., 5,000 years ago, the Minoans established the first advanced civilization of Europe, but their origin remains unclear. Here the authors show that the Minoans were a European population, genetically similar to other ancient European populations and to the present inhabitants of the island of Crete.

Published
2013

10. A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

Author

Zhi Lu, Giltae Song, Troy W. Whitfield, Vishwanath R. Iyer, Teresa Vales, Angelika Merkel, Max Libbrecht, David Haussler, Ting Wang, Kristen Lee, Lingyun Song, Richard M. Myers, Alfonso Valencia, Rachel A. Harte, Xiaoqin Xu, Lucas D. Ward, Hazuki Takahashi, Nathan C. Sheffield, Thomas Derrien, Georgi K. Marinov, Eric D. Nguyen, Bernard B. Suh, Brian J. Raney, Richard Sandstrom, Thomas D. Tullius, Benoit Miotto, Alexander Dobin, Youhan Xu, Lukas Habegger, Ian Dunham, Brian A. Risk, Paul G. Giresi, Morgan C. Giddings, Hualin Xi, Anshul Kundaje, Robert S. Harris, Devin Absher, Peter J. Bickel, Yanbao Yu, Browen Aken, Colin Kingswood, Bryan R. Lajoie, Peter J. Good, Katrina Learned, Laura Elnitski, Shirley Pepke, Brandon King, Piero Carninci, Xinqiong Yang, Ghia Euskirchen, Kathryn Beal, Christelle Borel, Michael Muratet, Robert L. Grossman, David G. Knowles, Zarmik Moqtaderi, Veronika Boychenko, Steven P. Wilder, Michael L. Tress, Florencia Pauli, Alan P. Boyle, Andrea Tanzer, Philipp Kapranov, Serafim Batzoglou, Audra K. Johnson, Jun Neri, Nitin Bhardwaj, Elise A. Feingold, Venkat S. Malladi, Michael M. Hoffman, William Stafford Noble, Andrea Sboner, Mark Gerstein, Stephanie L. Parker, Jacqueline Dumais, Felix Schlesinger, Deborah R. Winter, Randall H. Brown, Thanh Truong, Rebecca F. Lowdon, Paolo Ribeca, Brooke Rhead, Peggy J. Farnham, Krista Thibeault, Terrence S. Furey, Donna Karolchik, Alec Victorsen, Xiaoan Ruan, Rehab F. Abdelhamid, Amy S. Nesmith, Jing Wang, Nicholas M. Luscombe, Alina R. Cao, Diane Trout, Teri Slifer, Peter E. Newburger, Cricket A. Sloan, Dimitra Lotakis, Stephen M. J. Searle, Ali Mortazavi, Alexandra Bignell, Alex Reynolds, Orion J. Buske, Chris Zaleski, Theresa K. Canfield, Ian Bell, Jin Lian, Vanessa K. Swing, Katalin Toth Fejes, Catherine Ucla, Robert E. Thurman, Jacqueline Chrast, Wei Lin, Tim Hubbard, Gary Saunders, Minyi Shi, Vihra Sotirova, Sherman M. Weissman, Jason D. Lieb, Richard Humbert, Kevin M. Bowling, Assaf Gordon, Tarjei S. Mikkelsen, Jing Leng, Thomas R. Gingeras, Fabian Grubert, Nader Jameel, Jost Vielmetter, Hannah Monahan, Preti Jain, Lindsay L. Waite, Tony Shafer, Joel Rozowsky, Michael Coyne, Brian Reed, M. Kay, Harsha P. Gunawardena, Ross C. Hardison, Gavin Sherlock, Alexandra Charos, Joseph D. Fleming, Ann S. Zweig, Jason Gertz, Rajinder Kaul, Xianjun Dong, Alexandre Reymond, Carrie A. Davis, Haiyan Huang, Chao Cheng, Marco Mariotti, Phil Lacroute, Jason A. Dilocker, Kenneth McCue, R. Robilotto, Stylianos E. Antonarakis, Sridar V. Chittur, Justin Jee, Barbara J. Wold, Sudipto K. Chakrabortty, Erica Dumais, Amartya Sanyal, Nathan Boley, Tianyuan Wang, Julien Lagarde, Anthony Kirilusha, Jonathan B. Preall, Kevin Roberts, Erika Giste, Hugo Y. K. Lam, Alvis Brazma, Gregory J. Hannon, Eric Rynes, Philippe Batut, Kevin Struhl, Margus Lukk, Manching Ku, Suganthi Balasubramanian, Sonali Jha, Jorg Drenkow, W. James Kent, Michael Snyder, Jie Wang, Anna Battenhouse, Charles B. Epstein, Rami Rauch, Christopher Shestak, John A. Stamatoyannopoulos, Gaurab Mukherjee, Cédric Howald, Tanya Kutyavin, Huaien Wang, Scott A. Tenenbaum, Wan Ting Poh, Kate R. Rosenbloom, Manolis Kellis, Pauline A. Fujita, Linfeng Wu, Anita Bansal, Molly Weaver, Linda L. Grasfeder, Peter J. Sabo, Qiang Li, Melissa S. Cline, Robert M. Kuhn, Darin London, Seth Frietze, Atif Shahab, Shane Neph, Damian Keefe, James B. Brown, Mark Diekhans, Webb Miller, Katherine Aylor Fisher, Jiang Du, Hadar H. Sheffer, Sarah Djebali, Frank Doyle, Nathan Lamarre-Vincent, Chia-Lin Wei, Laura A.L. Dillon, Jennifer Harrow, Robert C. Altshuler, Tyler Alioto, Raymond K. Auerbach, Adam Frankish, Rebekka O. Sprouse, Patrick J. Collins, E. Christopher Partridge, Zheng Liu, Yoichiro Shibata, Elliott H. Margulies, Abigail K. Ebersol, Kimberly A. Showers, Eric D. Green, Krishna M. Roskin, Job Dekker, Barbara N. Pusey, Ekta Khurana, Gilberto DeSalvo, Yijun Ruan, Hao Wang, Jainab Khatun, Henriette O'Geen, Alexej Abyzov, Brian Williams, Ryan M. McDaniell, Maya Kasowski, Manoj Hariharan, Felix Kokocinski, Gloria Despacio-Reyes, Zhancheng Zhang, Subhradip Karmakar, Ewan Birney, Koon-Kiu Yan, Xian Chen, Shinny Vong, Daniel Sobral, Nick Bild, Seul K.C. Kim, Timo Lassmann, Li Wang, Minerva E. Sanchez, Vaughan Roach, Theodore Gibson, Stephen C. J. Parker, Michael F. Lin, Patrick A. Navas, Laurence R. Meyer, Luiz O. F. Penalva, Bradley E. Bernstein, Kevin P. White, Emilie Aït Yahya Graison, Juan M. Vaquerizas, Sushma Iyengar, Kimberly M. Newberry, Akshay Bhinge, Xiaolan Zhang, Kim Bell, Yoshihide Hayashizaki, Lucas Lochovsky, Noam Shoresh, Hagen Tilgner, Philip Cayting, Dorrelyn Patacsil, Timothy E. Reddy, Eric Haugen, Katherine E. Varley, M. van Baren, Nathan D. Trinklein, Bum Kyu Lee, Tristan Frum, Marianne Lindahl-Allen, Timothy Durham, Roderic Guigó, Christopher W. Maier, Micha Sammeth, Debasish Raha, Timothy R. Dreszer, Benedict Paten, Robbyn Issner, Michael R. Brent, Kevin Y. Yip, Kim Blahnik, Jason Ernst, Zhiping Weng, Henry Amrhein, Arend Sidow, Javier Herrero, Hui Gao, Stephen G. Landt, Pouya Kheradpour, Galt P. Barber, Gregory E. Crawford, Toby Hunt, HudsonAlpha Institute for Biotechnology [Huntsville, AL], ENCODE Project Consortium : Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE, Gingeras TR, Kent WJ, Birney E, Wold B, Crawford GE, Bernstein BE, Epstein CB, Shoresh N, Ernst J, Mikkelsen TS, Kheradpour P, Zhang X, Wang L, Issner R, Coyne MJ, Durham T, Ku M, Truong T, Ward LD, Altshuler RC, Lin MF, Kellis M, Gingeras TR, Davis CA, Kapranov P, Dobin A, Zaleski C, Schlesinger F, Batut P, Chakrabortty S, Jha S, Lin W, Drenkow J, Wang H, Bell K, Gao H, Bell I, Dumais E, Dumais J, Antonarakis SE, Ucla C, Borel C, Guigo R, Djebali S, Lagarde J, Kingswood C, Ribeca P, Sammeth M, Alioto T, Merkel A, Tilgner H, Carninci P, Hayashizaki Y, Lassmann T, Takahashi H, Abdelhamid RF, Hannon G, Fejes-Toth K, Preall J, Gordon A, Sotirova V, Reymond A, Howald C, Graison E, Chrast J, Ruan Y, Ruan X, Shahab A, Ting Poh W, Wei CL, Crawford GE, Furey TS, Boyle AP, Sheffield NC, Song L, Shibata Y, Vales T, Winter D, Zhang Z, London D, Wang T, Birney E, Keefe D, Iyer VR, Lee BK, McDaniell RM, Liu Z, Battenhouse A, Bhinge AA, Lieb JD, Grasfeder LL, Showers KA, Giresi PG, Kim SK, Shestak C, Myers RM, Pauli F, Reddy TE, Gertz J, Partridge EC, Jain P, Sprouse RO, Bansal A, Pusey B, Muratet MA, Varley KE, Bowling KM, Newberry KM, Nesmith AS, Dilocker JA, Parker SL, Waite LL, Thibeault K, Roberts K, Absher DM, Wold B, Mortazavi A, Williams B, Marinov G, Trout D, Pepke S, King B, McCue K, Kirilusha A, DeSalvo G, Fisher-Aylor K, Amrhein H, Vielmetter J, Sherlock G, Sidow A, Batzoglou S, Rauch R, Kundaje A, Libbrecht M, Margulies EH, Parker SC, Elnitski L, Green ED, Hubbard T, Harrow J, Searle S, Kokocinski F, Aken B, Frankish A, Hunt T, Despacio-Reyes G, Kay M, Mukherjee G, Bignell A, Saunders G, Boychenko V, Van Baren M, Brown RH, Khurana E, Balasubramanian S, Zhang Z, Lam H, Cayting P, Robilotto R, Lu Z, Guigo R, Derrien T, Tanzer A, Knowles DG, Mariotti M, James Kent W, Haussler D, Harte R, Diekhans M, Kellis M, Lin M, Kheradpour P, Ernst J, Reymond A, Howald C, Graison EA, Chrast J, Tress M, Rodriguez JM, Snyder M, Landt SG, Raha D, Shi M, Euskirchen G, Grubert F, Kasowski M, Lian J, Cayting P, Lacroute P, Xu Y, Monahan H, Patacsil D, Slifer T, Yang X, Charos A, Reed B, Wu L, Auerbach RK, Habegger L, Hariharan M, Rozowsky J, Abyzov A, Weissman SM, Gerstein M, Struhl K, Lamarre-Vincent N, Lindahl-Allen M, Miotto B, Moqtaderi Z, Fleming JD, Newburger P, Farnham PJ, Frietze S, O'Geen H, Xu X, Blahnik KR, Cao AR, Iyengar S, Stamatoyannopoulos JA, Kaul R, Thurman RE, Wang H, Navas PA, Sandstrom R, Sabo PJ, Weaver M, Canfield T, Lee K, Neph S, Roach V, Reynolds A, Johnson A, Rynes E, Giste E, Vong S, Neri J, Frum T, Johnson EM, Nguyen ED, Ebersol AK, Sanchez ME, Sheffer HH, Lotakis D, Haugen E, Humbert R, Kutyavin T, Shafer T, Dekker J, Lajoie BR, Sanyal A, James Kent W, Rosenbloom KR, Dreszer TR, Raney BJ, Barber GP, Meyer LR, Sloan CA, Malladi VS, Cline MS, Learned K, Swing VK, Zweig AS, Rhead B, Fujita PA, Roskin K, Karolchik D, Kuhn RM, Haussler D, Birney E, Dunham I, Wilder SP, Keefe D, Sobral D, Herrero J, Beal K, Lukk M, Brazma A, Vaquerizas JM, Luscombe NM, Bickel PJ, Boley N, Brown JB, Li Q, Huang H, Gerstein M, Habegger L, Sboner A, Rozowsky J, Auerbach RK, Yip KY, Cheng C, Yan KK, Bhardwaj N, Wang J, Lochovsky L, Jee J, Gibson T, Leng J, Du J, Hardison RC, Harris RS, Song G, Miller W, Haussler D, Roskin K, Suh B, Wang T, Paten B, Noble WS, Hoffman MM, Buske OJ, Weng Z, Dong X, Wang J, Xi H, Tenenbaum SA, Doyle F, Penalva LO, Chittur S, Tullius TD, Parker SC, White KP, Karmakar S, Victorsen A, Jameel N, Bild N, Grossman RL, Snyder M, Landt SG, Yang X, Patacsil D, Slifer T, Dekker J, Lajoie BR, Sanyal A, Weng Z, Whitfield TW, Wang J, Collins PJ, Trinklein ND, Partridge EC, Myers RM, Giddings MC, Chen X, Khatun J, Maier C, Yu Y, Gunawardena H, Risk B, Feingold EA, Lowdon RF, Dillon LA, Good PJ, Harrow J, Searle S., Becker, Peter B, Broad Institute of MIT and Harvard, Lincoln Laboratory, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology. Department of Physics, Kellis, Manolis, Epstein, Charles B., Bernstein, Bradley E., Shoresh, Noam, Ernst, Jason, Mikkelsen, Tarjei Sigurd, Kheradpour, Pouya, Zhang, Xiaolan, Wang, Li, Issner, Robbyn, Coyne, Michael J., Durham, Timothy, Ku, Manching, Truong, Thanh, Ward, Lucas D., Altshuler, Robert Charles, Lin, Michael F., ENCODE Project Consortium, Antonarakis, Stylianos, and Miotto, Benoit

Subjects
RNA, Messenger/genetics, [SDV]Life Sciences [q-bio], Messenger, Genoma humà, Genome, Medical and Health Sciences, 0302 clinical medicine, Models, ddc:576.5, Biology (General), Conserved Sequence, Genetics, 0303 health sciences, General Neuroscience, RNA-Binding Proteins, Genomics, Biological Sciences, Chromatin, 3. Good health, [SDV] Life Sciences [q-bio], DNA-Binding Proteins, Gene Components, 030220 oncology & carcinogenesis, DNA methylation, Encyclopedia, HIV/AIDS, Proteïnes de la sang -- Aspectes genètics, General Agricultural and Biological Sciences, Databases, Nucleic Acid, Human, Research Article, Quality Control, Process (engineering), QH301-705.5, 1.1 Normal biological development and functioning, Computational biology, Biology, ENCODE, General Biochemistry, Genetics and Molecular Biology, Chromatin/metabolism, Vaccine Related, 03 medical and health sciences, Databases, Genetic, Underpinning research, Humans, RNA, Messenger, RNA-Binding Proteins/genetics/metabolism, Vaccine Related (AIDS), Gene, 030304 developmental biology, Internet, General Immunology and Microbiology, Nucleic Acid, Agricultural and Veterinary Sciences, Base Sequence, Models, Genetic, Genome, Human, Prevention, Human Genome, Computational Biology, DNA Methylation, ENCODE Project Consortium, Gene Expression Regulation, DNA-Binding Proteins/genetics/metabolism, RNA, Human genome, Immunization, Generic health relevance, Developmental Biology
Abstract

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome., National Human Genome Research Institute (U.S.), National Institutes of Health (U.S.)

Published
2011

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