Table of Contents

Research

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Reconstructing genetic history of Siberian and Northeastern European populations
- Emily H.M. Wong,
- Andrey Khrunin,
- Larissa Nichols,
- Dmitry Pushkarev,
- Denis Khokhrin,
- Dmitry Verbenko,
- Oleg Evgrafov,
- James Knowles,
- John Novembre,
- Svetlana Limborska,
- and Anton Valouev
Genome Res. January 2017 27: 1-14; Published in Advance December 13, 2016, doi:10.1101/gr.202945.115
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Genome-wide uniformity of human ‘open’ pre-initiation complexes
- William K.M. Lai and
- B. Franklin Pugh
Genome Res. January 2017 27: 15-26; Published in Advance November 10, 2016, doi:10.1101/gr.210955.116
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Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs
- Marta Melé,
- Kaia Mattioli,
- William Mallard,
- David M. Shechner,
- Chiara Gerhardinger,
- and John L. Rinn
Genome Res. January 2017 27: 27-37; Published in Advance December 7, 2016, doi:10.1101/gr.214205.116
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A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity
- Fumitaka Inoue,
- Martin Kircher,
- Beth Martin,
- Gregory M. Cooper,
- Daniela M. Witten,
- Michael T. McManus,
- Nadav Ahituv,
- and Jay Shendure
Genome Res. January 2017 27: 38-52; Published in Advance November 9, 2016, doi:10.1101/gr.212092.116
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Evolutionary patterns of metazoan microRNAs reveal targeting principles in the let-7 and miR-10 families
- Justin M. Wolter,
- Hoai Huang Thi Le,
- Alexander Linse,
- Victoria A. Godlove,
- Thuy-Duyen Nguyen,
- Kasuen Kotagama,
- Alissa Lynch,
- Alan Rawls,
- and Marco Mangone
Genome Res. January 2017 27: 53-63; Published in Advance December 7, 2016, doi:10.1101/gr.209361.116
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Drosophila poised enhancers are generated during tissue patterning with the help of repression
- Nina Koenecke,
- Jeff Johnston,
- Qiye He,
- Samuel Meier,
- and Julia Zeitlinger
Genome Res. January 2017 27: 64-74; Published in Advance November 14, 2016, doi:10.1101/gr.209486.116
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Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans
- Tess E. Jeffers and
- Jason D. Lieb
Genome Res. January 2017 27: 75-86; Published in Advance November 14, 2016, doi:10.1101/gr.208173.116
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Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators
- David van Dijk,
- Eilon Sharon,
- Maya Lotan-Pompan,
- Adina Weinberger,
- Eran Segal,
- and Lucas B. Carey
Genome Res. January 2017 27: 87-94; Published in Advance December 13, 2016, doi:10.1101/gr.212316.116
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A novel translational control mechanism involving RNA structures within coding sequences
- Jennifer Jungfleisch,
- Danny D. Nedialkova,
- Ivan Dotu,
- Katherine E. Sloan,
- Neus Martinez-Bosch,
- Lukas Brüning,
- Emanuele Raineri,
- Pilar Navarro,
- Markus T. Bohnsack,
- Sebastian A. Leidel,
- and Juana Díez
Genome Res. January 2017 27: 95-106; Published in Advance November 7, 2016, doi:10.1101/gr.209015.116

Methods

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Identification of complex genomic rearrangements in cancers using CouGaR
- Misko Dzamba,
- Arun K. Ramani,
- Pawel Buczkowicz,
- Yue Jiang,
- Man Yu,
- Cynthia Hawkins,
- and Michael Brudno
Genome Res. January 2017 27: 107-117; Published in Advance November 14, 2016, doi:10.1101/gr.211201.116
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The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells
- Mireia Jordà,
- Anna Díez-Villanueva,
- Izaskun Mallona,
- Berta Martín,
- Sergi Lois,
- Víctor Barrera,
- Manel Esteller,
- Tanya Vavouri,
- and Miguel A. Peinado
Genome Res. January 2017 27: 118-132; Published in Advance December 20, 2016, doi:10.1101/gr.207522.116
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Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes
- T.S. Keshava Prasad,
- Ajeet Kumar Mohanty,
- Manish Kumar,
- Sreelakshmi K. Sreenivasamurthy,
- Gourav Dey,
- Raja Sekhar Nirujogi,
- Sneha M. Pinto,
- Anil K. Madugundu,
- Arun H. Patil,
- Jayshree Advani,
- Srikanth S. Manda,
- Manoj Kumar Gupta,
- Sutopa B. Dwivedi,
- Dhanashree S. Kelkar,
- Brantley Hall,
- Xiaofang Jiang,
- Ashley Peery,
- Pavithra Rajagopalan,
- Soujanya D. Yelamanchi,
- Hitendra S. Solanki,
- Remya Raja,
- Gajanan J. Sathe,
- Sandip Chavan,
- Renu Verma,
- Krishna M. Patel,
- Ankit P. Jain,
- Nazia Syed,
- Keshava K. Datta,
- Aafaque Ahmed Khan,
- Manjunath Dammalli,
- Savita Jayaram,
- Aneesha Radhakrishnan,
- Christopher J. Mitchell,
- Chan-Hyun Na,
- Nirbhay Kumar,
- Photini Sinnis,
- Igor V. Sharakhov,
- Charles Wang,
- Harsha Gowda,
- Zhijian Tu,
- Ashwani Kumar,
- and Akhilesh Pandey
Genome Res. January 2017 27: 133-144; Published in Advance November 15, 2016, doi:10.1101/gr.201368.115
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The dynamic landscape of fission yeast meiosis alternative-splice isoforms
- Zheng Kuang,
- Jef D. Boeke,
- and Stefan Canzar
Genome Res. January 2017 27: 145-156; Published in Advance November 17, 2016, doi:10.1101/gr.208041.116

Resources

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A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree
- Michael A. Eberle,
- Epameinondas Fritzilas,
- Peter Krusche,
- Morten Källberg,
- Benjamin L. Moore,
- Mitchell A. Bekritsky,
- Zamin Iqbal,
- Han-Yu Chuang,
- Sean J. Humphray,
- Aaron L. Halpern,
- Semyon Kruglyak,
- Elliott H. Margulies,
- Gil McVean,
- and David R. Bentley
Genome Res. January 2017 27: 157-164; Published in Advance November 30, 2016, doi:10.1101/gr.210500.116
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Genetic compendium of 1511 human brains available through the UK Medical Research Council Brain Banks Network Resource
- Michael J. Keogh,
- Wei Wei,
- Ian Wilson,
- Jon Coxhead,
- Sarah Ryan,
- Sara Rollinson,
- Helen Griffin,
- Marzena Kurzawa-Akanbi,
- Mauro Santibanez-Koref,
- Kevin Talbot,
- Martin R. Turner,
- Chris-Anne McKenzie,
- Claire Troakes,
- Johannes Attems,
- Colin Smith,
- Safa Al Sarraj,
- Chris M. Morris,
- Olaf Ansorge,
- Stuart Pickering-Brown,
- James W. Ironside,
- and Patrick F. Chinnery
Genome Res. January 2017 27: 165-173; Published in Advance December 21, 2016, doi:10.1101/gr.210609.116
OPEN ACCESS ARTICLE

Research

Reconstructing genetic history of Siberian and Northeastern European populations

Genome-wide uniformity of human ‘open’ pre-initiation complexes

Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

Evolutionary patterns of metazoan microRNAs reveal targeting principles in the let-7 and miR-10 families

Drosophila poised enhancers are generated during tissue patterning with the help of repression

Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans

Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators

A novel translational control mechanism involving RNA structures within coding sequences

Methods

Identification of complex genomic rearrangements in cancers using CouGaR

The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells

Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes

The dynamic landscape of fission yeast meiosis alternative-splice isoforms

Resources

A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree

Genetic compendium of 1511 human brains available through the UK Medical Research Council Brain Banks Network Resource

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