Munch Lab

Publications

The comparative genomics and complex population history of Papio baboons
Rogers J, Raveendran M, Harris A, Mailund T, Leppälä K, Athanasiadis G, Schierup MH, Cheng J, Munch K, Walker JA, Konkel MK, Jordan V, Steely CJ, Beckstrom TO, Bergey C, Burrell A, Schrempf D, Noll A, Kothe M, Kopp GH, Liu Y, Murali A, Billis K, Martin FJ, Muffato M, Cox L, Else J, Disotell T, Muzny DM, Phillips-Conroy J, Aken B, Eichler EE, Marques-Bonet T, Kosiol C, Batzer MA, Hahn MW, Tung J, Zinner D, Roos C, Jolly CJ, Gibbs RA, Worley KC, and the Baboon Genome Analysis Consortium
Science Advances IN PRESS

Dynamic Copy Number Evolution of X- and Y-Linked Ampliconic Genes in Human Populations
Lucotte EA, Skov L, Jensen JM, Macià MC, Munch K, Schierup MH
Genetics (2018)

A comprehensive genomic history of extinct and living elephants
Palkopoulou E, Lipson M, Mallick S, Nielsen S, Rohland N, Baleka S, Karpinski E, Ivancevic AM, To TH, R. Kortschak D, Raison JM, Qu Z, Chin TJ, Alt KW, Claesson S, Dalén L, MacPhee RDE, Meller H, Roca AL, Ryder OA, Heiman D, Young S, Breen M, Williams C, Aken BL, Ruffier M, Karlsson E, Johnson J, Palma FD, Alfoldi J, Adelson DL, Mailund T, Munch K, Lindblad-Toh K, Hofreiter M, Poinar H, Reich D
PNAS (2018)

Evidence that the Rate of Strong Selective Sweeps Increases with Population Size in the Great Apes
Nam K, Munch K, Mailund T, Nater A, Greminger M, Krützen M, Marquès-Bonet T, Schierup MH
PNAS (2017)

Selective Sweeps across Twenty Million Years of Primate Evolution
Munch K, Nam K, Schierup MH, Mailund M
Molecular Biology and Evolution (2016)

Strong selective sweeps on the X chromosome in the human-chimpanzee ancestor explain its low divergence
Dutheil JY, Munch K, Nam K, Mailund T, Schierup MH
PLoS Genetics (2015)

Extreme selective sweeps independently targeted the X chromosomes of the great apes
Nam K, Munch, K, Hobolth, A, Dutheil JY, Veeramah K, Woerner A, Hammer MH, Great Ape Diversity Project, Mailund T, Schierup MH.
PNAS (2015)

Inference of purifying and positive selection in three subspecies of chimpanzees (Pan troglodytes) from exome sequencing
Bataillon T, Duan J, Hvilsom C, Jin X, Li X, Skov L, Glemin S, Munch K, Jiang T, Qian Y, Hobolth A, Wang J, Mailund T, Siegismund HR, Schierup MH.
Genome Biology and Evolution (2015)

The Time-Scale Of Recombination Rate Evolution In Great Apes
Stevison LS, Woerner AE, Kidd JM, Kelley JL, Veeramah KR, McManus KF, Great Ape Genome Project, Bustamante CD, Hammer MF, Wall JD
Molecular Biology and Evolution (2015)

2014-12-12-Cover-AvianWhole Genome Analyses Resolve Early Branches in the Tree of Life of Modern Birds
Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, Fonseca RRd, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MdS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford M, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MPC, Prosdocimi F, Samaniego JA, Velazquez AMV, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman R, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker K, Jønsson KA, Johnson W, Koepfli KP, OBrien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SW, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MTP, Zhang G
Science (2014)

Lineage Sorting in Apes
Mailund T, Munch K, Schierup MH
Annual review of genetics (2014)

Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. rostrata)
Jacobsen LMW, Pujolar JM, Bernatchez L, Munch K, Jian J, Niu Y, Hansen MM.
Molecular Ecology (2014)

cover

Unraveling recombination rate evolution using ancestral recombination maps (Comissioned review)
Munch K, Schierup MH, Mailund T
BioEssays (2014)

Genome-wide single generation signatures of local selection in the panmictic European eel
Pujolar JM, Jacobsen LMW, Als TD, Frydenberg J, Munch K, Jonsson B, Jian JB, Cheng L, Maes GE, Bernatchez L, Hansen MM
Molecular Ecology (2014)

A fine-scale recombination map of the human–chimpanzee ancestor reveals faster change in humans than in chimpanzees and a strong impact of GC-biased gene conversion
Munch K, Mailund T, Dutheil JY, Schierup MH
Genome Research (2014)

Inferring the Process of Human–Chimpanzee Speciation
Mailund T, Munch K, Schierup MH
Wiley Online Library (2014)

Rates and patterns of great ape retrotransposition
Formozdiari F, Konkelb MK, Prado-Martinez J, Chiatanted G, Herraez IH, Walker JA, Nelson B, Alkan C, Sudmant PH, Huddleston J, Catacchio CR, Ko A, Malig M, Baker C, Great Ape Genome Project, Marques-Bonet T, Ventura M, Batzer MA, Eichler EE
PNAS (2013)

Great ape genetic diversity and population history
Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O’Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prufer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubi C, Carvalho T, Ruiz-Herrera A, Vives L, Mele1 M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers A, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH,  Hvilsom C, Andres AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T
Nature (2013)

A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species
T Mailund, AE Halager, M Westergaard, JY Dutheil, K Munch, LN Andersen, G Lunter, K Prüfer, A Scally, A Hobolth, MH Schierup
PLoS Genetics (2012)

The bonobo genome compared with the chimpanzee and human genomes
Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer T, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, Higashino S, Hobolth A, Dutheil J, Karakoc E, Alkan C, Sajjadian S, Catacchio CR, Ventura M, Marques-Bonet T, Eichler EE, Andre C, Atencia R, Mugisha L, Patterson P, Siebauer M, Good JM, Fischer A, Ptak SE, Lachmann M, Symer D, Mailund T, Schierup MH, Andres AM, Kelso J, Paabo S
Nature (2012)

Extensive X-linked adaptive evolution in central chimpanzees
Hvilsoma C, Qianc Y, Bataillonc B, Lid Y, Mailund T, Sallée B, Carlsena F, Lid R, Zhengd R, Jiangd R, Jiangd H, Jind X, Munch K, Hobolth A, Siegismund HR, Wang J, Schierupc MH
PNAS (2012)

Insights into hominid evolution from the gorilla genome sequence
Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O’Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R
Nature (2011)

Species-specific responses of Late Quaternary megafauna to climate and humans
Lorenzen ED, Nogués-Bravo D, Orlando L, Weinstock J, Binladen J, Marske KA, Ugan A, Borregaard MK, Gilbert MT, Nielsen R, Ho SY, Goebel T, Graf KE, Byers D, Stenderup JT, Rasmussen M, Campos PF, Leonard JA, Koepfli KP, Froese D, Zazula G, Stafford TW Jr, Aaris-Sørensen K, Batra P, Haywood AM, Singarayer JS, Valdes PJ, Boeskorov G, Burns JA, Davydov SP, Haile J, Jenkins DL, Kosintsev P, Kuznetsova T, Lai X, Martin LD, McDonald HG,
Mol D, Meldgaard M, Munch K, Stephan E, Sablin M, Sommer RS, Sipko T, Scott E, Suchard MA, Tikhonov A, Willerslev R, Wayne RK, Cooper A, Hofreiter M, Sher A, Shapiro B, Rahbek C, Willerslev E
Nature (2011)

Ancient DNA reveals late survival of mammoth and horse in interior Alaska
Haile J, Froese D, MacPhee R, Roberts R, Arnold L, Alberto R, Rasmussen M, Nielsen R, Brook B, Robinson S, Demuro M, Gilbert TM, Munch K, Austin J, Cooper A, Barnes I, Moller P, Willerslev E
PNAS (2009)

‘The Farm Beneath the Sand’ – an archaelogical case study on ancient ‘dirt’ DNA
Hebsgaard MB, Gilbert MTP, Arneborg J, Heyn, P, Allentoft ME, Bunce M, Munch K, Schweger C, Willerslev E
Antiquity (2009)

Non-Destructive Sampling of Ancient Insect DNA
Thomsen PF, Elias S, Gilbert MTP, Haile J, Munch K, Kuzmina S, Froese DG, Sher A, Holdaway RN, Willerslev E
PLoS ONE (2009)

Fast Phylogenetic DNA barcoding
Munch K, Boomsma W, Willerslev E, Nielsen R
Phil. Trans. R. Soc. B (2008)

Statistical Assignment of DNA Sequences using Bayesian Phylogenetics
Munch K, Boomsma W, Huelsenbeck J P, Willerslev E, Nielsen N
Systematic Biology (2008)

nGASP – the nematode genome annotation assessment project
Avril Coghlan,Tristan J Fiedler, Sheldon J McKay, Paul Flicek, Todd W Harris,
Darin Blasiar, _The nGASP Consortium_ and Lincoln D Stein
BMC Bioinformatics (2008)

Ancient Bacteria Show Evidence of DNA Repair
Johnson SS, Hebsgaard MB, Christensen T, Mastepanov M, Zuber MT, Nielsen R, Munch K, Brand T, Gilbert MTP, Bunce M, Ronn R, Gilichinsky D, Froese D, Willerslev E
PNAS (2007)

Ancient DNA Chronology within Sediment Deposits: Are Paleobiological Reconstructions
Possible and is DNA Leaching a Problem?

Haile J, Holdaway R, Oliver K, Bunce M, Gilbert MT, Nielsen R, Munch K, Ho SY, Shapiro B, Willerslev E
Molecular Biology Evolution (2007)

Automatic Generation of Gene Finders for Eukaryotic Species
Munch K and Krogh A
BMC Bioinformatics (2006)

A hidden Markov model approach for determining expression from genomic tiling micro arrays
Munch K, Gardner PP, Arctander P, and Krogh A
BMC Bioinformatics (2006)

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