Publications

MAKOVA, Kateryna D, Brandon D PICKETT, Robert S HARRIS, Gabrielle A HARTLEY, Monika Cechova, Karol PAL, Sergey NURK, Dongahn YOO, Qiuhui LI, Prajna HEBBAR, Barbara C MCGRATH, Francesca ANTONACCI, Margaux AUBEL, Arjun BIDDANDA, Matthew BORCHERS, Erich BORNBERG-BAUER, Gerard G BOUFFARD, Shelise Y BROOKS, Lucia CARBONE, Laura CARREL, Andrew CARROLL, Pi-Chuan CHANG, Chen-Shan CHIN, Daniel E COOK, Sarah J C CRAIG, de Gennaro LUCIANA, Mark DIEKHANS, Amalia DUTRA, Gage H GARCIA, Patrick G S GRADY, Richard E GREEN, Diana HADDAD, Pille HALLAST, William T HARVEY, Glenn HICKEY, David A HILLIS, Savannah J HOYT, Hyeonsoo JEONG, Kaivan KAMALI, Sergei L Kosakovsky POND, Troy M LAPOLICE, Charles LEE, Alexandra P LEWIS, Yong-Hwee E LOH, Patrick MASTERSON, Kelly M MCGARVEY, Rajiv C MCCOY, Paul MEDVEDEV, Karen H Miga, Katherine M MUNSON, Evgenia PAK, Benedict PATEN, Brendan J PINTO, Tamara POTAPOVA, Arang RHIE, Joana L ROCHA, Fedor RYABOV, Oliver A RYDER, Samuel SACCO, Kishwar SHAFIN, Valery A SHEPELEV, Viviane SLON, Steven J SOLAR, Jessica M STORER, Peter H SUDMANT, Alex SWEETEN, Michael G TASSIA, Francoise THIBAUD-NISSEN, Mario VENTURA, Melissa A WILSON, Alice C YOUNG, Huiqing ZENG, Xinru ZHANG, Zachary A SZPIECH, Christian D HUBER, Jennifer L GERTON, Soojin V YI, Michael C SCHATZ, Ivan A ALEXANDROV, Sergey KOREN, Rachel J O'NEILL, Evan E EICHLER, Adam M PHILLIPPY (2024). The complete sequence and comparative analysis of ape sex chromosomes. Nature.

WEISSENSTEINER, Matthias H, Marzia A CREMONA, Wilfried M GUIBLET, Nicholas STOLER, Robert S HARRIS, Monika Cechova, Kristin A ECKERT, Francesca CHIAROMONTE, Yi-Fei HUANG, Kateryna D MAKOVA (2023). Accurate sequencing of DNA motifs able to form alternative (non-B) structures. Genome Research.

RHIE, Arang, Sergey NURK, Monika Cechova, Savannah J HOYT, Dylan J TAYLOR, Nicolas ALTEMOSE, Paul W HOOK, Sergey KOREN, Mikko RAUTIAINEN, Ivan A ALEXANDROV, Jamie ALLEN, Mobin ASRI, Andrey V BZIKADZE, Nae-Chyun CHEN, Chen-Shan CHIN, Mark DIEKHANS, Paul FLICEK, Giulio FORMENTI, Arkarachai FUNGTAMMASAN, Garcia Giron CARLOS, Erik GARRISON, Ariel GERSHMAN, Jennifer L GERTON, Patrick G S GRADY, Andrea GUARRACINO, Leanne HAGGERTY, Reza HALABIAN, Nancy F HANSEN, Robert HARRIS, Gabrielle A HARTLEY, William T HARVEY, Marina HAUKNESS, Jakob HEINZ, Thibaut HOURLIER, Robert M HUBLEY, Sarah E HUNT, Stephen HWANG, Miten JAIN, Rupesh K KESHARWANI, Alexandra P LEWIS, Li HENG, Glennis A LOGSDON, Julian K LUCAS, Wojciech MAKALOWSKI, Christopher MARKOVIC, Fergal J MARTIN, Ann M Mc CARTNEY, Rajiv C MCCOY, Jennifer MCDANIEL, Brandy M MCNULTY, Paul MEDVEDEV, Alla MIKHEENKO, Katherine M MUNSON, Terence D MURPHY, Hugh E OLSEN, Nathan D OLSON, Luis F PAULIN, David PORUBSKY, Tamara POTAPOVA, Fedor RYABOV, Steven L SALZBERG, Michael E G SAURIA, Fritz J SEDLAZECK, Kishwar SHAFIN, Valery A SHEPELEV, Alaina SHUMATE, Jessica M STORER, Likhitha SURAPANENI, Angella M. Taravella OILL, Francoise THIBAUD-NISSEN, Winston TIMP, Marta TOMASZKIEWICZ, Mitchell R VOLLGER, Brian P WALENZ, Allison C WATWOOD, Matthias H WEISSENSTEINER, Aaron M WENGER, Melissa A WILSON, Samantha ZARATE, Yiming ZHU, Justin M ZOOK, Evan E EICHLER, Rachel J NEILL, Michael C SCHATZ, Karen H Miga, Kateryna D MAKOVA, Adam M PHILLIPPY (2022). The complete sequence of a human Y chromosome. Nature.

M Lexa, Monika Cechova, SH Nguyen, P Jedlicka, V Tokan, Z Kubat, R Hobza, R Kejnovsky (2022). HiC TE, a computational pipeline for HiC data analysis to study the role of repeat family interactions in the genome 3D organization. genes.

Monika Cechova, KH Miga (2022). Satellite DNAs and human sex chromosome variation. genes.

Monika Cechova (2020). Probably Correct -- Rescuing Repeats with Short and Long Reads. genes.

Monika Cechova (2020). Ten simple rules for biologists initiating a collaboration with computer scientists. genes.

Monika Cechova, Karen H Miga (2020). Comprehensive variant discovery in the era of complete human reference genomes. Nature methods.

Monika Cechova, Rahulsimham Vegesna, M Tomaszkiewicz, RS Harris, D Chen, S Rangavittal, P Medvedev, KD Makova. (2020). Dynamic evolution of great ape Y chromosomes. PNAS.

Monika Cechova, RS Harris, M Tomaszkiewicz, B Arbeithuber, F Chiaromonte (2019). Noise-cancelling repeat finder -- uncovering tandem repeats in error-prone long-read sequencing data. Bioinformatics.

RS Harris, Monika Cechova, KD Makova. (2019). High Satellite Repeat Turnover in Great Apes Studied with Short- and Long-Read Technologies. Mol Biol Evol.

WM Guiblet, MA Cremona, Monika Cechova, RS Harris, I Kejnovska, E Kejnovsky., KA Eckert, F Chiaromonte (2018). Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate. Genome Research.

S Rangavittal, RS Harris, Monika Cechova, M Tomaszkiewicz, R Chikhi, KD Makova., P Medvedev (2017). RecoverY -- k-mer-based read classification for Y-chromosome-specific sequencing and assembly. Bioinformatics.

M Tomaszkiewicz, S Rangavittal, Monika Cechova, R Campos-Sánchez, HW Fescemyer, RS Harris, D Ye, PCM O’Brien, R Chikhi, OA Ryder, MA Ferguson-Smith, P Medvedev, KD Makova. (2016). A time- and cost-effective strategy to sequence mammalian Y Chromosomes -- an application to the de novo assembly of gorilla Y. Genome Research.

Monika Cechova, Z Kubat, R Hobza, B Vyskot (2015). Fully automated pipeline for detection of sex linked genes using RNA-Seq data. BMC Bioinformatics.

Monika Cechova, B Vyskot, E Kejnovsky. (2013). Analysis of plastid and mitochondrial DNA insertions in the nucleus (NUPTs and NUMTs) of six plant species -- size, relative age and chromosomal localization. Heredity.

E Kejnovsky., Monika Cechova, P Steflova, I Kejnovska, S Manzano, R Hobza, Z Kubat, J Kovarik, M Jamilena, B Vyskot (2013). Expansion of microsatellites on evolutionary young Y chromosome. Plos One.