Search Results - "Goloborodko, Anton"

A pathway for mitotic chromosome formation by Gibcus, Johan H, Samejima, Kumiko, Goloborodko, Anton, Samejima, Itaru, Naumova, Natalia, Nuebler, Johannes, Kanemaki, Masato T, Xie, Linfeng, Paulson, James R, Earnshaw, William C, Mirny, Leonid A, Dekker, Job

“…Mitotic chromosomes fold as compact arrays of chromatin loops. To identify the pathway of mitotic chromosome formation, we combined imaging and Hi-C analysis…”
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Compaction and segregation of sister chromatids via active loop extrusion by Goloborodko, Anton, Imakaev, Maxim V, Marko, John F, Mirny, Leonid

“…The mechanism by which chromatids and chromosomes are segregated during mitosis and meiosis is a major puzzle of biology and biophysics. Using polymer…”
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Formation of Chromosomal Domains by Loop Extrusion by Fudenberg, Geoffrey, Imakaev, Maxim, Lu, Carolyn, Goloborodko, Anton, Abdennur, Nezar, Mirny, Leonid A.

“…Topologically associating domains (TADs) are fundamental structural and functional building blocks of human interphase chromosomes, yet the mechanisms of TAD…”
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Chromosome Compaction by Active Loop Extrusion by Goloborodko, Anton, Marko, John F., Mirny, Leonid A.

“…During cell division, chromosomes are compacted in length by more than a 100-fold. A wide range of experiments demonstrated that in their compacted state,…”
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Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization by Nora, Elphège P., Goloborodko, Anton, Valton, Anne-Laure, Gibcus, Johan H., Uebersohn, Alec, Abdennur, Nezar, Dekker, Job, Mirny, Leonid A., Bruneau, Benoit G.

“…The molecular mechanisms underlying folding of mammalian chromosomes remain poorly understood. The transcription factor CTCF is a candidate regulator of…”
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Emerging Evidence of Chromosome Folding by Loop Extrusion by Fudenberg, Geoffrey, Abdennur, Nezar, Imakaev, Maxim, Goloborodko, Anton, Mirny, Leonid A

“…Chromosome organization poses a remarkable physical problem with many biological consequences: How can molecular interactions between proteins at the nanometer…”
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Iterative correction of Hi-C data reveals hallmarks of chromosome organization by Imakaev, Maxim, Fudenberg, Geoffrey, McCord, Rachel Patton, Naumova, Natalia, Goloborodko, Anton, Lajoie, Bryan R, Dekker, Job, Mirny, Leonid A

“…ICE (iterative correction and eigenvector decomposition) provides insight into inter- and intrachromosome interaction patterns. Extracting biologically…”
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Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome by Hsieh, Tsung-Han S, Fudenberg, Geoffrey, Goloborodko, Anton, Rando, Oliver J

“…The combination of short and long crosslinkers during chromosome conformation capture allows the interrogation of structure from the nucleosome to the…”
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Hematopoietic Stem Cells Are the Major Source of Multilineage Hematopoiesis in Adult Animals by Sawai, Catherine M., Babovic, Sonja, Upadhaya, Samik, Knapp, David J.H.F., Lavin, Yonit, Lau, Colleen M., Goloborodko, Anton, Feng, Jue, Fujisaki, Joji, Ding, Lei, Mirny, Leonid A., Merad, Miriam, Eaves, Connie J., Reizis, Boris

“…Hematopoietic stem cells (HSCs) sustain long-term reconstitution of hematopoiesis in transplantation recipients, yet their role in the endogenous steady-state…”
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Pyteomics—a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics by Goloborodko, Anton A., Levitsky, Lev I., Ivanov, Mark V., Gorshkov, Mikhail V.

“…Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data,…”
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SMC complexes differentially compact mitotic chromosomes according to genomic context by Schalbetter, Stephanie Andrea, Goloborodko, Anton, Fudenberg, Geoffrey, Belton, Jon-Matthew, Miles, Catrina, Yu, Miao, Dekker, Job, Mirny, Leonid, Baxter, Jonathan

“…Structural maintenance of chromosomes (SMC) protein complexes are key determinants of chromosome conformation. Using Hi-C and polymer modelling, we study how…”
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Igh and Igk loci use different folding principles for V gene recombination due to distinct chromosomal architectures of pro-B and pre-B cells by Hill, Louisa, Wutz, Gordana, Jaritz, Markus, Tagoh, Hiromi, Calderón, Lesly, Peters, Jan-Michael, Goloborodko, Anton, Busslinger, Meinrad

“…Extended loop extrusion across the immunoglobulin heavy-chain ( Igh ) locus facilitates V H -DJ H recombination following downregulation of the cohesin-release…”
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Highly structured homolog pairing reflects functional organization of the Drosophila genome by AlHaj Abed, Jumana, Erceg, Jelena, Goloborodko, Anton, Nguyen, Son C., McCole, Ruth B., Saylor, Wren, Fudenberg, Geoffrey, Lajoie, Bryan R., Dekker, Job, Mirny, Leonid A., Wu, C.-ting

“…Trans -homolog interactions have been studied extensively in Drosophila , where homologs are paired in somatic cells and transvection is prevalent…”
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Cooltools: Enabling high-resolution Hi-C analysis in Python by Abdennur, Nezar, Abraham, Sameer, Fudenberg, Geoffrey, Flyamer, Ilya M, Galitsyna, Aleksandra A, Goloborodko, Anton, Imakaev, Maxim, Oksuz, Betul A, Venev, Sergey V, Xiao, Yao

“…Chromosome conformation capture (3C) technologies reveal the incredible complexity of genome organization. Maps of increasing size, depth, and resolution are…”
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The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos by Erceg, Jelena, AlHaj Abed, Jumana, Goloborodko, Anton, Lajoie, Bryan R., Fudenberg, Geoffrey, Abdennur, Nezar, Imakaev, Maxim, McCole, Ruth B., Nguyen, Son C., Saylor, Wren, Joyce, Eric F., Senaratne, T. Niroshini, Hannan, Mohammed A., Nir, Guy, Dekker, Job, Mirny, Leonid A., Wu, C.-ting

“…Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focus on trans…”
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Sequence Scrambling in Shotgun Proteomics is Negligible by Goloborodko, Anton A., Gorshkov, Mikhail V., Good, David M., Zubarev, Roman A.

“…Analysis of 15,897 low-energy (CAD) and 10,878 higher-energy (HCD) collisional dissociation mass spectra of doubly protonated tryptic peptides taken with high…”
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Application of Statistical Thermodynamics To Predict the Adsorption Properties of Polypeptides in Reversed-Phase HPLC by Tarasova, Irina A, Goloborodko, Anton A, Perlova, Tatyana Y, Pridatchenko, Marina L, Gorshkov, Alexander V, Evreinov, Victor V, Ivanov, Alexander R, Gorshkov, Mikhail V

“…The theory of critical chromatography for biomacromolecules (BioLCCC) describes polypeptide retention in reversed-phase HPLC using the basic principles of…”
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Sequence-specific predictive chromatography to assist mass spectrometric analysis of asparagine deamidation and aspartate isomerization in peptides by Sargaeva, Nadezda P., Goloborodko, Anton A., O'Connor, Peter B., Moskovets, Eugene, Gorshkov, Mikhail V.

“…Deamidation of asparagine and spontaneous isomerization of aspartic acid in proteins and peptides occur frequently. These modifications result in a mixture of…”
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Combination of Edman degradation of peptides with liquid chromatography/mass spectrometry workflow for peptide identification in bottom-up proteomics by Lobas, Anna A., Verenchikov, Anatoly N., Goloborodko, Anton A., Levitsky, Lev I., Gorshkov, Mikhail V.

“…RATIONALE High‐throughput methods of proteomics are essential for identification of proteins in a cell or tissue under certain conditions. Most of these…”
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Retention time prediction using the model of liquid chromatography of biomacromolecules at critical conditions in LC-MS phosphopeptide analysis by Perlova, Tatiana Yu, Goloborodko, Anton A, Margolin, Yelena, Pridatchenko, Marina L, Tarasova, Irina A, Gorshkov, Alexander V, Moskovets, Eugene, Ivanov, Alexander R, Gorshkov, Mikhail V

“…LC combined with MS/MS analysis of complex mixtures of protein digests is a reliable and sensitive method for characterization of protein phosphorylation…”
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