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A flying start to the second half ensured it was derby day delight for the U's as they kept up the pressure on the top of the table sides.
Phil Ifil and Anthony Wordsworth had scored the U's goals against Brighton in their last outing and the duo were on target again as they saw off Southend.
The Shrimpers gave it a real go in the latter part of the game, but the U's held on to send Southend to their first home defeat since October and grab bragging rights.
The U's made just the one change to their starting eleven, as a niggly back injury saw Kevin Lisbie drop to the bench to be replaced by Steven Gillespie.
The visitors were the first to get the ball into the area as Ifil swung in a dangerous ball into the penalty area from a free kick and Joyce was able to collect under pressure from Reid.
It was an open start to the game as the match went from end to end without too many penalty area entries, before Malone nutmegged White before Okuonghae nicked the ball away from danger.
The U's saw the resulting corner away from danger, with McCormack's shot deflecting off another Shrimpers player and away for a goal kick.
The visitors were trying to generate some tempo in the game with some early balls out from the back, but they didn't quite click into gear in those early stages.
But they should have been in front after eight minutes. The U's robbed the Southend defence and Platt did well to take the ball past his man and lay it back to Gillespie.
The front man received the ball slightly behind him, but his finish was still disappointing as he managed to scoop it well over the cross bar from a central position.
Just before the quarter hour mark, the Shrimpers went close as a dangerous cross was thrown in from the right hand side and Moussa's darting run to the far post just fell short of allowing him to connect with the ball.
The U's were next to go close as a clever ball over the top set Gillespie away in a foot race with Barrett. The ball fell between the keeper and the defender, but the U's striker toe poked past a shot wide of goal as the two home players hesitated.
Wordsworth then drove a shot into the area that was well blocked by Morison as it veered towards goal, as the U's enjoyed some possession around the home area.
Midway through the half though, it was the Southend fans with their heads in their hands, as a corner from Francis whipped across the face of goal and went behind for a goal kick.
The U's responded in kind as Tierney's throw caused chaos, before the Shrimpers twice failed to clear the resulting corner. The ball was returned into the danger area by Ifil and first Gillespie and then Reid from very close range couldn't force the ball home.
At the other end, a Southend corner was met with a free header by Christophe at the far post, but the Frenchman could only put his effort into the outside of the side netting.
His compatriot Laurent then sent another dangerous ball across the face of goal, but Williams was happy to watch it go past the far post with no Southend players taking a chance in the box.
O'Toole went into the book just after the half hour mark for a foul on McCormack, as the game started to gain a feisty edge. Moussa joined O'Toole in the book as it looked like White was escaping on a foray forward into space down the right hand side, and then Reid made it three just before half time.
The home side were edging possession, but it was the U's who were the more incisive around the area.
That was until, just as the half came to a close, Laurent escaped down the Southend left. He looked like he was in a good position to fire across Williams, but he hit a weak shot into the arms of the U's keeper.
The game got to the half at all square, and both sides started the second period without making any changes.
But the U's were in front 44 seconds after the restart. Gillespie veered out to the left hand side and dropped a cross into the area that clipped a Southend player, but found the onrushing Ifil, who buried a superb header into the bottom corner.
Two minutes later and White almost doubled the advantage. Great play by Platt saw the ball knocked back to the defender and he smacked in a fierce shot that curved only inches over the bar.
At the other end, Southend finally broke the U's shackles and Barnard drifted in a cross that Laurent flicked on towards goal, but Williams collected safely.
A miscontrol by Francis in a dangerous position saw Wordsworth capitalise and then fouled on the edge of the box. From the resulting free kick, the midfielder curled a superb left foot effort into the top corner to put the U's two up.
The U's were hunting the Southend players down in packs and again won the ball off Christophe. Wordsworth played it out to Platt with a clever flick and his low curled effort forced Joyce into a fine save with U's players waiting for a rebound.
The visitors fine start to the second half hit a blip twenty minutes after the break, as Gillespie picked up an injury as he chased down Joyce. But such was the U's strength that they were able to introduce Lisbie from the bench for the remainder of the game, with Gillespie seemingly only taken off as a precautionary measure.
The home side gained some territory in the next five minutes, and had the ball in the back of the net midway through the half. But the whistle had long gone for a foul on Williams before Barrett tucked home.
Seeking a path into the game, Shrimpers boss Tilson introduced James Walker for Christophe.
But the U's maintained their dominance territorially and made their next change with just under twenty to go, as Joel Thomas came on for Platt, whilst Scannell came on for the Shrimpers.
And the home side gave themselves hope as Francis sent over a superb cross from the right hand side for Barnard to bury a header into the bottom corner past Williams.
It put the home side's tails up with fourteen to go, and the U's would have a storm to ride in the dying stages of the match.
It looked like Walker had then got in with nine minutes left, but Okuonghae and White did superbly to shepherd him away from danger and eventually the U's cleared their lines.
Then the ball was flung into the danger area but Barnard's close range header was cleared over the bar by a brave header from White, before McCormack ran onto a ball in the area, but could only stab his shot on the move straight into the keeper's arms.
The U's needed to settle down on the ball but had a chance as Lisbie headed into Joyce's arms from a cross to the far post.
Ifil was replaced by Hackney with five minutes to go, with Wordsworth moving over to the right for the final stages of the game.
They had quelled much of the Southend storm, but the four minutes of injury time put up by the fourth official raised the volume in Roots Hall again as the home side sought an equaliser.
Hackney drove a shot wide on the angle midway through that additional time, but it was the home side finishing on the front foot.
However, the U's held firm to make sure that they keep pace with the sides at the top of the table.
Derby day delight for the U's!